Starting phenix.real_space_refine on Wed Nov 19 12:13:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sje_10215/11_2025/6sje_10215.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sje_10215/11_2025/6sje_10215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sje_10215/11_2025/6sje_10215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sje_10215/11_2025/6sje_10215.map" model { file = "/net/cci-nas-00/data/ceres_data/6sje_10215/11_2025/6sje_10215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sje_10215/11_2025/6sje_10215.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 101 5.16 5 C 15036 2.51 5 N 4236 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24115 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 9047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1129, 9047 Classifications: {'peptide': 1129} Link IDs: {'PTRANS': 51, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4603 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 25, 'TRANS': 571} Chain: "X" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1387 Classifications: {'DNA': 68} Link IDs: {'rna3p': 67} Chain breaks: 1 Time building chain proxies: 6.23, per 1000 atoms: 0.26 Number of scatterers: 24115 At special positions: 0 Unit cell: (151.815, 149.721, 124.593, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 68 15.00 O 4674 8.00 N 4236 7.00 C 15036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5372 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 16 sheets defined 53.8% alpha, 9.6% beta 17 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.678A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.743A pdb=" N ILE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.546A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 removed outlier: 3.841A pdb=" N TYR B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.261A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.780A pdb=" N LEU B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 removed outlier: 3.566A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.675A pdb=" N ASN B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.725A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.169A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.546A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 removed outlier: 3.584A pdb=" N MET B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 401 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.758A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.764A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 511 through 534 removed outlier: 3.568A pdb=" N GLN B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 573 removed outlier: 3.519A pdb=" N ALA B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 573 " --> pdb=" O ASP B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 removed outlier: 3.636A pdb=" N GLU B 589 " --> pdb=" O SER B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 586 through 589' Processing helix chain 'B' and resid 590 through 605 removed outlier: 3.872A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.969A pdb=" N LEU B 612 " --> pdb=" O ARG B 608 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 634 Processing helix chain 'B' and resid 634 through 655 removed outlier: 3.569A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 668 removed outlier: 3.821A pdb=" N MET B 660 " --> pdb=" O GLY B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.528A pdb=" N ASN B 673 " --> pdb=" O ASN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 699 Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.767A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.586A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 Processing helix chain 'B' and resid 837 through 843 removed outlier: 4.002A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.902A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 910 Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 948 through 962 Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 3.699A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 removed outlier: 3.782A pdb=" N GLN B1011 " --> pdb=" O SER B1008 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B1012 " --> pdb=" O LEU B1009 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1008 through 