Starting phenix.real_space_refine on Fri Jun 20 15:17:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t2v_10370/06_2025/6t2v_10370.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t2v_10370/06_2025/6t2v_10370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t2v_10370/06_2025/6t2v_10370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t2v_10370/06_2025/6t2v_10370.map" model { file = "/net/cci-nas-00/data/ceres_data/6t2v_10370/06_2025/6t2v_10370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t2v_10370/06_2025/6t2v_10370.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 54 5.49 5 S 101 5.16 5 C 14897 2.51 5 N 4192 2.21 5 O 4582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23826 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1098 Classifications: {'DNA': 54} Link IDs: {'rna3p': 53} Chain breaks: 1 Time building chain proxies: 13.89, per 1000 atoms: 0.58 Number of scatterers: 23826 At special positions: 0 Unit cell: (152.985, 150.815, 131.285, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 54 15.00 O 4582 8.00 N 4192 7.00 C 14897 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.61 Conformation dependent library (CDL) restraints added in 2.9 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 16 sheets defined 53.1% alpha, 9.2% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 8.50 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: 3.556A pdb=" N GLU B 58 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 55 through 59' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.642A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.622A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.820A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.256A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.678A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.559A 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: 3.625A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.760A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.251A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.469A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.529A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.756A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.829A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 Processing helix chain 'B' and resid 560 through 573 Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.953A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.801A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.613A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.806A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.607A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 removed outlier: 3.619A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 4.103A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.514A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 3.764A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.900A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 3.880A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.707A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.633A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 3.894A 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: 3.800A 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: 3.563A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.139A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.741A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.898A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 189 through 199 Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.568A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 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 removed outlier: 3.605A pdb=" N VAL C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 428 removed outlier: 3.667A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.868A pdb=" N ALA C 453 " --> pdb=" O PRO C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 474 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.593A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.786A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.575A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.726A pdb=" N MET C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.590A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.849A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 removed outlier: 3.546A pdb=" N GLN C 812 " --> pdb=" O PRO C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.521A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.833A 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: 3.621A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 904 " --> pdb=" O ARG C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.767A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.575A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.696A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1049 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.571A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1089 through 1094 removed outlier: 4.266A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.924A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C1119 " --> pdb=" O PRO C1115 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.766A 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: 3.970A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.547A pdb=" N LEU D 137 " --> pdb=" O ASP D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.515A 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: 3.647A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.563A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 286 removed