Starting phenix.real_space_refine on Sat Jul 4 22:48:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sje_10215/07_2026/6sje_10215.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sje_10215/07_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_10215/07_2026/6sje_10215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sje_10215/07_2026/6sje_10215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sje_10215/07_2026/6sje_10215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sje_10215/07_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-dev-6108/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: 5.04, 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 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: 2.61 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: 4.24 Time building geometry restraints manager: 2.41 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=" 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=" O3' DC X 80 " pdb=" P DT X 81 " ideal model delta sigma weight residual 1.607 1.681 -0.074 1.50e-02 4.44e+03 2.41e+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=" C3' DC X 80 " pdb=" O3' DC X 80 " ideal model delta sigma weight residual 1.435 1.473 -0.038 1.30e-02 5.92e+03 8.40e+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: 1.090 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.840 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.740 ------------------------------------------------------------------------------- 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= 0.238 Angle : 0.618 11.578 33908 Z= 0.425 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 0.61818 / 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 : 0.677 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: symmetry clash REVERT: B 56 VAL cc_start: 0.9226 (t) cc_final: 0.8942 (p) REVERT: B 133 CYS cc_start: 0.8532 (m) cc_final: 0.8207 (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: 0.8791 (mt) REVERT: B 348 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 518 MET cc_start: 0.8818 (mmm) cc_final: 0.8406 (mmp) REVERT: B 595 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8115 (pt0) REVERT: B 797 GLU cc_start: 0.8771 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 798 ASP cc_start: 0.7880 (m-30) cc_final: 0.6683 (m-30) REVERT: B 804 VAL cc_start: 0.9106 (t) cc_final: 0.8879 (p) REVERT: B 1066 ILE cc_start: 0.9334 (mt) cc_final: 0.8430 (mt) REVERT: B 1078 LEU cc_start: 0.8187 (tt) cc_final: 0.7923 (mt) REVERT: B 1111 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6035 (t80) REVERT: B 1114 TYR cc_start: 0.8663 (m-10) cc_final: 0.8389 (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: 0.8439 (tt) REVERT: C 385 GLU cc_start: 0.8458 (tt0) cc_final: 0.8010 (tt0) REVERT: C 465 PHE cc_start: 0.8098 (m-80) cc_final: 0.7867 (m-80) REVERT: C 492 TYR cc_start: 0.7657 (m-80) cc_final: 0.6891 (m-80) REVERT: C 550 TYR cc_start: 0.7484 (t80) cc_final: 0.6527 (t80) REVERT: C 571 LEU cc_start: 0.8955 (mt) cc_final: 0.8730 (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: 0.6979 (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: 0.6535 (t80) REVERT: C 730 SER cc_start: 0.9204 (t) cc_final: 0.8672 (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: 0.7176 (mtt) REVERT: D 407 MET cc_start: 0.8926 (ttp) cc_final: 0.8696 (tmm) REVERT: D 444 LEU cc_start: 0.8735 (mt) cc_final: 0.8531 (tp) REVERT: D 484 ILE cc_start: 0.8703 (mm) cc_final: 0.7986 (tp) REVERT: D 537 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.7959 (p) REVERT: D 600 LEU cc_start: 0.8546 (mt) cc_final: 0.8193 (mp) outliers start: 74 outliers final: 12 residues processed: 750 average time/residue: 0.1622 time to fit residues: 183.2607 Evaluate side-chains 350 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 336 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.079011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063933 restraints weight = 107420.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.065645 restraints weight = 63006.