1012' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.672A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1048 removed outlier: 3.890A pdb=" N ALA B1048 " --> pdb=" O PRO B1045 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1045 through 1048' Processing helix chain 'B' and resid 1094 through 1106 Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1144 through 1146 No H-bonds generated for 'chain 'B' and resid 1144 through 1146' Processing helix chain 'B' and resid 1163 through 1174 removed outlier: 3.668A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.907A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 99 removed outlier: 3.664A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 116 removed outlier: 3.792A pdb=" N HIS C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.729A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 185 through 199 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 253 through 263 removed outlier: 3.556A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.670A pdb=" N PHE C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'C' and resid 381 through 400 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 418 through 428 Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.642A pdb=" N GLU C 452 " --> pdb=" O HIS C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.589A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.868A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.535A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.827A pdb=" N GLN C 570 " --> pdb=" O SER C 566 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 599 removed outlier: 4.468A pdb=" N CYS C 591 " --> pdb=" O TRP C 587 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 625 Processing helix chain 'C' and resid 633 through 646 removed outlier: 4.020A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 700 removed outlier: 3.885A pdb=" N GLN C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 723 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 769 through 780 Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 833 through 843 removed outlier: 3.568A pdb=" N LEU C 837 " --> pdb=" O PRO C 833 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 874 through 889 Processing helix chain 'C' and resid 893 through 904 removed outlier: 3.630A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.799A pdb=" N GLU C 914 " --> pdb=" O GLY C 910 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 935 No H-bonds generated for 'chain 'C' and resid 933 through 935' Processing helix chain 'C' and resid 973 through 989 removed outlier: 3.542A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 4.017A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 removed outlier: 3.639A pdb=" N ARG C1068 " --> pdb=" O LEU C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1113 Processing helix chain 'C' and resid 1113 through 1119 removed outlier: 3.823A pdb=" N PHE C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.580A pdb=" N GLN D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 15' Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 32 through 49 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.957A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.547A pdb=" N ARG D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 221 removed outlier: 3.526A pdb=" N ARG D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.571A pdb=" N LYS D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.610A pdb=" N MET D 273 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.510A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.770A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 removed outlier: 3.554A pdb=" N ALA D 319 " --> pdb=" O TYR D 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 316 through 319' Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.618A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 365 through 375 removed outlier: 3.940A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.641A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN D 387 " --> pdb=" O LYS D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 391 removed outlier: 3.856A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 400 through 415 Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.587A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.528A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 571 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.695A pdb=" N ILE D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.362A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 439 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 20 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL B 62 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.520A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.370A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.701A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.262A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B1076 " --> pdb=" O PHE B1135 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B1137 " --> pdb=" O TYR B1076 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.262A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 34 through 36 removed outlier: 4.460A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG C 266 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.020A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.273A pdb=" N ILE C 408 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N CYS C 662 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL C 410 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS C 782 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 939 through 947 removed outlier: 5.469A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 15.483A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.158A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.039A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 170 removed outlier: 6.604A pdb=" N ARG D 200 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.236A pdb=" N ASP D 547 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.561A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 80 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6608 1.33 - 1.45: 4535 1.45 - 1.57: 13328 1.57 - 1.69: 134 1.69 - 1.81: 169 Bond restraints: 24774 Sorted by residual: bond pdb=" C ASN C 660 " pdb=" N ILE C 661 " ideal model delta sigma weight residual 1.330 1.246 0.084 1.25e-02 6.40e+03 4.53e+01 bond pdb=" C LEU C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.331 1.376 -0.045 7.90e-03 1.60e+04 3.20e+01 bond pdb=" O3' DC X 80 " pdb=" P DT X 81 " ideal model delta sigma weight residual 1.607 1.681 -0.074 1.50e-02 4.44e+03 2.41e+01 bond pdb=" P DT X 81 " pdb=" OP1 DT X 81 " ideal model delta sigma weight residual 1.480 1.553 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 1.523 1.561 -0.037 1.30e-02 5.92e+03 8.20e+00 ... (remaining 24769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 33551 2.32 - 4.63: 317 4.63 - 6.95: 29 6.95 - 9.26: 9 9.26 - 11.58: 2 Bond angle restraints: 33908 Sorted by residual: angle pdb=" N LEU C 664 " pdb=" CA LEU C 664 " pdb=" C LEU C 664 " ideal model delta sigma weight residual 111.28 122.86 -11.58 1.09e+00 8.42e-01 1.13e+02 angle pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" C MET C 665 " ideal model delta sigma weight residual 113.16 123.91 -10.75 1.42e+00 4.96e-01 5.73e+01 angle pdb=" C PHE B 468 " pdb=" N MET B 469 " pdb=" CA MET B 469 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C2' DC X 80 " pdb=" C1' DC X 80 " pdb=" N1 DC X 80 " ideal model delta sigma weight residual 113.50 119.69 -6.19 1.50e+00 4.44e-01 1.71e+01 angle pdb=" O3' DC X 80 " pdb=" C3' DC X 80 " pdb=" C2' DC X 80 " ideal model delta sigma weight residual 111.50 117.44 -5.94 1.50e+00 4.44e-01 1.57e+01 ... (remaining 33903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 13467 17.11 - 34.22: 826 34.22 - 51.33: 368 51.33 - 68.44: 85 68.44 - 85.55: 9 Dihedral angle restraints: 14755 sinusoidal: 6466 harmonic: 8289 Sorted by residual: dihedral pdb=" CA PRO B1051 " pdb=" C PRO B1051 " pdb=" N PRO B1052 " pdb=" CA PRO B1052 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual 122.80 131.61 -8.81 0 2.50e+00 1.60e-01 1.24e+01 dihedral pdb=" C MET C 665 " pdb=" N MET C 665 " pdb=" CA MET C 665 " pdb=" CB MET C 665 " ideal model delta harmonic sigma weight residual -122.60 -131.32 8.72 0 2.50e+00 1.60e-01 1.22e+01 ... (remaining 14752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3569 0.094 - 0.188: 154 0.188 - 0.282: 3 0.282 - 0.376: 2 0.376 - 0.470: 1 Chirality