outlier: 3.569A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.739A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.519A 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: 3.813A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.537A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.539A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.534A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.661A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.749A 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: 6.497A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.777A 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: 6.294A 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: 6.591A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.643A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1155 through 1158 removed outlier: 7.225A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N MET B1061 " --> pdb=" O PRO B1026 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.370A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 266 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 324 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.928A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 3.645A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.723A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.653A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.752A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.340A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.516A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.198A 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: 6.585A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.395A 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: 7.199A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN D 439 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ILE D 552 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 441 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.459A 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: 4.488A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 10.33 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7590 1.34 - 1.45: 3403 1.45 - 1.57: 13184 1.57 - 1.69: 106 1.69 - 1.81: 169 Bond restraints: 24452 Sorted by residual: bond pdb=" N GLU B1073 " pdb=" CA GLU B1073 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.19e+00 bond pdb=" C PRO C 823 " pdb=" N LEU C 824 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.17e+00 bond pdb=" C ILE C 670 " pdb=" O ILE C 670 " ideal model delta sigma weight residual 1.232 1.240 -0.008 8.90e-03 1.26e+04 8.47e-01 bond pdb=" C SER C 419 " pdb=" N PRO C 420 " ideal model delta sigma weight residual 1.335 1.348 -0.012 1.36e-02 5.41e+03 8.32e-01 bond pdb=" CB PRO C 63 " pdb=" CG PRO C 63 " ideal model delta sigma weight residual 1.492 1.537 -0.045 5.00e-02 4.00e+02 8.22e-01 ... (remaining 24447 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 32753 1.39 - 2.78: 577 2.78 - 4.17: 60 4.17 - 5.56: 17 5.56 - 6.95: 2 Bond angle restraints: 33409 Sorted by residual: angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" N GLY B 898 " pdb=" CA GLY B 898 " pdb=" C GLY B 898 " ideal model delta sigma weight residual 110.87 115.76 -4.89 1.54e+00 4.22e-01 1.01e+01 angle pdb=" N TRP B 878 " pdb=" CA TRP B 878 " pdb=" C TRP B 878 " ideal model delta sigma weight residual 107.88 112.25 -4.37 1.41e+00 5.03e-01 9.59e+00 angle pdb=" C SER C 447 " pdb=" N HIS C 448 " pdb=" CA HIS C 448 " ideal model delta sigma weight residual 119.78 123.18 -3.40 1.24e+00 6.50e-01 7.51e+00 angle pdb=" CA GLY C 938 " pdb=" C GLY C 938 " pdb=" N GLN C 939 " ideal model delta sigma weight residual 114.98 117.50 -2.52 1.14e+00 7.69e-01 4.90e+00 ... (remaining 33404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.26: 13284 15.26 - 30.53: 832 30.53 - 45.79: 325 45.79 - 61.06: 164 61.06 - 76.32: 10 Dihedral angle restraints: 14615 sinusoidal: 6326 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 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA GLY C 657 " pdb=" C GLY C 657 " pdb=" N PRO C 658 " pdb=" CA PRO C 658 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR B 304 " pdb=" C THR B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.90e+00 ... (remaining 14612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2423 0.026 - 0.052: 828 0.052 - 0.078: 240 0.078 - 0.104: 134 0.104 - 0.131: 48 Chirality restraints: 3673 Sorted by residual: chirality pdb=" CA ILE D 233 " pdb=" N ILE D 233 " pdb=" C ILE D 233 " pdb=" CB ILE D 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL D 337 " pdb=" N VAL D 337 " pdb=" C VAL D 337 " pdb=" CB VAL D 337 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 3670 not shown) Planarity restraints: 4205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 992 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLU B 992 " -0.057 2.00e-02 2.50e+03 pdb=" O GLU B 992 " 0.021 2.00e-02 2.50e+03 pdb=" N TRP B 993 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO C 658 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 469 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP C 469 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP C 469 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 470 " 0.016 2.00e-02 2.50e+03 ... (remaining 4202 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2695 2.75 - 3.29: 21379 3.29 - 3.83: 39009 3.83 - 4.36: 44859 4.36 - 4.90: 77256 Nonbonded interactions: 185198 Sorted by model distance: nonbonded pdb=" OD1 ASN B 759 " pdb=" NH2 ARG B 822 " model vdw 2.213 3.120 nonbonded pdb=" OG SER D 303 " pdb=" O GLY D 307 " model vdw 2.285 3.040 nonbonded pdb=" NH2 