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.066838 restraints weight = 42829.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.067589 restraints weight = 32158.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.068161 restraints weight = 26417.019| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24774 Z= 0.147 Angle : 0.614 9.055 33908 Z= 0.318 Chirality : 0.041 0.179 3729 Planarity : 0.005 0.082 4219 Dihedral : 14.710 84.899 3843 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % 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: -1.78 (0.14), residues: 2837 helix: -0.55 (0.12), residues: 1414 sheet: -0.76 (0.29), residues: 290 loop : -2.02 (0.15), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 559 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 0.00308 / 0.15 (24774) covalent geometry : angle 0.61441 / 0.32 (33908) hydrogen bonds : bond 0.04237 / 2.71 ( 1106) hydrogen bonds : angle 4.59093 / 3.25 ( 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 420 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.867 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: 0.9166 (t) cc_final: 0.8831 (p) REVERT: B 499 MET cc_start: 0.7488 (tpt) cc_final: 0.6908 (tpt) REVERT: B 518 MET cc_start: 0.8760 (mmm) cc_final: 0.8308 (mmp) REVERT: B 557 LEU cc_start: 0.9492 (mp) cc_final: 0.9266 (mp) REVERT: B 599 LEU cc_start: 0.9467 (mp) cc_final: 0.9106 (mt) REVERT: B 797 GLU cc_start: 0.8788 (tt0) cc_final: 0.8337 (tm-30) REVERT: B 798 ASP cc_start: 0.8003 (m-30) cc_final: 0.7632 (m-30) REVERT: B 1078 LEU cc_start: 0.8154 (tt) cc_final: 0.7923 (mt) REVERT: B 1114 TYR cc_start: 0.8608 (m-10) cc_final: 0.8359 (m-10) REVERT: C 12 VAL cc_start: 0.9212 (t) cc_final: 0.8983 (t) REVERT: C 34 MET cc_start: 0.8621 (mmt) cc_final: 0.8253 (mmm) REVERT: C 49 THR cc_start: 0.8663 (p) cc_final: 0.8099 (t) REVERT: C 103 LEU cc_start: 0.8885 (mt) cc_final: 0.8394 (tt) REVERT: C 115 LEU cc_start: 0.9137 (mp) cc_final: 0.8753 (pp) REVERT: C 385 GLU cc_start: 0.8513 (tt0) cc_final: 0.7897 (tt0) REVERT: C 550 TYR cc_start: 0.7474 (t80) cc_final: 0.5727 (t80) REVERT: C 571 LEU cc_start: 0.9214 (mt) cc_final: 0.8894 (mm) REVERT: C 676 CYS cc_start: 0.8555 (m) cc_final: 0.8236 (m) REVERT: C 680 MET cc_start: 0.8672 (mmp) cc_final: 0.8391 (mmp) REVERT: C 714 TYR cc_start: 0.8862 (t80) cc_final: 0.8020 (t80) REVERT: C 728 TYR cc_start: 0.7958 (t80) cc_final: 0.6417 (t80) REVERT: C 730 SER cc_start: 0.9285 (t) cc_final: 0.8576 (t) REVERT: C 790 ASP cc_start: 0.7602 (t0) cc_final: 0.7175 (t0) REVERT: C 1102 MET cc_start: 0.9164 (ttp) cc_final: 0.8904 (tmm) REVERT: D 275 ASP cc_start: 0.8322 (p0) cc_final: 0.8029 (p0) REVERT: D 393 ILE cc_start: 0.7958 (pt) cc_final: 0.7691 (pt) REVERT: D 407 MET cc_start: 0.8844 (ttp) cc_final: 0.8631 (tmm) REVERT: D 444 LEU cc_start: 0.8767 (mt) cc_final: 0.8542 (tp) outliers start: 1 outliers final: 1 residues processed: 420 average time/residue: 0.1518 time to fit residues: 99.9789 Evaluate side-chains 275 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 10.0000 chunk 233 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 179 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 224 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 237 HIS C 660 ASN C 817 HIS ** C1078 ASN ** 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 = 0.3616 r_free = 0.3616 target = 0.077659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.062538 restraints weight = 109630.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064197 restraints weight = 64760.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.065352 restraints weight = 44183.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.066067 restraints weight = 33570.