Starting phenix.real_space_refine on Sun Sep 13 14:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sje_10215/09_2026/6sje_10215.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sje_10215/09_2026/6sje_10215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sje_10215/09_2026/6sje_10215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sje_10215/09_2026/6sje_10215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sje_10215/09_2026/6sje_10215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sje_10215/09_2026/6sje_10215.map" } resolution = 4.1 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= 0.002 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 68 5.49 5 S 101 5.16 5 C 15036 2.51 5 N 4236 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 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: 24115 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: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1387 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain breaks: 1 Time building chain proxies: 4.96, per 1000 atoms: 0.21 Number of scatterers: 24115 At special positions: 0 Unit cell: (151.815, 149.721, 124.593, 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 68 15.00 O 4674 8.00 N 4236 7.00 C 15036 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: 1.95 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: 129 helices and 16 sheets defined 53.8% alpha, 9.6% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.60 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: 3.678A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.743A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.546A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.841A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.261A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.780A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.566A 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: 3.675A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.725A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.169A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.546A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.584A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.758A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.764A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 removed outlier: 3.568A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.519A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.636A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.872A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.969A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.569A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.821A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.528A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.767A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.586A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 4.002A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.902A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 941 through 945 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: 3.699A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.782A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.672A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.890A 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: 3.668A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.907A 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 99 removed outlier: 3.664A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.792A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.729A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.556A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.670A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 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 418 through 428 Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.642A pdb=" N GLU C 452 " --> pdb=" O HIS C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.589A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.868A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.535A 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 578 removed outlier: 3.827A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.468A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.602A 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: 4.020A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.885A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.568A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.726A 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: 3.630A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.799A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.542A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 4.017A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.639A 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: 3.823A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.580A 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: 3.957A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.547A 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: 3.526A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.571A pdb=" N LYS D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.610A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.510A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.770A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.554A 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: 3.618A 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: 3.940A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.641A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.856A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.587A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.528A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.695A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.839A 