ARG B 254 " pdb=" O3' DG X 61 " model vdw 2.292 3.120 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR B 394 " pdb=" OE1 GLU B 436 " model vdw 2.304 3.040 ... (remaining 185193 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 60.300 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24452 Z= 0.099 Angle : 0.453 6.953 33409 Z= 0.287 Chirality : 0.034 0.131 3673 Planarity : 0.005 0.074 4205 Dihedral : 13.085 76.320 9243 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.01 % Favored : 97.96 % Rotamer: Outliers : 3.02 % Allowed : 5.18 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.11), residues: 2837 helix: -2.53 (0.09), residues: 1409 sheet: -0.87 (0.29), residues: 276 loop : -2.44 (0.14), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 652 HIS 0.002 0.000 HIS C 377 PHE 0.007 0.000 PHE B1023 TYR 0.007 0.001 TYR B1093 ARG 0.003 0.000 ARG B 800 Details of bonding type rmsd hydrogen bonds : bond 0.14798 ( 1097) hydrogen bonds : angle 6.30144 ( 3179) covalent geometry : bond 0.00167 (24452) covalent geometry : angle 0.45276 (33409) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 441 time to evaluate : 2.815 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: B 166 ASP cc_start: 0.9158 (m-30) cc_final: 0.8830 (m-30) REVERT: B 269 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.5762 (mm) REVERT: B 354 MET cc_start: 0.7717 (mtt) cc_final: 0.7479 (mtm) REVERT: B 431 MET cc_start: 0.9115 (mtm) cc_final: 0.8620 (mtp) REVERT: B 499 MET cc_start: 0.8110 (ttp) cc_final: 0.7780 (tpp) REVERT: B 501 MET cc_start: 0.9116 (mtm) cc_final: 0.8339 (mpp) REVERT: B 518 MET cc_start: 0.7577 (mmm) cc_final: 0.6306 (mmm) REVERT: B 541 MET cc_start: 0.8598 (mtp) cc_final: 0.7617 (tpp) REVERT: B 588 PHE cc_start: 0.8255 (m-80) cc_final: 0.7894 (m-80) REVERT: B 594 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8458 (tp-100) REVERT: B 658 MET cc_start: 0.8796 (tpp) cc_final: 0.8531 (tpt) REVERT: B 711 LEU cc_start: 0.9635 (tp) cc_final: 0.9386 (tp) REVERT: B 753 TRP cc_start: 0.9178 (OUTLIER) cc_final: 0.7614 (t60) REVERT: B 964 PHE cc_start: 0.8239 (m-80) cc_final: 0.7892 (m-10) REVERT: B 1021 MET cc_start: 0.9165 (ttp) cc_final: 0.8732 (ppp) REVERT: C 50 LEU cc_start: 0.9252 (mt) cc_final: 0.9011 (tt) REVERT: C 91 MET cc_start: 0.8431 (mtm) cc_final: 0.8100 (mtm) REVERT: C 133 ASP cc_start: 0.8831 (t0) cc_final: 0.8506 (m-30) REVERT: C 165 GLN cc_start: 0.9140 (mt0) cc_final: 0.8781 (mt0) REVERT: C 234 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6812 (mm) REVERT: C 408 ILE cc_start: 0.9364 (mt) cc_final: 0.8940 (pt) REVERT: C 465 PHE cc_start: 0.8373 (m-80) cc_final: 0.7752 (m-80) REVERT: C 471 LEU cc_start: 0.8936 (mt) cc_final: 0.8544 (pp) REVERT: C 906 ASP cc_start: 0.8350 (m-30) cc_final: 0.8019 (t0) REVERT: C 980 LEU cc_start: 0.8905 (tp) cc_final: 0.8663 (tp) REVERT: D 25 LEU cc_start: 0.9307 (mt) cc_final: 0.8994 (pp) REVERT: D 100 MET cc_start: 0.9257 (mtm) cc_final: 0.8885 (mpp) REVERT: D 108 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.5915 (p90) REVERT: D 201 LEU cc_start: 0.9360 (mt) cc_final: 0.9097 (tp) REVERT: D 212 LEU cc_start: 0.9492 (tp) cc_final: 0.8917 (tp) REVERT: D 273 MET cc_start: 0.8275 (mtm) cc_final: 0.8005 (ttt) REVERT: D 280 SER cc_start: 0.7789 (p) cc_final: 0.6701 (p) REVERT: D 282 LEU cc_start: 0.9357 (tp) cc_final: 0.9063 (pp) outliers start: 73 outliers final: 13 residues processed: 508 average time/residue: 0.3746 time to fit residues: 291.5969 Evaluate side-chains 257 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 746 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 493 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 116 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 GLN B 120 GLN B 150 GLN B 181 GLN B 222 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 455 ASN B 458 ASN B 463 GLN B 562 GLN B 566 GLN B 610 ASN B 650 GLN B 713 GLN B 765 GLN B 769 HIS B 848 GLN B 943 HIS B 944 GLN B1072 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 HIS B1134 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 390 HIS C 510 ASN C 570 GLN C 614 GLN ** C 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 749 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 ASN C 817 HIS C 822 GLN C 843 HIS C 883 GLN C 925 GLN C 951 GLN C1091 GLN C1108 GLN D 22 GLN D 89 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 152 ASN D 251 GLN D 328 GLN D 469 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.067188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.048385 restraints weight = 143774.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.049993 restraints weight = 82206.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.050982 restraints weight = 57772.362| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 24452 Z= 0.333 Angle : 0.848 14.501 33409 Z= 0.429 Chirality : 0.044 0.171 3673 Planarity : 0.006 0.081 4205 Dihedral : 13.859 82.437 3732 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.35 % Allowed : 10.81 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 2837 helix: -0.06 (0.13), residues: 1435 sheet: -0.54 (0.29), residues: 276 loop : -1.94 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 272 HIS 0.012 0.002 HIS C 233 PHE 0.024 0.003 PHE C 526 TYR 0.022 0.003 TYR C 728 ARG 0.017 0.001 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.05788 ( 1097) hydrogen bonds : angle 4.79274 ( 3179) covalent geometry : bond 0.00720 (24452) covalent geometry : angle 0.84827 (33409) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 186 time to evaluate : 2.