restraints: 3729 Sorted by residual: chirality pdb=" CA MET C 665 " pdb=" N MET C 665 " pdb=" C MET C 665 " pdb=" CB MET C 665 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" P DT X 81 " pdb=" OP1 DT X 81 " pdb=" OP2 DT X 81 " pdb=" O5' DT X 81 " both_signs ideal model delta sigma weight residual True 2.35 -2.65 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LEU C 664 " pdb=" N LEU C 664 " pdb=" C LEU C 664 " pdb=" CB LEU C 664 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 3726 not shown) Planarity restraints: 4219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 419 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 420 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 420 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 420 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 304 " 0.038 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO B 305 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG X 83 " -0.025 2.00e-02 2.50e+03 1.17e-02 4.09e+00 pdb=" N9 DG X 83 " 0.024 2.00e-02 2.50e+03 pdb=" C8 DG X 83 " 0.013 2.00e-02 2.50e+03 pdb=" N7 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG X 83 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG X 83 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG X 83 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG X 83 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG X 83 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DG X 83 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG X 83 " -0.009 2.00e-02 2.50e+03 ... (remaining 4216 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5611 2.79 - 3.32: 20052 3.32 - 3.85: 40337 3.85 - 4.37: 45746 4.37 - 4.90: 77972 Nonbonded interactions: 189718 Sorted by model distance: nonbonded pdb=" O PHE C 62 " pdb=" N1 DG X 86 " model vdw 2.264 3.120 nonbonded pdb=" O2 DC X 27 " pdb=" N2 DG X 59 " model vdw 2.304 2.496 nonbonded pdb=" O LEU D 67 " pdb=" OG1 THR D 70 " model vdw 2.332 3.040 nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.336 3.040 nonbonded pdb=" O TYR C 754 " pdb=" OG SER C 758 " model vdw 2.341 3.040 ... (remaining 189713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.340 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24774 Z= 0.166 Angle : 0.595 11.578 33908 Z= 0.362 Chirality : 0.041 0.470 3729 Planarity : 0.005 0.060 4219 Dihedral : 13.750 85.548 9383 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.06 % Allowed : 5.34 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.11), residues: 2837 helix: -2.50 (0.09), residues: 1382 sheet: -1.20 (0.28), residues: 299 loop : -2.38 (0.14), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 708 TYR 0.012 0.001 TYR B1111 PHE 0.014 0.001 PHE B1023 TRP 0.015 0.001 TRP B 652 HIS 0.005 0.000 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00282 (24774) covalent geometry : angle 0.59481 (33908) hydrogen bonds : bond 0.15023 ( 1106) hydrogen bonds : angle 6.45258 ( 3197) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 694 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9226 (t) cc_final: 0.8942 (p) REVERT: B 133 CYS cc_start: 0.8532 (m) cc_final: 0.8207 (m) REVERT: B 152 LEU cc_start: 0.8526 (tp) cc_final: 0.8223 (mt) REVERT: B 335 ILE cc_start: 0.9066 (mt) cc_final: 0.8791 (mt) REVERT: B 348 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7207 (mt-10) REVERT: B 518 MET cc_start: 0.8818 (mmm) cc_final: 0.8406 (mmp) REVERT: B 595 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8115 (pt0) REVERT: B 797 GLU cc_start: 0.8771 (tt0) cc_final: 0.8454 (tm-30) REVERT: B 798 ASP cc_start: 0.7880 (m-30) cc_final: 0.6683 (m-30) REVERT: B 804 VAL cc_start: 0.9106 (t) cc_final: 0.8879 (p) REVERT: B 1066 ILE cc_start: 0.9334 (mt) cc_final: 0.8430 (mt) REVERT: B 1078 LEU cc_start: 0.8187 (tt) cc_final: 0.7923 (mt) REVERT: B 1111 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6035 (t80) REVERT: B 1114 TYR cc_start: 0.8663 (m-10) cc_final: 0.8389 (m-10) REVERT: C 12 VAL cc_start: 0.9109 (t) cc_final: 0.8852 (t) REVERT: C 37 VAL cc_start: 0.7673 (m) cc_final: 0.7427 (p) REVERT: C 69 ILE cc_start: 0.9099 (mm) cc_final: 0.8823 (mt) REVERT: C 103 LEU cc_start: 0.8895 (mt) cc_final: 0.8439 (tt) REVERT: C 385 GLU cc_start: 0.8458 (tt0) cc_final: 0.8010 (tt0) REVERT: C 465 PHE cc_start: 0.8098 (m-80) cc_final: 0.7867 (m-80) REVERT: C 492 TYR cc_start: 0.7657 (m-80) cc_final: 0.6891 (m-80) REVERT: C 550 TYR cc_start: 0.7484 (t80) cc_final: 0.6527 (t80) REVERT: C 571 LEU cc_start: 0.8955 (mt) cc_final: 0.8730 (mm) REVERT: C 676 CYS cc_start: 0.8160 (m) cc_final: 0.7836 (m) REVERT: C 685 TYR cc_start: 0.8182 (t80) cc_final: 0.6979 (t80) REVERT: C 714 TYR cc_start: 0.8815 (t80) cc_final: 0.8112 (t80) REVERT: C 728 TYR cc_start: 0.7963 (t80) cc_final: 0.6535 (t80) REVERT: C 730 SER cc_start: 0.9204 (t) cc_final: 0.8672 (t) REVERT: C 861 ASP cc_start: 0.8116 (p0) cc_final: 0.7428 (p0) REVERT: D 273 MET cc_start: 0.7489 (mtm) cc_final: 0.7176 (mtt) REVERT: D 407 MET cc_start: 0.8926 (ttp) cc_final: 0.8696 (tmm) REVERT: D 444 LEU cc_start: 0.8735 (mt) cc_final: 0.8531 (tp) REVERT: D 484 ILE cc_start: 0.8703 (mm) cc_final: 0.7986 (tp) REVERT: D 537 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.7959 (p) REVERT: D 600 LEU cc_start: 0.8546 (mt) cc_final: 0.8193 (mp) outliers start: 74 outliers final: 12 residues processed: 750 average time/residue: 0.2000 time to fit residues: 224.8860 Evaluate side-chains 350 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 336 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.0670 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 134 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 224 GLN B 455 ASN B 458 ASN B 463 GLN B 531 GLN B 566 GLN B 594 GLN B 610 ASN B 650 GLN B 713 GLN B 765 GLN B 834 HIS B 843 GLN B 848 GLN B 900 ASN B 944 GLN B1084 ASN B1095 GLN B1133 HIS B1134 HIS C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN C 321 GLN C 336 HIS C 423 GLN C 510 ASN C 563 HIS C 570 GLN C 614 GLN C 660 ASN C 699 GLN C 724 GLN C 749 GLN C 759 HIS C 792 GLN C 822 GLN C 883 GLN C 925 GLN C 979 GLN C1091 GLN D 128 HIS D 469 HIS D 523 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.078869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063500 restraints weight = 108204.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065250 restraints weight = 62604.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.066453 restraints weight = 42350.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.067261 restraints weight = 31880.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.067832 restraints weight = 25999.140| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24774 Z= 0.128 Angle : 0.588 9.559 33908 Z= 0.300 Chirality : 0.039 0.172 3729 Planarity : 0.005 0.070 4219 Dihedral : 14.543 86.072 3843 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.14), residues: 2837 helix: -0.30 (0.13), residues: 1413 sheet: -0.71 (0.29), residues: 284 loop : -1.90 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 728 TYR 0.023 0.001 TYR D 108 PHE 0.025 0.001 PHE D 386 TRP 0.035 0.001 TRP C 149 HIS 0.011 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00281 (24774) covalent geometry : angle 0.58811 (33908) hydrogen bonds : bond 0.03674 ( 1106) hydrogen bonds : angle 4.37760 ( 3197) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9251 (t) cc_final: 0.8895 (p) REVERT: B 518 MET cc_start: 0.8810 (mmm) cc_final: 0.8334 (mmp) REVERT: B 599 LEU cc_start: 0.9502 (mp) cc_final: 0.9143 (mt) REVERT: B 731 SER cc_start: 0.8372 (t) cc_final: 0.7979 (m) REVERT: B 797 GLU cc_start: 0.8855 (tt0) cc_final: 0.8303 (tm-30) REVERT: B 798 ASP cc_start: 0.8187 (m-30) cc_final: 0.7772 (m-30) REVERT: B 804 VAL cc_start: 0.9306 (t) cc_final: 0.9089 (p) REVERT: B 1078 LEU cc_start: 0.8284 (tt) cc_final: 0.7987 (mt) REVERT: B 1114 TYR cc_start: 0.8654 (m-10) cc_final: 0.8385 (m-10) REVERT: B 1170 GLU cc_start: 0.8496 (tp30) cc_final: 0.8296 (pt0) REVERT: C 12 VAL cc_start: 0.9285 (t) cc_final: 0.9048 (t) REVERT: C 34 MET cc_start: 0.8736 (mmt) cc_final: 0.8280 (mmm) REVERT: C 72 MET cc_start: 0.8837 (mmp) cc_final: 0.8628 (mmp) REVERT: C 103 LEU cc_start: 0.9044 (mt) cc_final: 0.8581 (tt) REVERT: C 115 LEU cc_start: 0.9281 (mp) cc_final: 0.8799 (pp) REVERT: C 342 ILE cc_start: 0.9501 (tt) cc_final: 0.9248 (tp) REVERT: C 385 GLU cc_start: 0.8604 (tt0) cc_final: 0.7858 (tt0) REVERT: C 550 TYR cc_start: 0.7644 (t80) cc_final: 0.5739 (t80) REVERT: C 571 LEU cc_start: 0.9252 (mt) cc_final: 0.8960 (mm) REVERT: C 676 CYS cc_start: 0.8760 (m) cc_final: 0.8342 (m) REVERT: C 680 MET cc_start: 0.8873 (mmp) cc_final: 0.8592 (mmp) REVERT: C 714 TYR cc_start: 