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: 6.362A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.548A 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: 7.575A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.962A 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: 6.520A 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: 6.370A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.701A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.262A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.262A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 36 removed outlier: 4.460A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.020A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.273A pdb=" N ILE C 408 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N CYS C 662 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 410 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.469A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.483A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.158A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.039A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 6.604A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.236A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.561A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6608 1.33 - 1.45: 4535 1.45 - 1.57: 13328 1.57 - 1.69: 134 1.69 - 1.81: 169 Bond restraints: 24774 Sorted by residual: bond pdb=" C ASN C 660 " pdb=" N ILE C 661 " ideal model delta sigma weight residual 1.330 1.246 0.084 1.25e-02 6.40e+03 4.53e+01 bond pdb=" O3' DC X 80 " pdb=" P DT X 81 " ideal model delta sigma weight residual 1.607 1.681 -0.074 1.20e-02 6.94e+03 3.76e+01 bond pdb=" C LEU C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.20e+01 bond pdb=" P DT X 81 " pdb=" OP1 DT X 81 " ideal model delta sigma weight residual 1.480 1.553 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O3' DG X 86 " pdb=" P DT X 87 " ideal model delta sigma weight residual 1.607 1.643 -0.036 1.20e-02 6.94e+03 8.83e+00 ... (remaining 24769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 33477 2.32 - 4.63: 389 4.63 - 6.95: 30 6.95 - 9.26: 10 9.26 - 11.58: 2 Bond angle restraints: 33908 Sorted by residual: angle pdb=" N LEU C 664 " pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 111.28 122.86 -11.58 1.09e+00 8.42e-01 1.13e+02 angle pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" C MET C 665 " ideal model delta sigma weight residual 113.16 123.91 -10.75 1.42e+00 4.96e-01 5.73e+01 angle pdb=" O5' DC X 80 " pdb=" C5' DC X 80 " pdb=" C4' DC X 80 " ideal model delta sigma weight residual 109.40 114.58 -5.18 8.00e-01 1.56e+00 4.19e+01 angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" N3 DT X 54 " pdb=" C4 DT X 54 " pdb=" O4 DT X 54 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 33903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 13467 17.11 - 34.22: 826 34.22 - 51.33: 368 51.33 - 68.44: 85 68.44 - 85.55: 9 Dihedral angle restraints: 14755 sinusoidal: 6466 harmonic: 8289 Sorted by residual: dihedral pdb=" CA PRO B1051 " pdb=" C PRO B1051 " pdb=" N PRO B1052 " pdb=" CA PRO B1052 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual 122.80 131.61 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C MET C 665 " pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual -122.60 -131.32 8.72 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3564 0.094 - 0.188: 158 0.188 - 0.282: 4 0.282 - 0.376: 2 0.376 - 0.470: 1 Chirality restraints: 3729 Sorted by residual: chirality pdb=" CA MET C 665 " pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CB MET C 665 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" P DT X 81 " pdb=" OP1 DT X 81 " pdb=" OP2 DT X 81 " pdb=" O5' DT X 81 " both_signs ideal model delta sigma weight residual True 2.34 -2.65 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA LEU C 664 " pdb=" N LEU C 664 " pdb=" C LEU C 664 " pdb=" CB LEU C 664 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3726 not shown) Planarity restraints: 4219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 420 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 304 " 0.038 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO B 305 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG X 83 " -0.025 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG X 83 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG X 83 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG X 83 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG X 83 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG X 83 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG X 83 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG X 83 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG X 83 " -0.009 2.00e-02 2.50e+03 ... (remaining 4216 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5611 2.79 - 3.32: 20052 3.32 - 3.85: 40337 3.85 - 4.37: 45746 4.37 - 4.90: 77972 Nonbonded interactions: 189718 Sorted by model distance: nonbonded pdb=" O PHE C 62 " pdb=" N1 DG X 86 " model vdw 2.264 3.120 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.304 2.496 nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.332 3.040 nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.336 3.040 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.341 3.040 ... (remaining 189713 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.750 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: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24774 Z= 0.239 Angle : 0.619 11.578 33908 Z= 0.426 Chirality : 0.042 0.470 3729 Planarity : 0.005 0.060 4219 Dihedral : 13.750 85.548 9383 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.06 % Allowed : 5.34 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.11), residues: 