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9257 (pttm) cc_final: 0.8992 (pttm) REVERT: B 354 MET cc_start: 0.8167 (mtt) cc_final: 0.7788 (mtm) REVERT: B 431 MET cc_start: 0.8998 (mtm) cc_final: 0.8776 (mtp) REVERT: B 501 MET cc_start: 0.9381 (mtm) cc_final: 0.8815 (mtm) REVERT: B 518 MET cc_start: 0.8360 (mmm) cc_final: 0.8032 (mmm) REVERT: B 541 MET cc_start: 0.8602 (mtp) cc_final: 0.7514 (tpp) REVERT: B 559 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8103 (ttt90) REVERT: B 658 MET cc_start: 0.9089 (tpp) cc_final: 0.8575 (tpt) REVERT: B 753 TRP cc_start: 0.9233 (OUTLIER) cc_final: 0.7806 (t60) REVERT: B 794 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7836 (ttp80) REVERT: B 1102 MET cc_start: 0.9107 (tmm) cc_final: 0.8195 (tmm) REVERT: B 1111 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8343 (p90) REVERT: C 1 MET cc_start: 0.7297 (tpp) cc_final: 0.7073 (tmm) REVERT: C 17 MET cc_start: 0.9213 (ptm) cc_final: 0.8980 (ptp) REVERT: C 89 GLN cc_start: 0.8505 (pm20) cc_final: 0.8153 (pm20) REVERT: C 133 ASP cc_start: 0.8873 (t0) cc_final: 0.8642 (t0) REVERT: C 408 ILE cc_start: 0.9609 (mt) cc_final: 0.9310 (pt) REVERT: C 665 MET cc_start: 0.7700 (mtp) cc_final: 0.7270 (mtp) REVERT: C 667 MET cc_start: 0.6053 (ttm) cc_final: 0.5122 (ttm) REVERT: C 906 ASP cc_start: 0.8515 (m-30) cc_final: 0.8280 (t0) REVERT: C 1102 MET cc_start: 0.9458 (ttt) cc_final: 0.9188 (ttp) REVERT: D 25 LEU cc_start: 0.9341 (mt) cc_final: 0.9098 (tt) REVERT: D 108 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6209 (p90) REVERT: D 112 MET cc_start: 0.8885 (tpp) cc_final: 0.8644 (ttm) REVERT: D 471 HIS cc_start: 0.8623 (m90) cc_final: 0.8150 (m-70) REVERT: D 512 PHE cc_start: 0.9315 (m-80) cc_final: 0.8999 (m-10) REVERT: D 514 MET cc_start: 0.7961 (mmm) cc_final: 0.7646 (mmm) REVERT: D 520 LYS cc_start: 0.9011 (tttt) cc_final: 0.8679 (mtpt) REVERT: D 536 MET cc_start: 0.5788 (tpt) cc_final: 0.5231 (tpt) outliers start: 81 outliers final: 45 residues processed: 256 average time/residue: 0.3317 time to fit residues: 138.4351 Evaluate side-chains 202 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 3 optimal weight: 0.9990 chunk 268 optimal weight: 8.9990 chunk 253 optimal weight: 40.0000 chunk 224 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 GLN B 689 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 336 HIS C 725 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.068062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.049241 restraints weight = 141992.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.050902 restraints weight = 79963.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.052000 restraints weight = 55514.080| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24452 Z= 0.141 Angle : 0.586 10.940 33409 Z= 0.294 Chirality : 0.039 0.336 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.810 88.479 3722 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.40 % Allowed : 11.30 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2837 helix: 0.86 (0.14), residues: 1442 sheet: -0.49 (0.29), residues: 275 loop : -1.67 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 972 HIS 0.005 0.001 HIS D 289 PHE 0.017 0.001 PHE B 351 TYR 0.013 0.001 TYR B 394 ARG 0.011 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03712 ( 1097) hydrogen bonds : angle 4.18748 ( 3179) covalent geometry : bond 0.00311 (24452) covalent geometry : angle 0.58642 (33409) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 172 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9220 (pttm) cc_final: 0.8922 (pttm) REVERT: B 354 MET cc_start: 0.8110 (mtt) cc_final: 0.7751 (mtm) REVERT: B 499 MET cc_start: 0.6706 (ppp) cc_final: 0.6289 (ppp) REVERT: B 501 MET cc_start: 0.9223 (mtm) cc_final: 0.8931 (mtm) REVERT: B 518 MET cc_start: 0.8348 (mmm) cc_final: 0.7483 (mmm) REVERT: B 541 MET cc_start: 0.8646 (mtp) cc_final: 0.7543 (tpp) REVERT: B 559 ARG cc_start: 0.8433 (ttp-170) cc_final: 0.8207 (ttt90) REVERT: B 658 MET cc_start: 0.9168 (tpp) cc_final: 0.8780 (tpt) REVERT: B 660 MET cc_start: 0.8556 (tpt) cc_final: 0.7962 (tpt) REVERT: B 748 GLU cc_start: 0.8833 (tt0) cc_final: 0.8537 (mt-10) REVERT: B 753 TRP cc_start: 0.9169 (OUTLIER) cc_final: 0.8009 (t60) REVERT: B 1102 MET cc_start: 0.9381 (tmm) cc_final: 0.9035 (tmm) REVERT: B 1111 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8344 (p90) REVERT: B 1168 MET cc_start: 0.7799 (mmm) cc_final: 0.7503 (mmm) REVERT: B 1171 MET cc_start: 0.7616 (ptt) cc_final: 0.7033 (ppp) REVERT: C 1 MET cc_start: 0.7413 (tpp) cc_final: 0.7121 (tmm) REVERT: C 96 MET cc_start: 0.8904 (ttm) cc_final: 0.8478 (tpp) REVERT: C 227 LEU cc_start: 0.9642 (mt) cc_final: 0.9244 (pp) REVERT: C 408 ILE cc_start: 0.9592 (mt) cc_final: 0.9278 (pt) REVERT: C 471 LEU cc_start: 0.8886 (mt) cc_final: 0.8526 (pp) REVERT: C 665 MET cc_start: 0.7629 (mtp) cc_final: 0.7300 (mtm) REVERT: C 667 MET cc_start: 0.6085 (ttm) cc_final: 0.5293 (ttm) REVERT: C 787 MET cc_start: 0.7375 (pmm) cc_final: 0.6817 (ptt) REVERT: C 906 ASP cc_start: 0.8506 (m-30) cc_final: 0.8197 (t0) REVERT: C 1102 MET cc_start: 0.9465 (ttt) cc_final: 0.9221 (ttp) REVERT: D 25 LEU cc_start: 0.9304 (mt) cc_final: 0.9024 (pp) REVERT: D 100 MET cc_start: 0.8904 (mpp) cc_final: 0.8607 (mpp) REVERT: D 108 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.6077 (p90) REVERT: D 112 MET cc_start: 0.8896 (tpp) cc_final: 0.8612 (ttm) REVERT: D 278 MET cc_start: 0.8464 (mtm) cc_final: 0.7886 (ptp) REVERT: D 471 HIS cc_start: 0.8614 (m90) cc_final: 0.8067 (m-70) REVERT: D 512 PHE cc_start: 0.9331 (m-80) cc_final: 0.9059 (m-10) REVERT: D 520 LYS cc_start: 0.8969 (tttt) cc_final: 0.8650 (mtpt) REVERT: D 536 MET cc_start: 0.5532 (tpt) cc_final: 0.4954 (tpt) outliers start: 58 outliers final: 31 residues processed: 217 average time/residue: 0.3215 time to fit residues: 116.5301 Evaluate side-chains 180 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1116 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 22 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 103 optimal weight: 30.0000 chunk 150 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 223 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 4 optimal weight: 0.0030 chunk 255 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 overall best weight: 6.