0.8853 (t80) cc_final: 0.7940 (t80) REVERT: C 728 TYR cc_start: 0.8003 (t80) cc_final: 0.6253 (t80) REVERT: C 730 SER cc_start: 0.9337 (t) cc_final: 0.8574 (t) REVERT: C 790 ASP cc_start: 0.7802 (t0) cc_final: 0.7175 (t0) REVERT: C 1102 MET cc_start: 0.9339 (ttp) cc_final: 0.9021 (tmm) REVERT: D 100 MET cc_start: 0.9061 (mpp) cc_final: 0.8851 (mpp) REVERT: D 191 MET cc_start: 0.8063 (mmp) cc_final: 0.7849 (mmp) REVERT: D 275 ASP cc_start: 0.8464 (p0) cc_final: 0.8211 (p0) REVERT: D 393 ILE cc_start: 0.7992 (pt) cc_final: 0.7689 (pt) REVERT: D 407 MET cc_start: 0.8941 (ttp) cc_final: 0.8711 (tmm) outliers start: 1 outliers final: 0 residues processed: 421 average time/residue: 0.1798 time to fit residues: 117.5382 Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 48 optimal weight: 30.0000 chunk 233 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN B 162 GLN B 222 HIS B 224 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 531 GLN B 610 ASN B 689 HIS B 713 GLN B 876 GLN B 956 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 HIS C 126 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 660 ASN C 793 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.075274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060081 restraints weight = 109968.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.061706 restraints weight = 64983.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.062804 restraints weight = 44588.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063575 restraints weight = 33945.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064020 restraints weight = 27899.949| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 24774 Z= 0.169 Angle : 0.590 7.848 33908 Z= 0.303 Chirality : 0.040 0.203 3729 Planarity : 0.005 0.073 4219 Dihedral : 14.642 89.597 3843 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.12 % Allowed : 2.24 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 2837 helix: 0.71 (0.14), residues: 1423 sheet: -0.43 (0.29), residues: 293 loop : -1.57 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 559 TYR 0.013 0.001 TYR C 550 PHE 0.028 0.002 PHE C 193 TRP 0.017 0.001 TRP B 652 HIS 0.007 0.001 HIS D 548 Details of bonding type rmsd covalent geometry : bond 0.00372 (24774) covalent geometry : angle 0.59002 (33908) hydrogen bonds : bond 0.03628 ( 1106) hydrogen bonds : angle 4.10905 ( 3197) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 56 VAL cc_start: 0.9188 (t) cc_final: 0.8984 (p) REVERT: B 499 MET cc_start: 0.8057 (tpp) cc_final: 0.7354 (tpt) REVERT: B 518 MET cc_start: 0.8882 (mmm) cc_final: 0.8423 (mmp) REVERT: B 520 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 595 GLU cc_start: 0.8496 (pt0) cc_final: 0.7245 (pt0) REVERT: B 731 SER cc_start: 0.8598 (t) cc_final: 0.8189 (m) REVERT: B 797 GLU cc_start: 0.9026 (tt0) cc_final: 0.8606 (tm-30) REVERT: B 798 ASP cc_start: 0.8370 (m-30) cc_final: 0.7951 (m-30) REVERT: B 1078 LEU cc_start: 0.8306 (tt) cc_final: 0.8066 (mt) REVERT: B 1112 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 1114 TYR cc_start: 0.8805 (m-10) cc_final: 0.8503 (m-10) REVERT: B 1170 GLU cc_start: 0.8543 (tp30) cc_final: 0.8297 (pt0) REVERT: C 91 MET cc_start: 0.8654 (mtm) cc_final: 0.8303 (ttp) REVERT: C 103 LEU cc_start: 0.9000 (mt) cc_final: 0.8747 (mt) REVERT: C 115 LEU cc_start: 0.9246 (mp) cc_final: 0.8800 (pp) REVERT: C 714 TYR cc_start: 0.8887 (t80) cc_final: 0.7998 (t80) REVERT: C 790 ASP cc_start: 0.7807 (t0) cc_final: 0.7433 (t0) REVERT: C 851 MET cc_start: 0.8633 (mtt) cc_final: 0.8405 (mtp) REVERT: C 1057 MET cc_start: 0.7177 (mmm) cc_final: 0.6963 (mmm) REVERT: D 100 MET cc_start: 0.9038 (mpp) cc_final: 0.8802 (mpp) REVERT: D 393 ILE cc_start: 0.8035 (pt) cc_final: 0.7729 (pt) REVERT: D 484 ILE cc_start: 0.8437 (mm) cc_final: 0.7662 (tp) REVERT: D 545 GLU cc_start: 0.8120 (tt0) cc_final: 0.7891 (tt0) outliers start: 3 outliers final: 2 residues processed: 331 average time/residue: 0.1710 time to fit residues: 90.1917 Evaluate side-chains 225 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 277 optimal weight: 20.0000 chunk 267 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 141 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 227 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN B 496 GLN B 601 GLN B 624 ASN B 705 HIS B 956 HIS B1133 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C 793 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058529 restraints weight = 110516.