2837 helix: -2.50 (0.09), residues: 1382 sheet: -1.20 (0.28), residues: 299 loop : -2.38 (0.14), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 708 TYR 0.012 0.001 TYR B1111 PHE 0.014 0.001 PHE B1023 TRP 0.015 0.001 TRP B 652 HIS 0.005 0.000 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.24 (24774) covalent geometry : angle 0.61900 / 0.43 (33908) hydrogen bonds : bond 0.15023 / 10.23 ( 1106) hydrogen bonds : angle 6.45258 / 4.57 ( 3197) *********************** 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 768 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 694 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9226 (t) cc_final: 0.8941 (p) REVERT: B 133 CYS cc_start: 0.8532 (m) cc_final: 0.8198 (m) REVERT: B 152 LEU cc_start: 0.8526 (tp) cc_final: 0.8223 (mt) REVERT: B 335 ILE cc_start: 0.9066 (mt) cc_final: 0.8790 (mt) REVERT: B 348 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7205 (mt-10) REVERT: B 518 MET cc_start: 0.8818 (mmm) cc_final: 0.8403 (mmp) REVERT: B 595 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8114 (pt0) REVERT: B 725 GLN cc_start: 0.8399 (mt0) cc_final: 0.8136 (mm-40) REVERT: B 797 GLU cc_start: 0.8771 (tt0) cc_final: 0.8456 (tm-30) REVERT: B 798 ASP cc_start: 0.7880 (m-30) cc_final: 0.6684 (m-30) REVERT: B 804 VAL cc_start: 0.9106 (t) cc_final: 0.8874 (p) REVERT: B 1066 ILE cc_start: 0.9334 (mt) cc_final: 0.8429 (mt) REVERT: B 1078 LEU cc_start: 0.8187 (tt) cc_final: 0.7922 (mt) REVERT: B 1111 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6036 (t80) REVERT: B 1114 TYR cc_start: 0.8663 (m-10) cc_final: 0.8390 (m-10) REVERT: C 12 VAL cc_start: 0.9109 (t) cc_final: 0.8852 (t) REVERT: C 37 VAL cc_start: 0.7674 (m) cc_final: 0.7427 (p) REVERT: C 69 ILE cc_start: 0.9099 (mm) cc_final: 0.8823 (mt) REVERT: C 103 LEU cc_start: 0.8895 (mt) cc_final: 0.8438 (tt) REVERT: C 385 GLU cc_start: 0.8458 (tt0) cc_final: 0.8009 (tt0) REVERT: C 465 PHE cc_start: 0.8098 (m-80) cc_final: 0.7866 (m-80) REVERT: C 492 TYR cc_start: 0.7657 (m-80) cc_final: 0.6894 (m-80) REVERT: C 550 TYR cc_start: 0.7484 (t80) cc_final: 0.6526 (t80) REVERT: C 571 LEU cc_start: 0.8955 (mt) cc_final: 0.8729 (mm) REVERT: C 676 CYS cc_start: 0.8160 (m) cc_final: 0.7836 (m) REVERT: C 685 TYR cc_start: 0.8181 (t80) cc_final: 0.6978 (t80) REVERT: C 714 TYR cc_start: 0.8815 (t80) cc_final: 0.8112 (t80) REVERT: C 728 TYR cc_start: 0.7963 (t80) cc_final: 0.6536 (t80) REVERT: C 730 SER cc_start: 0.9204 (t) cc_final: 0.8673 (t) REVERT: C 861 ASP cc_start: 0.8116 (p0) cc_final: 0.7428 (p0) REVERT: D 273 MET cc_start: 0.7489 (mtm) cc_final: 0.7173 (mtt) REVERT: D 407 MET cc_start: 0.8926 (ttp) cc_final: 0.8697 (tmm) REVERT: D 484 ILE cc_start: 0.8703 (mm) cc_final: 0.7981 (tp) REVERT: D 537 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8199 (p) REVERT: D 600 LEU cc_start: 0.8546 (mt) cc_final: 0.8196 (mp) outliers start: 74 outliers final: 12 residues processed: 750 average time/residue: 0.1885 time to fit residues: 214.1165 Evaluate side-chains 351 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 337 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 134 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN B 181 GLN B 224 GLN B 455 ASN B 458 ASN B 463 GLN B 531 GLN B 566 GLN B 594 GLN B 610 ASN B 650 GLN B 725 GLN B 765 GLN B 834 HIS B 843 GLN B 848 GLN B 900 ASN B 944 GLN B 956 HIS B1084 ASN B1095 GLN B1133 HIS B1134 HIS C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 321 GLN C 336 HIS C 423 GLN C 563 HIS C 570 GLN C 614 GLN C 699 GLN C 749 GLN C 759 HIS C 792 GLN C 822 GLN C 883 GLN C 925 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 979 GLN C1091 GLN D 128 HIS D 369 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 = 0.3643 r_free = 0.3643 target = 0.078945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.063906 restraints weight = 107305.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.065591 restraints weight = 63010.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.066789 restraints weight = 42898.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067609 restraints weight = 32242.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.068108 restraints weight = 26123.488| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24774 Z= 0.140 Angle : 0.613 9.200 33908 Z= 0.317 Chirality : 0.041 0.182 3729 Planarity : 0.005 0.084 4219 Dihedral : 14.676 84.894 3843 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.04 % Allowed : 2.48 % Favored : 97.47 % 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: -1.74 (0.14), residues: 2837 helix: -0.52 (0.12), residues: 1414 sheet: -0.76 (0.29), residues: 290 loop : -2.00 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 728 TYR 0.049 0.002 TYR D 108 PHE 0.026 0.002 PHE B 428 TRP 0.032 0.002 TRP C 149 HIS 0.012 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (24774) covalent geometry : angle 0.61259 / 0.32 (33908) hydrogen bonds : bond 0.04192 / 2.68 ( 1106) hydrogen bonds : angle 4.58011 / 3.24 ( 3197) *********************** 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 419 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 418 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9179 (t) cc_final: 0.8845 (p) REVERT: B 499 MET cc_start: 0.7535 (tpt) cc_final: 0.6975 (tpt) REVERT: B 518 MET cc_start: 0.8789 (mmm) cc_final: 0.8316 (mmp) REVERT: B 557 LEU cc_start: 0.9486 (mp) cc_final: 0.9236 (mp) REVERT: B 599 LEU cc_start: 0.9464 (mp) cc_final: 0.9112 (mt) REVERT: B 797 GLU cc_start: 0.8827 (tt0) cc_final: 0.8329 (tm-30) REVERT: B 798 ASP cc_start: 0.8101 (m-30) cc_final: 0.7715 (m-30) REVERT: B 804 VAL cc_start: 0.9256 (t) cc_final: 0.9049 (p) REVERT: B 1078 LEU cc_start: 0.8219 (tt) cc_final: 0.7952 (mt) REVERT: B 1114 TYR cc_start: 0.8609 (m-10) cc_final: 0.8357 (m-10) REVERT: C 12 VAL cc_start: 0.9243 (t) cc_final: 0.9017 (t) REVERT: C 34 MET cc_start: 