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 GLN B 695 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 65 HIS ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 HIS ** D 495 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.065072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046401 restraints weight = 146478.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.047956 restraints weight = 83548.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.048975 restraints weight = 58735.909| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24452 Z= 0.221 Angle : 0.659 11.551 33409 Z= 0.332 Chirality : 0.042 0.309 3673 Planarity : 0.004 0.052 4205 Dihedral : 13.956 89.328 3720 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.06 % Allowed : 11.30 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 2837 helix: 0.93 (0.13), residues: 1459 sheet: -0.37 (0.30), residues: 265 loop : -1.52 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 272 HIS 0.008 0.001 HIS D 289 PHE 0.013 0.002 PHE C 526 TYR 0.034 0.002 TYR B1107 ARG 0.010 0.001 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.04456 ( 1097) hydrogen bonds : angle 4.36944 ( 3179) covalent geometry : bond 0.00487 (24452) covalent geometry : angle 0.65940 (33409) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 141 time to evaluate : 2.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 LYS cc_start: 0.9209 (pttm) cc_final: 0.8870 (pttp) REVERT: B 354 MET cc_start: 0.8097 (mtt) cc_final: 0.7749 (mtm) REVERT: B 499 MET cc_start: 0.7166 (ppp) cc_final: 0.6457 (ppp) REVERT: B 501 MET cc_start: 0.9335 (mtm) cc_final: 0.9034 (mtm) REVERT: B 518 MET cc_start: 0.8583 (mmm) cc_final: 0.8087 (mmm) REVERT: B 541 MET cc_start: 0.8618 (mtp) cc_final: 0.7463 (tpp) REVERT: B 660 MET cc_start: 0.8552 (tpt) cc_final: 0.7833 (tpt) REVERT: B 748 GLU cc_start: 0.8895 (tt0) cc_final: 0.8631 (tt0) REVERT: B 753 TRP cc_start: 0.9078 (OUTLIER) cc_final: 0.7968 (t60) REVERT: B 794 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7852 (ttp80) REVERT: B 798 ASP cc_start: 0.8482 (t0) cc_final: 0.8270 (t0) REVERT: B 1102 MET cc_start: 0.9347 (tmm) cc_final: 0.9027 (tmm) REVERT: B 1111 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8441 (p90) REVERT: B 1168 MET cc_start: 0.8338 (mmm) cc_final: 0.8002 (mmm) REVERT: B 1171 MET cc_start: 0.7794 (ptt) cc_final: 0.7312 (ppp) REVERT: C 1 MET cc_start: 0.7480 (tpp) cc_final: 0.7196 (tmm) REVERT: C 42 MET cc_start: 0.8270 (tpp) cc_final: 0.8047 (tpp) REVERT: C 408 ILE cc_start: 0.9598 (mt) cc_final: 0.9345 (pt) REVERT: C 665 MET cc_start: 0.7906 (mtp) cc_final: 0.7552 (mtp) REVERT: C 667 MET cc_start: 0.6230 (ttm) cc_final: 0.5540 (ttm) REVERT: C 787 MET cc_start: 0.7543 (pmm) cc_final: 0.7136 (ptp) REVERT: C 906 ASP cc_start: 0.8599 (m-30) cc_final: 0.8236 (t0) REVERT: C 1102 MET cc_start: 0.9478 (ttt) cc_final: 0.9258 (ttp) REVERT: D 100 MET cc_start: 0.8995 (mpp) cc_final: 0.8740 (mpp) REVERT: D 112 MET cc_start: 0.8938 (tpp) cc_final: 0.8712 (ttm) REVERT: D 273 MET cc_start: 0.8094 (ptt) cc_final: 0.6782 (ppp) REVERT: D 278 MET cc_start: 0.8617 (mtm) cc_final: 0.7932 (ptp) REVERT: D 396 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7659 (ttm170) REVERT: D 407 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9045 (mpp) REVERT: D 471 HIS cc_start: 0.8726 (m170) cc_final: 0.8130 (m-70) REVERT: D 483 MET cc_start: 0.2691 (tmm) cc_final: 0.2377 (tmm) REVERT: D 536 MET cc_start: 0.5761 (tpt) cc_final: 0.5223 (tpt) outliers start: 74 outliers final: 47 residues processed: 203 average time/residue: 0.3281 time to fit residues: 110.4843 Evaluate side-chains 183 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 954 PHE Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain B residue 1170 GLU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 892 ASP Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 191 optimal weight: 30.0000 chunk 108 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 149 optimal weight: 0.0470 chunk 283 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 210 optimal weight: 8.9990 chunk 259 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN D 471 HIS ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.066593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.047947 restraints weight = 144308.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049620 restraints weight = 80833.