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066637 restraints weight = 27707.843| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24774 Z= 0.134 Angle : 0.574 8.734 33908 Z= 0.300 Chirality : 0.040 0.200 3729 Planarity : 0.004 0.064 4219 Dihedral : 14.749 86.830 3843 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.08 % Allowed : 2.44 % 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: -0.83 (0.15), residues: 2837 helix: 0.38 (0.13), residues: 1421 sheet: -0.51 (0.29), residues: 293 loop : -1.74 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 974 TYR 0.014 0.001 TYR C 492 PHE 0.023 0.001 PHE B 756 TRP 0.014 0.001 TRP B 652 HIS 0.015 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (24774) covalent geometry : angle 0.57414 / 0.30 (33908) hydrogen bonds : bond 0.03795 / 2.41 ( 1106) hydrogen bonds : angle 4.29631 / 3.05 ( 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 356 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9119 (t) cc_final: 0.8870 (p) REVERT: B 499 MET cc_start: 0.7533 (tpt) cc_final: 0.6949 (tpt) REVERT: B 518 MET cc_start: 0.8841 (mmm) cc_final: 0.8383 (mmp) REVERT: B 584 ARG cc_start: 0.8551 (mtp85) cc_final: 0.8173 (mtt-85) REVERT: B 596 MET cc_start: 0.9117 (mmt) cc_final: 0.8804 (mmp) REVERT: B 599 LEU cc_start: 0.9507 (mp) cc_final: 0.9130 (mt) REVERT: B 731 SER cc_start: 0.8517 (t) cc_final: 0.8107 (m) REVERT: B 797 GLU cc_start: 0.8927 (tt0) cc_final: 0.8413 (tm-30) REVERT: B 798 ASP cc_start: 0.8167 (m-30) cc_final: 0.7716 (m-30) REVERT: B 1024 TYR cc_start: 0.6886 (m-10) cc_final: 0.6682 (m-10) REVERT: B 1078 LEU cc_start: 0.8256 (tt) cc_final: 0.8013 (mt) REVERT: B 1112 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8351 (tm-30) REVERT: B 1114 TYR cc_start: 0.8642 (m-10) cc_final: 0.8380 (m-10) REVERT: B 1170 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: C 12 VAL cc_start: 0.9286 (t) cc_final: 0.9062 (t) REVERT: C 91 MET cc_start: 0.8660 (mtm) cc_final: 0.8321 (ttp) REVERT: C 103 LEU cc_start: 0.9008 (mt) cc_final: 0.8525 (tt) REVERT: C 115 LEU cc_start: 0.9224 (mp) cc_final: 0.8800 (pp) REVERT: C 230 LEU cc_start: 0.9099 (mt) cc_final: 0.8878 (mt) REVERT: C 342 ILE cc_start: 0.9558 (tt) cc_final: 0.9287 (tp) REVERT: C 385 GLU cc_start: 0.8556 (tt0) cc_final: 0.8329 (tt0) REVERT: C 714 TYR cc_start: 0.8855 (t80) cc_final: 0.7969 (t80) REVERT: C 790 ASP cc_start: 0.7616 (t0) cc_final: 0.7279 (t0) REVERT: D 112 MET cc_start: 0.8324 (ttm) cc_final: 0.8101 (ttm) REVERT: D 324 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7924 (pp20) REVERT: D 393 ILE cc_start: 0.7996 (pt) cc_final: 0.7734 (pt) REVERT: D 484 ILE cc_start: 0.8578 (mm) cc_final: 0.7874 (tp) outliers start: 2 outliers final: 1 residues processed: 356 average time/residue: 0.1594 time to fit residues: 90.4248 Evaluate side-chains 244 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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: 8.9990 chunk 267 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 141 optimal weight: 0.0040 chunk 153 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 196 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 130 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 610 ASN B 624 ASN B 956 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN C 724 GLN C 958 GLN D 369 GLN ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.075458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060381 restraints weight = 110439.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.061966 restraints weight = 65452.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.063078 restraints weight = 45095.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063808 restraints weight = 34299.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064344 restraints weight = 28299.213| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 24774 Z= 0.180 Angle : 0.595 9.898 33908 Z= 0.307 Chirality : 0.040 0.158 3729 Planarity : 0.004 0.065 4219 Dihedral : 14.815 88.983 3843 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % 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: -0.22 (0.15), residues: 2837 helix: 0.90 (0.14), residues: 1429 sheet: -0.36 (0.29), residues: 289 loop : -1.46 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 448 TYR 0.029 0.002 TYR D 108 PHE 0.025 0.002 PHE D 386 TRP 0.015 0.001 TRP B 652 HIS 0.011 0.001 HIS D 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (24774) covalent