0.8701 (mmt) cc_final: 0.8290 (mmm) REVERT: C 37 VAL cc_start: 0.7774 (m) cc_final: 0.7553 (p) REVERT: C 49 THR cc_start: 0.8658 (p) cc_final: 0.8130 (t) REVERT: C 103 LEU cc_start: 0.8967 (mt) cc_final: 0.8479 (tt) REVERT: C 115 LEU cc_start: 0.9183 (mp) cc_final: 0.8777 (pp) REVERT: C 137 GLN cc_start: 0.8926 (tt0) cc_final: 0.8532 (tt0) REVERT: C 385 GLU cc_start: 0.8568 (tt0) cc_final: 0.7942 (tt0) REVERT: C 550 TYR cc_start: 0.7553 (t80) cc_final: 0.5738 (t80) REVERT: C 571 LEU cc_start: 0.9228 (mt) cc_final: 0.8933 (mm) REVERT: C 676 CYS cc_start: 0.8659 (m) cc_final: 0.8301 (m) REVERT: C 680 MET cc_start: 0.8744 (mmp) cc_final: 0.8468 (mmp) REVERT: C 714 TYR cc_start: 0.8893 (t80) cc_final: 0.8010 (t80) REVERT: C 728 TYR cc_start: 0.8015 (t80) cc_final: 0.6413 (t80) REVERT: C 730 SER cc_start: 0.9302 (t) cc_final: 0.8595 (t) REVERT: C 790 ASP cc_start: 0.7699 (t0) cc_final: 0.7206 (t0) REVERT: C 1102 MET cc_start: 0.9262 (ttp) cc_final: 0.8955 (tmm) REVERT: D 275 ASP cc_start: 0.8400 (p0) cc_final: 0.8074 (p0) REVERT: D 393 ILE cc_start: 0.7983 (pt) cc_final: 0.7705 (pt) REVERT: D 407 MET cc_start: 0.8897 (ttp) cc_final: 0.8666 (tmm) REVERT: D 445 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7828 (mtp85) outliers start: 1 outliers final: 1 residues processed: 419 average time/residue: 0.1755 time to fit residues: 115.2882 Evaluate side-chains 279 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 278 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 48 optimal weight: 0.0060 chunk 233 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 279 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 GLN B 262 GLN B 281 GLN B 610 ASN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 817 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.078416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.063263 restraints weight = 107990.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064964 restraints weight = 62937.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.066136 restraints weight = 42693.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066947 restraints weight = 32088.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.067433 restraints weight = 26084.468| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24774 Z= 0.125 Angle : 0.562 8.936 33908 Z= 0.293 Chirality : 0.040 0.171 3729 Planarity : 0.004 0.063 4219 Dihedral : 14.679 86.337 3843 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 2837 helix: 0.35 (0.13), residues: 1414 sheet: -0.55 (0.30), residues: 287 loop : -1.74 (0.16), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 974 TYR 0.034 0.001 TYR D 108 PHE 0.025 0.001 PHE D 386 TRP 0.013 0.001 TRP D 113 HIS 0.015 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (24774) covalent geometry : angle 0.56207 / 0.29 (33908) hydrogen bonds : bond 0.03774 / 2.38 ( 1106) hydrogen bonds : angle 4.30268 / 3.06 ( 3197) *********************** 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 363 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 361 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9087 (t) cc_final: 0.8811 (p) REVERT: B 499 MET cc_start: 0.7495 (tpt) cc_final: 0.6856 (tpt) REVERT: B 518 MET cc_start: 0.8804 (mmm) cc_final: 0.8345 (mmp) REVERT: B 599 LEU cc_start: 0.9484 (mp) cc_final: 0.9166 (mt) REVERT: B 731 SER cc_start: 0.8493 (t) cc_final: 0.8088 (m) REVERT: B 797 GLU cc_start: 0.8880 (tt0) cc_final: 0.8376 (tm-30) REVERT: B 798 ASP cc_start: 0.8190 (m-30) cc_final: 0.7748 (m-30) REVERT: B 804 VAL cc_start: 0.9239 (t) cc_final: 0.9034 (p) REVERT: B 1078 LEU cc_start: 0.8220 (tt) cc_final: 0.7980 (mt) REVERT: B 1112 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 1114 TYR cc_start: 0.8596 (m-10) cc_final: 0.8375 (m-10) REVERT: B 1170 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: C 12 VAL cc_start: 0.9253 (t) cc_final: 0.9028 (t) REVERT: C 103 LEU cc_start: 0.8952 (mt) cc_final: 0.8479 (tt) REVERT: C 115 LEU cc_start: 0.9198 (mp) cc_final: 0.8790 (pp) REVERT: C 230 LEU cc_start: 0.9076 (mt) cc_final: 0.8828 (mt) REVERT: C 342 ILE cc_start: 0.9557 (tt) cc_final: 0.9275 (tp) REVERT: C 714 TYR cc_start: 0.8839 (t80) cc_final: 0.8424 (t80) REVERT: C 790 ASP cc_start: 0.7515 (t0) cc_final: 0.7189 (t0) REVERT: D 169 ILE cc_start: 0.9275 (pt) cc_final: 0.8799 (tp) REVERT: D 324 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7879 (pp20) REVERT: D 393 ILE cc_start: 0.7985 (pt) cc_final: 0.7717 (pt) REVERT: D 445 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7920 (mtp85) REVERT: D 484 ILE cc_start: 0.8554 (mm) cc_final: 0.7813 (tp) REVERT: D 536 MET cc_start: 0.9029 (ttm) cc_final: 0.8730 (ttm) outliers start: 2 outliers final: 1 residues processed: 363 average time/residue: 0.1671 time to fit residues: 96.7633 Evaluate side-chains 248 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 277 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 197 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 130 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 485 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN B 610 ASN B 624 ASN ** B 689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS B 956 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 660 ASN C 724 GLN C 958 GLN D 369 GLN D 542 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.058936 restraints weight = 111640.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060566 restraints weight = 65119.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.061677 restraints weight = 44402.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062454 restraints weight = 33626.