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.050686 restraints weight = 55816.594| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24452 Z= 0.113 Angle : 0.562 12.936 33409 Z= 0.281 Chirality : 0.039 0.257 3673 Planarity : 0.004 0.054 4205 Dihedral : 13.884 88.521 3720 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.11 % Allowed : 12.38 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2837 helix: 1.40 (0.14), residues: 1444 sheet: -0.24 (0.31), residues: 265 loop : -1.36 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 972 HIS 0.003 0.001 HIS C 377 PHE 0.009 0.001 PHE B 959 TYR 0.014 0.001 TYR B1107 ARG 0.008 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1097) hydrogen bonds : angle 4.03044 ( 3179) covalent geometry : bond 0.00250 (24452) covalent geometry : angle 0.56224 (33409) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 143 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 354 MET cc_start: 0.8070 (mtt) cc_final: 0.7701 (mtm) REVERT: B 499 MET cc_start: 0.7335 (ppp) cc_final: 0.6632 (ppp) REVERT: B 501 MET cc_start: 0.9289 (mtm) cc_final: 0.8999 (mtm) REVERT: B 541 MET cc_start: 0.8640 (mtp) cc_final: 0.7533 (tpp) REVERT: B 594 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8338 (tp-100) REVERT: B 660 MET cc_start: 0.8462 (tpt) cc_final: 0.7895 (tpt) REVERT: B 748 GLU cc_start: 0.8902 (tt0) cc_final: 0.8586 (mt-10) REVERT: B 753 TRP cc_start: 0.9078 (OUTLIER) cc_final: 0.7968 (t60) REVERT: B 794 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7790 (ttp80) REVERT: B 798 ASP cc_start: 0.8427 (t0) cc_final: 0.8226 (t0) REVERT: B 1102 MET cc_start: 0.9320 (tmm) cc_final: 0.9035 (tmm) REVERT: B 1111 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8372 (p90) REVERT: B 1168 MET cc_start: 0.8175 (mmm) cc_final: 0.7973 (mmm) REVERT: B 1171 MET cc_start: 0.7974 (ptt) cc_final: 0.7625 (ppp) REVERT: C 408 ILE cc_start: 0.9580 (mt) cc_final: 0.9309 (pt) REVERT: C 471 LEU cc_start: 0.9095 (mt) cc_final: 0.8632 (pp) REVERT: C 665 MET cc_start: 0.7798 (mtp) cc_final: 0.7406 (mtp) REVERT: C 667 MET cc_start: 0.6087 (ttm) cc_final: 0.5481 (ttm) REVERT: C 787 MET cc_start: 0.7563 (pmm) cc_final: 0.7187 (ptp) REVERT: C 906 ASP cc_start: 0.8510 (m-30) cc_final: 0.8129 (t0) REVERT: C 1102 MET cc_start: 0.9440 (ttt) cc_final: 0.9213 (ttp) REVERT: D 25 LEU cc_start: 0.9244 (mt) cc_final: 0.8889 (pp) REVERT: D 112 MET cc_start: 0.8961 (tpp) cc_final: 0.8693 (ttm) REVERT: D 278 MET cc_start: 0.8381 (mtm) cc_final: 0.7839 (ptp) REVERT: D 396 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7525 (ttm170) REVERT: D 407 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.9040 (mpp) REVERT: D 471 HIS cc_start: 0.8539 (m90) cc_final: 0.8258 (m90) REVERT: D 504 ARG cc_start: 0.8293 (tpm170) cc_final: 0.8009 (tpm170) REVERT: D 536 MET cc_start: 0.5575 (tpt) cc_final: 0.5151 (tpt) outliers start: 51 outliers final: 32 residues processed: 187 average time/residue: 0.3246 time to fit residues: 101.5376 Evaluate side-chains 172 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 794 ARG Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 134 optimal weight: 10.0000 chunk 162 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 208 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 277 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 194 optimal weight: 0.2980 chunk 182 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 overall best weight: 5.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1084 ASN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** 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 = 0.3728 r_free = 0.3728 target = 0.064616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046407 restraints weight = 146686.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.047913 restraints weight = 85317.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.048894 restraints weight = 60429.884| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24452 Z= 0.183 Angle : 0.623 13.925 33409 Z= 0.313 Chirality : 0.040 0.183 3673 Planarity : 0.004 0.051 4205 Dihedral : 13.934 88.287 3720 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.82 % Allowed : 12.38 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.16), residues: 2837 helix: 1.36 (0.14), residues: 1450 sheet: -0.35 (0.31), residues: 260 loop : -1.35 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 511 HIS 0.005 0.001 HIS C 233 PHE 0.014 0.002 PHE B 428 TYR 0.016 0.001 TYR C 728 ARG 0.007 0.000 ARG B 974 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 1097) hydrogen bonds : angle 4.22888 ( 3179) covalent geometry : bond 0.00402 (24452) covalent geometry : angle 0.62304 (33409) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 141 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7092 (mm) REVERT: B 354 MET cc_start: 0.8109 (mtt) cc_final: 0.7645 (mtm) REVERT: B 499 MET cc_start: 0.7540 (ppp) cc_final: 0.6799 (ppp) REVERT: B 501 MET cc_start: 0.9312 (mtm) cc_final: 0.8959 (mtm) REVERT: B 541 MET cc_start: 0.8591 (mtp) cc_final: 0.7447 (tpp) REVERT: B 748 GLU cc_start: 0.8917 (tt0) cc_final: 0.8641 (tt0) REVERT: B 753 TRP cc_start: 0.9104 (OUTLIER) cc_final: 0.8044 (t60) REVERT: B 798 ASP cc_start: 0.8443 (t0) cc_final: 0.8176 (t0) REVERT: B 1021 MET cc_start: 0.8963 (tpp) cc_final: 0.8260 (tpp) REVERT: B 1061 MET cc_start: 0.7190 (tpp) cc_final: 0.6743 (tpp) REVERT: B 1102 MET cc_start: 0.9307 (tmm) cc_final: 0.9007 (tmm) REVERT: B 1111 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.8392 (p90) REVERT: B 1168 MET cc_start: 0.8424 (mmm) cc_final: 0.8207 (mmm) REVERT: B 1171 MET cc_start: 0.8243 (ptt) cc_final: 0.8042 (ppp) REVERT: C 46 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 96 MET cc_start: 0.8917 (tpp) cc_final: 0.8052 (tpp) REVERT: C 408 ILE cc_start: 0.9579 (mt) cc_final: 0.9313 (pt) REVERT: C 537 MET cc_start: 0.6890 (tpp) cc_final: 0.6030 (tpp) REVERT: C 665 MET cc_start: 0.7804 (mtp) cc_final: 0.7418 (mtp) REVERT: C 667 MET cc_start: 0.6122 (ttm) cc_final: 0.5414 (ttm) REVERT: C 787 MET cc_start: 0.7632 (pmm) cc_final: 0.7144 (ptt) REVERT: C 906 ASP cc_start: 0.8574 (m-30) cc_final: 0.8196 (t0) REVERT: C 1102 MET cc_start: 0.9467 (ttt) cc_final: 0.9243 (ttp) REVERT: D 25 LEU cc_start: 0.9292 (mt) cc_final: 0.8953 (pp) REVERT: D 100 MET cc_start: 0.8926 (mpp) cc_final: 0.8655 (mmm) REVERT: D 112 MET cc_start: 0.8981 (tpp) cc_final: 0.8727 (ttm) REVERT: D 273 MET cc_start: 0.8143 (ptt) cc_final: 0.6969 (ppp) REVERT: D 278 MET cc_start: 0.8568 (mtm) cc_final: 0.8126 (ptp) REVERT: D 396 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7527 (ttm170) REVERT: D 407 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8952 (mpp) REVERT: D 471 HIS cc_start: 0.8770 (m90) cc_final: 0.8354 (m-70) REVERT: D 483 MET cc_start: 0.2510 (tmm) cc_final: 0.2215 (tmm) REVERT: D 504 ARG cc_start: 0.8252 (tpm170) cc_final: 0.8010 (tpm170) REVERT: D 520 LYS cc_start: 0.8966 (tttt) cc_final: 0.8678 (mtpt) REVERT: D 536 MET cc_start: 0.6108 (tpt) cc_final: 0.5565 (tpt) outliers start: 68 outliers final: 50 residues processed: 198 average time/residue: 0.3144 time to fit residues: 103.0525 Evaluate side-chains 192 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 257 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 180 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 273 optimal weight: 50.0000 chunk 28 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 120 optimal weight: 0.0050 chunk 4 optimal weight: 0.0870 chunk 55 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 overall best weight: 3.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** 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 = 0.3748 r_free = 0.3748 target = 0.065400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047058 restraints weight = 144726.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.048655 restraints weight = 81768.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.049680 restraints weight = 56962.671| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24452 Z= 0.125 Angle : 0.570 12.285 33409 Z= 0.284 Chirality : 0.039 0.295 3673 Planarity : 0.004 0.053 4205 Dihedral : 13.918 88.057 3720 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.03 % Allowed : 13.46 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.16), residues: 2837 helix: 1.61 (0.14), residues: 1441 sheet: -0.29 (0.31), residues: 261 loop : -1.28 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 972 HIS 0.004 0.001 HIS B 689 PHE 0.010 0.001 PHE B 428 TYR 0.012 0.001 TYR B1107 ARG 0.009 0.000 ARG B 794 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 1097) hydrogen bonds : angle 4.05717 ( 3179) covalent geometry : bond 0.00277 (24452) covalent geometry : angle 0.56991 (33409) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 2.679 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 354 MET cc_start: 0.8100 (mtt) cc_final: 0.7623 (mtm) REVERT: B 499 MET cc_start: 0.7557 (ppp) cc_final: 0.6822 (ppp) REVERT: B 501 MET cc_start: 0.9224 (mtm) cc_final: 0.8847 (mtm) REVERT: B 541 MET cc_start: 0.8659 (mtp) cc_final: 0.7484 (tpp) REVERT: B 753 TRP cc_start: 0.9073 (OUTLIER) cc_final: 0.7828 (t60) REVERT: B 1021 MET cc_start: 0.8841 (tpp) cc_final: 0.8171 (tpp) REVERT: B 1102 MET cc_start: 0.9327 (tmm) cc_final: 0.9060 (tmm) REVERT: B 1111 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (p90) REVERT: C 42 MET cc_start: 0.8230 (tpp) cc_final: 0.8017 (tpp) REVERT: C 96 MET cc_start: 0.8954 (tpp) cc_final: 0.8083 (tpp) REVERT: C 408 ILE cc_start: 0.9553 (mt) cc_final: 0.9327 (pt) REVERT: C 537 MET cc_start: 0.6977 (tpp) cc_final: 0.6043 (tpp) REVERT: C 646 ASP cc_start: 0.8834 (t0) cc_final: 0.8160 (t0) REVERT: C 665 MET cc_start: 0.7769 (mtp) cc_final: 0.7389 (mtp) REVERT: C 667 MET cc_start: 0.6071 (ttm) cc_final: 0.5388 (ttm) REVERT: C 787 MET cc_start: 0.7689 (pmm) cc_final: 0.7254 (ptt) REVERT: C 906 ASP cc_start: 0.8445 (m-30) cc_final: 0.8110 (t0) REVERT: C 1102 MET cc_start: 0.9425 (ttt) cc_final: 0.9198 (ttp) REVERT: D 100 MET cc_start: 0.8825 (mpp) cc_final: 0.8564 (mmm) REVERT: D 112 MET cc_start: 0.8979 (tpp) cc_final: 0.8739 (ttm) REVERT: D 273 MET cc_start: 0.7978 (ptt) cc_final: 0.6918 (ppp) REVERT: D 278 MET cc_start: 0.8460 (mtm) cc_final: 0.7909 (ptp) REVERT: D 396 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7598 (ttm170) REVERT: D 407 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8916 (mpp) REVERT: D 471 HIS cc_start: 0.8834 (m90) cc_final: 0.8367 (m-70) REVERT: D 483 MET cc_start: 0.2449 (tmm) cc_final: 0.2107 (tmm) REVERT: D 504 ARG cc_start: 0.8297 (tpm170) cc_final: 0.8045 (tpm170) REVERT: D 520 LYS cc_start: 0.8953 (tttt) cc_final: 0.8680 (mtpt) outliers start: 49 outliers final: 37 residues processed: 186 average time/residue: 0.3462 time to fit residues: 107.4307 Evaluate side-chains 181 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 212 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 chunk 94 optimal weight: 40.0000 chunk 255 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 95 optimal weight: 0.0870 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 ASN B 531 GLN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 GLN ** C 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.064173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.046560 restraints weight = 156065.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.047983 restraints weight = 91692.