geometry : angle 0.59476 / 0.31 (33908) hydrogen bonds : bond 0.03714 / 2.36 ( 1106) hydrogen bonds : angle 4.21421 / 3.00 ( 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 316 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 1.010 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: 0.9188 (t) cc_final: 0.8972 (p) REVERT: B 133 CYS cc_start: 0.8520 (m) cc_final: 0.8256 (m) REVERT: B 384 ASP cc_start: 0.8847 (t70) cc_final: 0.8607 (t0) REVERT: B 419 ILE cc_start: 0.9353 (pt) cc_final: 0.9102 (pt) REVERT: B 499 MET cc_start: 0.7991 (tpt) cc_final: 0.7356 (tpt) REVERT: B 518 MET cc_start: 0.8937 (mmm) cc_final: 0.8514 (mmp) REVERT: B 604 MET cc_start: 0.8845 (ttp) cc_final: 0.8592 (ttt) REVERT: B 731 SER cc_start: 0.8580 (t) cc_final: 0.8169 (m) REVERT: B 797 GLU cc_start: 0.9041 (tt0) cc_final: 0.8532 (tm-30) REVERT: B 798 ASP cc_start: 0.8234 (m-30) cc_final: 0.7952 (m-30) REVERT: B 1078 LEU cc_start: 0.8264 (tt) cc_final: 0.7843 (mp) REVERT: B 1112 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 1114 TYR cc_start: 0.8734 (m-10) cc_final: 0.8370 (m-10) REVERT: C 91 MET cc_start: 0.8695 (mtm) cc_final: 0.8377 (ttp) REVERT: C 385 GLU cc_start: 0.8853 (tt0) cc_final: 0.8471 (tt0) REVERT: C 685 TYR cc_start: 0.8536 (t80) cc_final: 0.8232 (t80) REVERT: C 714 TYR cc_start: 0.8883 (t80) cc_final: 0.8007 (t80) REVERT: C 790 ASP cc_start: 0.8045 (t0) cc_final: 0.7456 (t0) REVERT: C 851 MET cc_start: 0.8553 (mtt) cc_final: 0.8340 (mtp) REVERT: C 1080 MET cc_start: 0.8202 (ppp) cc_final: 0.7840 (ppp) REVERT: D 269 ASP cc_start: 0.8260 (t0) cc_final: 0.7654 (p0) REVERT: D 275 ASP cc_start: 0.8499 (p0) cc_final: 0.8188 (p0) REVERT: D 393 ILE cc_start: 0.8000 (pt) cc_final: 0.7684 (pt) REVERT: D 484 ILE cc_start: 0.8656 (mm) cc_final: 0.7926 (tp) REVERT: D 600 LEU cc_start: 0.8977 (mt) cc_final: 0.8736 (mp) outliers start: 1 outliers final: 0 residues processed: 316 average time/residue: 0.1571 time to fit residues: 80.4129 Evaluate side-chains 210 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6344 > 50: distance: 38 - 43: 33.377 distance: 43 - 44: 41.047 distance: 44 - 45: 39.715 distance: 45 - 47: 8.783 distance: 47 - 48: 27.453 distance: 48 - 49: 16.002 distance: 48 - 51: 27.751 distance: 49 - 50: 15.685 distance: 49 - 53: 12.667 distance: 51 - 52: 23.538 distance: 53 - 54: 9.655 distance: 54 - 55: 6.292 distance: 54 - 57: 5.093 distance: 55 - 56: 10.982 distance: 55 - 62: 4.434 distance: 57 - 58: 3.269 distance: 58 - 59: 12.415 distance: 59 - 60: 8.287 distance: 59 - 61: 5.774 distance: 62 - 63: 14.918 distance: 63 - 64: 12.569 distance: 63 - 66: 19.889 distance: 64 - 65: 27.989 distance: 64 - 73: 27.712 distance: 66 - 67: 9.897 distance: 67 - 68: 17.880 distance: 68 - 69: 8.104 distance: 69 - 70: 5.018 distance: 70 - 71: 7.243 distance: 70 - 72: 4.551 distance: 73 - 74: 9.935 distance: 74 - 75: 13.213 distance: 74 - 77: 11.115 distance: 75 - 76: 17.619 distance: 75 - 81: 14.894 distance: 77 - 78: 14.686 distance: 78 - 79: 7.304 distance: 78 - 80: 8.302 distance: 82 - 83: 9.845 distance: 82 - 85: 3.637 distance: 83 - 84: 7.961 distance: 83 - 92: 9.354 distance: 85 - 86: 3.860 distance: 86 - 87: 9.394 distance: 87 - 88: 4.620 distance: 88 - 89: 6.853 distance: 89 - 90: 7.090 distance: 89 - 91: 7.204 distance: 92 - 93: 11.516 distance: 93 - 94: 13.498 distance: 93 - 96: 9.944 distance: 94 - 95: 6.219 distance: 94 - 102: 12.230 distance: 96 - 97: 9.389 distance: 97 - 98: 11.263 distance: 97 - 99: 7.593 distance: 98 - 100: 8.542 distance: 99 - 101: 9.241 distance: 100 - 101: 6.140 distance: 102 - 103: 9.056 distance: 103 - 104: 9.214 distance: 103 - 106: 12.486 distance: 104 - 105: 10.003 distance: 104 - 112: 16.320 distance: 106 - 107: 6.240 distance: 107 - 108: 10.118 distance: 108 - 110: 7.603 distance: 109 - 111: 13.693 distance: 110 - 111: 8.170 distance: 112 - 113: 25.334 distance: 113 - 114: 20.892 distance: 113 - 116: 15.063 distance: 114 - 115: 31.194 distance: 114 - 117: 19.105 distance: 117 - 118: 9.391 distance: 118 - 119: 24.339 distance: 119 - 120: 34.932 distance: 119 - 121: 17.779