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.062974 restraints weight = 27515.994| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 24774 Z= 0.244 Angle : 0.655 9.931 33908 Z= 0.337 Chirality : 0.042 0.171 3729 Planarity : 0.005 0.062 4219 Dihedral : 14.835 89.668 3843 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.08 % Allowed : 2.73 % Favored : 97.18 % 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: -0.20 (0.15), residues: 2837 helix: 0.89 (0.14), residues: 1420 sheet: -0.34 (0.29), residues: 293 loop : -1.38 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 254 TYR 0.026 0.002 TYR D 108 PHE 0.034 0.002 PHE D 386 TRP 0.018 0.002 TRP B 652 HIS 0.010 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.24 (24774) covalent geometry : angle 0.65545 / 0.34 (33908) hydrogen bonds : bond 0.03956 / 2.55 ( 1106) hydrogen bonds : angle 4.31088 / 3.08 ( 3197) *********************** 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 312 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8608 (m) cc_final: 0.8332 (m) REVERT: B 384 ASP cc_start: 0.8866 (t70) cc_final: 0.8632 (t0) REVERT: B 499 MET cc_start: 0.8013 (tpt) cc_final: 0.7558 (tpt) REVERT: B 518 MET cc_start: 0.8980 (mmm) cc_final: 0.8540 (mmp) REVERT: B 520 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 604 MET cc_start: 0.8936 (ttp) cc_final: 0.8698 (ttt) REVERT: B 660 MET cc_start: 0.9057 (tmm) cc_final: 0.8833 (tmm) REVERT: B 797 GLU cc_start: 0.9126 (tt0) cc_final: 0.8653 (tm-30) REVERT: B 798 ASP cc_start: 0.8372 (m-30) cc_final: 0.7962 (m-30) REVERT: B 1078 LEU cc_start: 0.8360 (tt) cc_final: 0.7929 (mp) REVERT: B 1112 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 1114 TYR cc_start: 0.8819 (m-10) cc_final: 0.8465 (m-10) REVERT: C 2 LEU cc_start: 0.7885 (tp) cc_final: 0.7564 (mp) REVERT: C 91 MET cc_start: 0.8767 (mtm) cc_final: 0.8406 (ttp) REVERT: C 571 LEU cc_start: 0.9317 (mt) cc_final: 0.8907 (mt) REVERT: C 685 TYR cc_start: 0.8623 (t80) cc_final: 0.8202 (t80) REVERT: C 714 TYR cc_start: 0.8906 (t80) cc_final: 0.8681 (t80) REVERT: C 790 ASP cc_start: 0.8232 (t0) cc_final: 0.7623 (t0) REVERT: C 851 MET cc_start: 0.8731 (mtt) cc_final: 0.8455 (mtp) REVERT: D 169 ILE cc_start: 0.9355 (pt) cc_final: 0.8960 (mp) REVERT: D 393 ILE cc_start: 0.7999 (pt) cc_final: 0.7682 (pt) REVERT: D 484 ILE cc_start: 0.8623 (mm) cc_final: 0.7917 (tp) REVERT: D 488 ASP cc_start: 0.8212 (t0) cc_final: 0.8003 (t0) REVERT: D 600 LEU cc_start: 0.9009 (mt) cc_final: 0.8777 (mp) outliers start: 2 outliers final: 0 residues processed: 312 average time/residue: 0.1638 time to fit residues: 82.5021 Evaluate side-chains 202 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 252 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN B 485 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN B 956 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** 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 = 0.3530 r_free = 0.3530 target = 0.073699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058569 restraints weight = 110772.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060203 restraints weight = 64146.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061343 restraints weight = 43420.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.062111 restraints weight = 32882.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.062567 restraints weight = 26959.167| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24774 Z= 0.190 Angle : 0.619 9.033 33908 Z= 0.320 Chirality : 0.041 0.178 3729 Planarity : 0.004 0.064 4219 Dihedral : 14.984 88.483 3843 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.08 % Allowed : 1.70 % Favored : 98.22 % 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: 0.04 (0.16), residues: 2837 helix: 1.11 (0.14), residues: 1423 sheet: -0.28 (0.29), residues: 293 loop : -1.29 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 445 TYR 0.023 0.002 TYR D 108 PHE 0.021 0.002 PHE B 645 TRP 0.015 0.001 TRP B 652 HIS 0.009 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (24774) covalent geometry : angle 0.61946 / 0.32 (33908) hydrogen bonds : bond 0.03749 / 2.40 ( 1106) hydrogen bonds : angle 4.23816 / 3.01 ( 3197) *********************** 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 283 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8703 (tpp) cc_final: 0.8015 (tpp) REVERT: B 384 ASP cc_start: 0.8818 (t70) cc_final: 0.8540 (t0) REVERT: B 499 MET cc_start: 0.8072 (tpt) cc_final: 0.7588 (tpt) REVERT: B 518 MET cc_start: 0.8923 (mmm) cc_final: 0.8505 (mmp) REVERT: B 520 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8310 (tm-30) REVERT: B 727 MET cc_start: 0.7899 (mtp) cc_final: 0.7550 (mtp) REVERT: B 797 GLU cc_start: 0.9149 (tt0) cc_final: 0.8515 (tm-30) REVERT: B 902 ARG cc_start: 0.8300 (ptm-80) cc_final: 0.8088 (ptm-80) REVERT: B 1078 LEU cc_start: 0.8368 (tt) cc_final: 0.8055 (mt) REVERT: B 1112 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 1114 TYR cc_start: 0.8846 (m-10) cc_final: 0.8466 (m-10) REVERT: B 1135 PHE cc_start: 0.7786 (t80) cc_final: 0.7524 (t80) REVERT: C 2 LEU cc_start: 0.7843 (tp) cc_final: 0.7527 (mp) REVERT: C 91 MET cc_start: 0.8760 (mtm) cc_final: 0.8406 (ttp) REVERT: C 411 MET cc_start: 0.9141 (mtm) cc_final: 0.8708 (ttm) REVERT: C 667 MET cc_start: 0.9020 (mpp) cc_final: 0.8733 (mtm) REVERT: C 685 TYR cc_start: 0.8500 (t80) cc_final: 0.7897 (t80) REVERT: C 714 TYR cc_start: 0.8892 (t80) cc_final: 0.8598 (t80) REVERT: C 790 ASP cc_start: 0.8300 (t0) cc_final: 0.7727 (t0) REVERT: C 851 MET cc_start: 0.8768 (mtt) cc_final: 0.8485 (mtp) REVERT: C 1057 MET cc_start: 0.7392 (mmm) cc_final: 0.7096 (mmm) REVERT: D 100 MET cc_start: 0.8951 (mpp) cc_final: 0.8685 (mpp) REVERT: D 169 ILE cc_start: 0.9325 (pt) cc_final: 0.8933 (mp) REVERT: D 275 ASP cc_start: 0.8619 (p0) cc_final: 0.8303 (p0) REVERT: D 393 ILE cc_start: 0.8043 (pt) cc_final: 0.7652 (pt) REVERT: D 488 ASP cc_start: 0.8128 (t0) cc_final: 0.7886 (t0) REVERT: D 545 GLU cc_start: 0.8008 (tt0) cc_final: 0.7267 (pm20) outliers start: 2 outliers final: 0 residues processed: 283 average time/residue: 0.1561 time to fit residues: 72.7519 Evaluate side-chains 200 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 90 optimal weight: 6.9990 chunk 246 optimal weight: 30.0000 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 260 optimal weight: 20.0000 chunk 284 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN B 705 HIS B 956 HIS B1133 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055501 restraints weight = 114690.