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.048903 restraints weight = 65539.841| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24452 Z= 0.202 Angle : 0.658 11.213 33409 Z= 0.329 Chirality : 0.041 0.218 3673 Planarity : 0.004 0.050 4205 Dihedral : 14.047 88.489 3720 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.44 % Allowed : 13.83 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2837 helix: 1.28 (0.14), residues: 1454 sheet: -0.37 (0.32), residues: 244 loop : -1.31 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 272 HIS 0.006 0.001 HIS C 233 PHE 0.013 0.002 PHE C1112 TYR 0.018 0.002 TYR B 394 ARG 0.007 0.001 ARG B 794 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 1097) hydrogen bonds : angle 4.34455 ( 3179) covalent geometry : bond 0.00443 (24452) covalent geometry : angle 0.65798 (33409) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 141 time to evaluate : 2.609 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 269 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7488 (mm) REVERT: B 354 MET cc_start: 0.8121 (mtt) cc_final: 0.7641 (mtm) REVERT: B 499 MET cc_start: 0.7697 (ppp) cc_final: 0.6932 (ppp) REVERT: B 501 MET cc_start: 0.9314 (mtm) cc_final: 0.8870 (mtm) REVERT: B 541 MET cc_start: 0.8698 (mtp) cc_final: 0.7549 (tpp) REVERT: B 660 MET cc_start: 0.8211 (tpt) cc_final: 0.7403 (tpt) REVERT: B 753 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.7983 (t60) REVERT: B 1021 MET cc_start: 0.8902 (tpp) cc_final: 0.8265 (tpp) REVERT: B 1061 MET cc_start: 0.7349 (tpp) cc_final: 0.7029 (tpp) REVERT: B 1102 MET cc_start: 0.9313 (tmm) cc_final: 0.9088 (tmm) REVERT: B 1111 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8539 (p90) REVERT: B 1168 MET cc_start: 0.7482 (mmm) cc_final: 0.7125 (mpp) REVERT: B 1171 MET cc_start: 0.8677 (ptm) cc_final: 0.8378 (ppp) REVERT: C 96 MET cc_start: 0.9072 (tpp) cc_final: 0.8785 (tpp) REVERT: C 387 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8690 (mm-30) REVERT: C 537 MET cc_start: 0.6815 (tpp) cc_final: 0.6089 (tpp) REVERT: C 606 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: C 646 ASP cc_start: 0.8847 (t0) cc_final: 0.8193 (t0) REVERT: C 665 MET cc_start: 0.7822 (mtp) cc_final: 0.7457 (mtp) REVERT: C 787 MET cc_start: 0.7634 (pmm) cc_final: 0.7303 (ptp) REVERT: C 1102 MET cc_start: 0.9469 (ttt) cc_final: 0.9243 (ttp) REVERT: D 100 MET cc_start: 0.9022 (mpp) cc_final: 0.8657 (mmm) REVERT: D 112 MET cc_start: 0.9006 (tpp) cc_final: 0.8733 (ttm) REVERT: D 273 MET cc_start: 0.8316 (ptt) cc_final: 0.7222 (ppp) REVERT: D 278 MET cc_start: 0.8456 (mtm) cc_final: 0.8025 (ptp) REVERT: D 396 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7532 (ttm170) REVERT: D 407 MET cc_start: 0.9305 (OUTLIER) cc_final: 0.8980 (mpp) REVERT: D 471 HIS cc_start: 0.9054 (m90) cc_final: 0.8683 (m-70) REVERT: D 504 ARG cc_start: 0.8265 (tpm170) cc_final: 0.8023 (tpm170) REVERT: D 520 LYS cc_start: 0.8979 (tttt) cc_final: 0.8728 (mtpt) REVERT: D 536 MET cc_start: 0.8958 (mpp) cc_final: 0.8376 (tpt) outliers start: 59 outliers final: 42 residues processed: 190 average time/residue: 0.3129 time to fit residues: 99.5620 Evaluate side-chains 182 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 254 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 753 TRP Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain B residue 1085 TRP Chi-restraints excluded: chain B residue 1093 TYR Chi-restraints excluded: chain B residue 1111 TYR Chi-restraints excluded: chain C residue 82 LYS Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 362 ASP Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 506 ILE Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 CYS Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 689 LEU Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 970 SER Chi-restraints excluded: chain C residue 1035 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 108 TYR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 191 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 350 ASP Chi-restraints excluded: chain D residue 396 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 533 THR Chi-restraints excluded: chain D residue 579 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6008 > 50: distance: 29 - 35: 9.222 distance: 35 - 36: 27.396 distance: 36 - 37: 21.147 distance: 36 - 39: 14.225 distance: 37 - 46: 33.508 distance: 39 - 40: 18.676 distance: 40 - 41: 11.499 distance: 40 - 42: 10.223 distance: 41 - 43: 22.314 distance: 42 - 44: 23.668 distance: 43 - 45: 12.947 distance: 44 - 45: 25.925 distance: 46 - 47: 29.420 distance: 47 - 48: 24.822 distance: 47 - 50: 42.407 distance: 48 - 49: 26.835 distance: 48 - 53: 22.174 distance: 50 - 51: 8.229 distance: 50 - 52: 33.587 distance: 53 - 54: 24.474 distance: 54 - 55: 20.232 distance: 54 - 57: 21.232 distance: 55 - 56: 4.264 distance: 55 - 62: 20.990 distance: 57 - 58: 13.239 distance: 58 - 59: 23.070 distance: 59 - 60: 25.535 distance: 59 - 61: 20.935 distance: 62 - 63: 15.638 distance: 62 - 68: 44.828 distance: 63 - 64: 10.606 distance: 63 - 66: 41.237 distance: 64 - 65: 18.944 distance: 64 - 69: 27.183 distance: 66 - 67: 12.330 distance: 67 - 68: 6.604 distance: 69 - 70: 16.066 distance: 70 - 71: 38.525 distance: 70 - 73: 42.981 distance: 71 - 72: 40.665 distance: 71 - 77: 20.983 distance: 73 - 74: 21.891 distance: 74 - 75: 36.955 distance: 74 - 76: 54.719 distance: 77 - 78: 10.344 distance: 77 - 83: 27.467 distance: 78 - 79: 41.357 distance: 78 - 81: 26.594 distance: 79 - 80: 23.454 distance: 79 - 84: 36.025 distance: 81 - 82: 5.198 distance: 82 - 83: 11.789 distance: 84 - 85: 5.846 distance: 85 - 86: 40.317 distance: 85 - 88: 19.799 distance: 86 - 95: 23.792 distance: 88 - 89: 10.179 distance: 89 - 90: 4.035 distance: 89 - 91: 7.144 distance: 90 - 92: 10.119 distance: 91 - 93: 19.280 distance: 92 - 94: 10.651 distance: 93 - 94: 10.283 distance: 95 - 96: 21.091 distance: 96 - 97: 13.220 distance: 96 - 99: 34.283 distance: 97 - 98: 11.320 distance: 97 - 102: 8.087 distance: 99 - 100: 31.336 distance: 99 - 101: 28.513 distance: 102 - 103: 19.495 distance: 103 - 104: 17.608 distance: 103 - 106: 19.311 distance: 104 - 105: 20.476 distance: 104 - 110: 26.632 distance: 106 - 107: 25.210 distance: 107 - 108: 30.095 distance: 107 - 109: 25.862 distance: 110 - 111: 18.394 distance: 110 - 116: 19.888 distance: 111 - 112: 11.877 distance: 111 - 114: 13.034 distance: 112 - 113: 20.602 distance: 112 - 117: 12.593 distance: 114 - 115: 22.187 distance: 115 - 116: 18.624