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.056918 restraints weight = 69109.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.057890 restraints weight = 48384.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.058571 restraints weight = 37560.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.058945 restraints weight = 31395.782| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 24774 Z= 0.327 Angle : 0.800 13.154 33908 Z= 0.403 Chirality : 0.045 0.181 3729 Planarity : 0.006 0.086 4219 Dihedral : 15.283 89.876 3843 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.25 (0.15), residues: 2837 helix: 0.80 (0.13), residues: 1429 sheet: -0.27 (0.29), residues: 294 loop : -1.38 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 433 TYR 0.024 0.003 TYR C 714 PHE 0.034 0.003 PHE D 386 TRP 0.021 0.002 TRP B 272 HIS 0.010 0.002 HIS B 705 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.33 (24774) covalent geometry : angle 0.80011 / 0.40 (33908) hydrogen bonds : bond 0.04583 / 2.97 ( 1106) hydrogen bonds : angle 4.63981 / 3.31 ( 3197) *********************** 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 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8511 (tpp) cc_final: 0.8065 (tpp) REVERT: B 384 ASP cc_start: 0.8775 (t70) cc_final: 0.8554 (t0) REVERT: B 499 MET cc_start: 0.8268 (tpt) cc_final: 0.7908 (tpt) REVERT: B 621 MET cc_start: 0.8893 (mmm) cc_final: 0.8661 (mmp) REVERT: B 727 MET cc_start: 0.8386 (mtp) cc_final: 0.8108 (mtp) REVERT: B 797 GLU cc_start: 0.9213 (tt0) cc_final: 0.8709 (tm-30) REVERT: B 1078 LEU cc_start: 0.8366 (tt) cc_final: 0.8120 (mt) REVERT: B 1112 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 91 MET cc_start: 0.8735 (mtm) cc_final: 0.8342 (ttp) REVERT: C 571 LEU cc_start: 0.9427 (mt) cc_final: 0.9112 (mt) REVERT: C 685 TYR cc_start: 0.8605 (t80) cc_final: 0.7710 (t80) REVERT: C 790 ASP cc_start: 0.8424 (t0) cc_final: 0.8019 (t0) REVERT: C 851 MET cc_start: 0.8667 (mtt) cc_final: 0.8339 (mtp) REVERT: C 1057 MET cc_start: 0.7330 (mmm) cc_final: 0.6994 (mmm) REVERT: D 169 ILE cc_start: 0.9261 (pt) cc_final: 0.8886 (mp) REVERT: D 393 ILE cc_start: 0.8080 (pt) cc_final: 0.7854 (pt) REVERT: D 484 ILE cc_start: 0.8537 (mm) cc_final: 0.8009 (tp) REVERT: D 488 ASP cc_start: 0.8220 (t0) cc_final: 0.7979 (t0) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1574 time to fit residues: 69.2305 Evaluate side-chains 179 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 43 optimal weight: 0.9980 chunk 206 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 224 GLN ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN B 843 GLN B1072 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.057849 restraints weight = 111747.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059384 restraints weight = 65594.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.060457 restraints weight = 44978.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.061183 restraints weight = 34341.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061648 restraints weight = 28328.557| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24774 Z= 0.131 Angle : 0.594 10.303 33908 Z= 0.304 Chirality : 0.041 0.164 3729 Planarity : 0.004 0.048 4219 Dihedral : 15.252 89.844 3843 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2837 helix: 1.23 (0.14), residues: 1421 sheet: -0.18 (0.30), residues: 275 loop : -1.21 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 255 TYR 0.034 0.002 TYR C 550 PHE 0.022 0.001 PHE D 386 TRP 0.012 0.001 TRP B 652 HIS 0.010 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (24774) covalent geometry : angle 0.59442 / 0.30 (33908) hydrogen bonds : bond 0.03702 / 2.36 ( 1106) hydrogen bonds : angle 4.21028 / 2.99 ( 3197) *********************** 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 277 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8404 (tpp) cc_final: 0.7883 (tpp) REVERT: B 499 MET cc_start: 0.8266 (tpt) cc_final: 0.7897 (tpt) REVERT: B 520 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 525 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8527 (tp-100) REVERT: B 621 MET cc_start: 0.8810 (mmm) cc_final: 0.8532 (mmp) REVERT: B 661 LEU cc_start: 0.9563 (mt) cc_final: 0.9311 (mt) REVERT: B 793 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 797 GLU cc_start: 0.9184 (tt0) cc_final: 0.8365 (tm-30) REVERT: B 1078 LEU cc_start: 0.8251 (tt) cc_final: 0.7952 (mt) REVERT: B 1109 LEU cc_start: 0.9450 (tp) cc_final: 0.9202 (tp) REVERT: B 1112 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 1114 TYR cc_start: 0.8867 (m-10) cc_final: 0.8405 (m-10) REVERT: C 91 MET cc_start: 0.8693 (mtm) cc_final: 0.8326 (ttp) REVERT: C 115 LEU cc_start: 0.9131 (mt) cc_final: 0.8904 (mp) REVERT: C 385 GLU cc_start: 0.8891 (tt0) cc_final: 0.8439 (tt0) REVERT: C 571 LEU cc_start: 0.9377 (mt) cc_final: 0.9057 (mt) REVERT: C 667 MET cc_start: 0.9119 (mpp) cc_final: 0.8675 (mtm) REVERT: C 685 TYR cc_start: 0.8425 (t80) cc_final: 0.7621 (t80) REVERT: C 790 ASP cc_start: 0.8266 (t0) cc_final: 0.7805 (t0) REVERT: D 169 ILE cc_start: 0.9248 (pt) cc_final: 0.8912 (mp) REVERT: D 270 GLU cc_start: 0.6487 (tm-30) cc_final: 0.5299 (tm-30) REVERT: D 484 ILE cc_start: 0.8445 (mm) cc_final: 0.8007 (tp) REVERT: D 488 ASP cc_start: 0.8345 (t0) cc_final: 0.8119 (t0) REVERT: D 545 GLU cc_start: 0.8007 (tt0) cc_final: 0.7271 (pm20) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1582 time to fit residues: 71.9850 Evaluate side-chains 189 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 0.0870 chunk 231 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 155 optimal weight: 0.1980 chunk 244 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 166 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS C 38 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN C 792 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058748 restraints weight = 111003.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060341 restraints weight = 64791.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061424 restraints weight = 44300.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.062086 restraints weight = 33663.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.062613 restraints weight = 28038.572| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24774 Z= 0.117 Angle : 0.600 12.706 33908 Z= 0.304 Chirality : 0.040 0.170 3729 Planarity : 0.004 0.061 4219 Dihedral : 15.223 87.392 3843 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.37 (0.16), residues: 2837 helix: 1.35 (0.14), residues: 1421 sheet: -0.05 (0.30), residues: 289 loop : -1.09 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 445 TYR 0.014 0.001 TYR C 714 PHE 0.021 0.001 PHE D 386 TRP 0.012 0.001 TRP C 841 HIS 0.009 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (24774) covalent geometry : angle 0.60029 / 0.30 (33908) hydrogen bonds : bond 0.03585 / 2.25 ( 1106) hydrogen bonds : angle 4.15221 / 2.95 ( 3197) *********************** 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 269 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8354 (tpp) cc_final: 0.7881 (tpp) REVERT: B 499 MET cc_start: 0.8228 (tpt) cc_final: 0.7880 (tpt) REVERT: B 525 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8588 (tp-100) REVERT: B 621 MET cc_start: 0.8859 (mmm) cc_final: 0.8579 (mmp) REVERT: B 727 MET cc_start: 0.8378 (mtt) cc_final: 0.8018 (mtt) REVERT: B 797 GLU cc_start: 0.9135 (tt0) cc_final: 0.8417 (tm-30) REVERT: B 1066 ILE cc_start: 0.9231 (mt) cc_final: 0.7857 (mt) REVERT: B 1078 LEU cc_start: 0.8154 (tt) cc_final: 0.7878 (mt) REVERT: B 1109 LEU cc_start: 0.9444 (tp) cc_final: 0.9236 (tp) REVERT: B 1112 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 1114 TYR cc_start: 0.8843 (m-10) cc_final: 0.8378 (m-10) REVERT: C 2 LEU cc_start: 0.7477 (tt) cc_final: 0.7206 (tt) REVERT: C 91 MET cc_start: 0.8669 (mtm) cc_final: 0.8255 (ttp) REVERT: C 115 LEU cc_start: 0.9145 (mt) cc_final: 0.8933 (mp) REVERT: C 260 LEU cc_start: 0.8239 (tp) cc_final: 0.8025 (tp) REVERT: C 385 GLU cc_start: 0.8784 (tt0) cc_final: 0.8305 (tt0) REVERT: C 571 LEU cc_start: 0.9419 (mt) cc_final: 0.9003 (mt) REVERT: C 667 MET cc_start: 0.8977 (mpp) cc_final: 0.8564 (mtm) REVERT: C 685 TYR cc_start: 0.8183 (t80) cc_final: 0.7412 (t80) REVERT: C 790 ASP cc_start: 0.8211 (t0) cc_final: 0.7780 (t0) REVERT: C 851 MET cc_start: 0.8702 (mtt) cc_final: 0.8360 (mtp) REVERT: C 965 LEU cc_start: 0.8579 (tp) cc_final: 0.8372 (tp) REVERT: D 169 ILE cc_start: 0.9183 (pt) cc_final: 0.8861 (mp) REVERT: D 275 ASP cc_start: 0.8626 (p0) cc_final: 0.8139 (p0) REVERT: D 484 ILE cc_start: 0.8454 (mm) cc_final: 0.8049 (tp) REVERT: D 488 ASP cc_start: 0.8299 (t0) cc_final: 0.8073 (t0) REVERT: D 545 GLU cc_start: 0.7973 (tt0) cc_final: 0.7287 (pm20) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1553 time to fit residues: 68.9482 Evaluate side-chains 192 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 104 optimal weight: 30.0000 chunk 172 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS B1150 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 979 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.056843 restraints weight = 113297.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058365 restraints weight = 66487.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059417 restraints weight = 45615.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.060108 restraints weight = 34921.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060543 restraints weight = 28925.156| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 24774 Z= 0.209 Angle : 0.659 9.436 33908 Z= 0.337 Chirality : 0.042 0.198 3729 Planarity : 0.004 0.059 4219 Dihedral : 15.314 88.232 3843 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.36 (0.16), residues: 2837 helix: 1.29 (0.14), residues: 1427 sheet: -0.04 (0.30), residues: 293 loop : -1.05 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 255 TYR 0.018 0.002 TYR C 492 PHE 0.017 0.002 PHE C 68 TRP 0.016 0.002 TRP B 652 HIS 0.007 0.001 HIS B 689 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (24774) covalent geometry : angle 0.65860 / 0.34 (33908) hydrogen bonds : bond 0.03947 / 2.52 ( 1106) hydrogen bonds : angle 4.33354 / 3.08 ( 3197) *********************** 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 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8441 (tpp) cc_final: 0.7958 (tpp) REVERT: B 384 ASP cc_start: 0.8818 (t70) cc_final: 0.8569 (t0) REVERT: B 499 MET cc_start: 0.8234 (tpt) cc_final: 0.7944 (tpt) REVERT: B 525 GLN cc_start: 0.9072 (mm-40) cc_final: 0.8602 (tp-100) REVERT: B 621 MET cc_start: 0.9048 (mmm) cc_final: 0.8743 (mmp) REVERT: B 661 LEU cc_start: 0.9500 (mt) cc_final: 0.9212 (mt) REVERT: B 727 MET cc_start: 0.8515 (mtt) cc_final: 0.8091 (mtt) REVERT: B 797 GLU cc_start: 0.9238 (tt0) cc_final: 0.8511 (tm-30) REVERT: B 1078 LEU cc_start: 0.8231 (tt) cc_final: 0.7951 (mt) REVERT: B 1109 LEU cc_start: 0.9475 (tp) cc_final: 0.9215 (tp) REVERT: B 1112 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 1114 TYR cc_start: 0.8899 (m-10) cc_final: 0.8450 (m-10) REVERT: C 2 LEU cc_start: 0.7463 (tt) cc_final: 0.7262 (tt) REVERT: C 91 MET cc_start: 0.8735 (mtm) cc_final: 0.8380 (ttp) REVERT: C 115 LEU cc_start: 0.9141 (mt) cc_final: 0.8928 (mp) REVERT: C 342 ILE cc_start: 0.9572 (tt) cc_final: 0.9311 (tp) REVERT: C 396 MET cc_start: 0.8645 (tpp) cc_final: 0.8440 (tpp) REVERT: C 571 LEU cc_start: 0.9440 (mt) cc_final: 0.9075 (mt) REVERT: C 685 TYR cc_start: 0.8347 (t80) cc_final: 0.7568 (t80) REVERT: C 790 ASP cc_start: 0.8467 (t0) cc_final: 0.8109 (t0) REVERT: C 851 MET cc_start: 0.8762 (mtt) cc_final: 0.8293 (mtp) REVERT: D 169 ILE cc_start: 0.9322 (pt) cc_final: 0.8924 (mp) REVERT: D 273 MET cc_start: 0.8559 (mtm) cc_final: 0.8338 (mtt) REVERT: D 484 ILE cc_start: 0.8460 (mm) cc_final: 0.8070 (tp) REVERT: D 488 ASP cc_start: 0.8351 (t0) cc_final: 0.8078 (t0) REVERT: D 545 GLU cc_start: 0.7997 (tt0) cc_final: 0.7291 (pm20) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1534 time to fit residues: 62.1627 Evaluate side-chains 178 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 130 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.072753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057887 restraints weight = 112029.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.059439 restraints weight = 65839.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060495 restraints weight = 45164.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061208 restraints weight = 34494.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.061675 restraints weight = 28480.199| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24774 Z= 0.133 Angle : 0.611 11.998 33908 Z= 0.310 Chirality : 0.041 0.216 3729 Planarity : 0.004 0.047 4219 Dihedral : 15.289 88.661 3843 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2837 helix: 1.39 (0.14), residues: 1426 sheet: 0.01 (0.31), residues: 283 loop : -1.01 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 662 TYR 0.020 0.001 TYR C 492 PHE 0.017 0.001 PHE C 68 TRP 0.044 0.001 TRP C 248 HIS 0.011 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24774) covalent geometry : angle 0.61127 / 0.31 (33908) hydrogen bonds : bond 0.03694 / 2.34 ( 1106) hydrogen bonds : angle 4.20375 / 3.00 ( 3197) ********************** 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 249 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 MET cc_start: 0.8328 (tpp) cc_final: 0.7882 (tpp) REVERT: B 384 ASP cc_start: 0.8805 (t70) cc_final: 0.8569 (t0) REVERT: B 499 MET cc_start: 0.8265 (tpt) cc_final: 0.7964 (tpt) REVERT: B 525 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8527 (tp-100) REVERT: B 621 MET cc_start: 0.8985 (mmm) cc_final: 0.8621 (mmp) REVERT: B 658 MET cc_start: 0.8723 (tpt) cc_final: 0.8348 (tmm) REVERT: B 661 LEU cc_start: 0.9550 (mt) cc_final: 0.9333 (mt) REVERT: B 727 MET cc_start: 0.8497 (mtt) cc_final: 0.8035 (mtt) REVERT: B 797 GLU cc_start: 0.9168 (tt0) cc_final: 0.8515 (tm-30) REVERT: B 1066 ILE cc_start: 0.9237 (mt) cc_final: 0.7793 (mt) REVERT: B 1109 LEU cc_start: 0.9498 (tp) cc_final: 0.9297 (tp) REVERT: B 1112 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8374 (tm-30) REVERT: B 1114 TYR cc_start: 0.8861 (m-10) cc_final: 0.8419 (m-10) REVERT: C 91 MET cc_start: 0.8699 (mtm) cc_final: 0.8352 (ttp) REVERT: C 115 LEU cc_start: 0.9128 (mt) cc_final: 0.8893 (mp) REVERT: C 230 LEU cc_start: 0.9221 (mt) cc_final: 0.8952 (mt) REVERT: C 260 LEU cc_start: 0.8217 (tp) cc_final: 0.8006 (tp) REVERT: C 309 ASP cc_start: 0.8858 (m-30) cc_final: 0.8518 (m-30) REVERT: C 342 ILE cc_start: 0.9559 (tt) cc_final: 0.9317 (tp) REVERT: C 385 GLU cc_start: 0.8662 (tt0) cc_final: 0.8217 (tt0) REVERT: C 571 LEU cc_start: 0.9431 (mt) cc_final: 0.9045 (mt) REVERT: C 667 MET cc_start: 0.8870 (mpp) cc_final: 0.8551 (mtm) REVERT: C 685 TYR cc_start: 0.8279 (t80) cc_final: 0.7460 (t80) REVERT: C 790 ASP cc_start: 0.8327 (t0) cc_final: 0.8033 (t0) REVERT: C 851 MET cc_start: 0.8732 (mtt) cc_final: 0.8300 (mtp) REVERT: D 169 ILE cc_start: 0.9322 (pt) cc_final: 0.8969 (mp) REVERT: D 275 ASP cc_start: 0.8649 (p0) cc_final: 0.8334 (p0) REVERT: D 324 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8138 (pp20) REVERT: D 484 ILE cc_start: 0.8458 (mm) cc_final: 0.8091 (tp) REVERT: D 488 ASP cc_start: 0.8296 (t0) cc_final: 0.8020 (t0) REVERT: D 545 GLU cc_start: 0.7977 (tt0) cc_final: 0.7268 (pm20) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1500 time to fit residues: 62.3557 Evaluate side-chains 190 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 286 optimal weight: 50.0000 chunk 198 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 17 optimal weight: 0.0020 chunk 9 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 238 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 chunk 202 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.072985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.057828 restraints weight = 111810.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059424 restraints weight = 64462.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.060513 restraints weight = 43826.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.061273 restraints weight = 33372.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061757 restraints weight = 27442.863| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24774 Z= 0.128 Angle : 0.598 9.206 33908 Z= 0.305 Chirality : 0.040 0.165 3729 Planarity : 0.004 0.051 4219 Dihedral : 15.245 87.858 3843 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.51 (0.16), residues: 2837 helix: 1.39 (0.14), residues: 1428 sheet: 0.08 (0.30), residues: 289 loop : -0.95 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 662 TYR 0.020 0.001 TYR C 492 PHE 0.019 0.001 PHE C 68 TRP 0.016 0.001 TRP C 248 HIS 0.010 0.001 HIS B 956 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (24774) covalent geometry : angle 0.59786 / 0.31 (33908) hydrogen bonds : bond 0.03653 / 2.31 ( 1106) hydrogen bonds : angle 4.19060 / 2.99 ( 3197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3695.48 seconds wall clock time: 64 minutes 54.83 seconds (3894.83 seconds total)