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.060130 restraints weight = 64878.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.061216 restraints weight = 44248.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.061952 restraints weight = 33609.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062398 restraints weight = 27603.778| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24774 Z= 0.189 Angle : 0.596 9.354 33908 Z= 0.304 Chirality : 0.040 0.170 3729 Planarity : 0.004 0.042 4219 Dihedral : 14.780 85.278 3843 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2837 helix: 1.14 (0.14), residues: 1427 sheet: -0.29 (0.29), residues: 293 loop : -1.30 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 255 TYR 0.020 0.002 TYR D 108 PHE 0.023 0.002 PHE B 645 TRP 0.018 0.002 TRP D 113 HIS 0.007 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00413 (24774) covalent geometry : angle 0.59635 (33908) hydrogen bonds : bond 0.03541 ( 1106) hydrogen bonds : angle 4.11057 ( 3197) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 287 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 256 LYS cc_start: 0.7960 (pttp) cc_final: 0.7726 (mmmm) REVERT: B 499 MET cc_start: 0.8479 (tpp) cc_final: 0.7870 (tpt) REVERT: B 518 MET cc_start: 0.8952 (mmm) cc_final: 0.8578 (mmp) REVERT: B 595 GLU cc_start: 0.8271 (pt0) cc_final: 0.7767 (pt0) REVERT: B 596 MET cc_start: 0.9155 (mmt) cc_final: 0.8853 (mmp) REVERT: B 621 MET cc_start: 0.8934 (mmm) cc_final: 0.8543 (mmp) REVERT: B 797 GLU cc_start: 0.9217 (tt0) cc_final: 0.8518 (tm-30) REVERT: B 798 ASP cc_start: 0.8391 (m-30) cc_final: 0.7852 (m-30) REVERT: B 902 ARG cc_start: 0.8386 (ptm-80) cc_final: 0.8125 (ptm-80) REVERT: B 1068 LEU cc_start: 0.9339 (tt) cc_final: 0.9112 (tt) REVERT: B 1078 LEU cc_start: 0.8276 (tt) cc_final: 0.7995 (mt) REVERT: B 1112 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8259 (tm-30) REVERT: B 1114 TYR cc_start: 0.8874 (m-10) cc_final: 0.8530 (m-10) REVERT: B 1135 PHE cc_start: 0.7708 (t80) cc_final: 0.7463 (t80) REVERT: C 2 LEU cc_start: 0.7656 (tp) cc_final: 0.7392 (tp) REVERT: C 91 MET cc_start: 0.8676 (mtm) cc_final: 0.8359 (ttp) REVERT: C 260 LEU cc_start: 0.8279 (tp) cc_final: 0.8072 (tp) REVERT: C 685 TYR cc_start: 0.8534 (t80) cc_final: 0.8076 (t80) REVERT: C 714 TYR cc_start: 0.8859 (t80) cc_final: 0.8024 (t80) REVERT: C 790 ASP cc_start: 0.8049 (t0) cc_final: 0.7728 (t0) REVERT: C 1102 MET cc_start: 0.9147 (ttm) cc_final: 0.8941 (tmm) REVERT: D 100 MET cc_start: 0.9064 (mpp) cc_final: 0.8807 (mpp) REVERT: D 393 ILE cc_start: 0.7987 (pt) cc_final: 0.7686 (pt) REVERT: D 484 ILE cc_start: 0.8457 (mm) cc_final: 0.7749 (tp) REVERT: D 488 ASP cc_start: 0.8162 (t0) cc_final: 0.7927 (t0) outliers start: 1 outliers final: 0 residues processed: 288 average time/residue: 0.1620 time to fit residues: 74.8939 Evaluate side-chains 208 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 172 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 169 optimal weight: 0.9980 chunk 224 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 252 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.055929 restraints weight = 111795.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057502 restraints weight = 64746.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.058593 restraints weight = 43890.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059345 restraints weight = 33401.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.059837 restraints weight = 27406.880| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 24774 Z= 0.247 Angle : 0.679 11.958 33908 Z= 0.343 Chirality : 0.042 0.177 3729 Planarity : 0.005 0.060 4219 Dihedral : 15.073 89.441 3843 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.04 % Allowed : 2.53 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2837 helix: 1.08 (0.14), residues: 1429 sheet: -0.23 (0.29), residues: 287 loop : -1.29 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 433 TYR 0.017 0.002 TYR C 190 PHE 0.023 0.002 PHE B 64 TRP 0.019 0.002 TRP B 652 HIS 0.007 0.002 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00544 (24774) covalent geometry : angle 0.67859 (33908) hydrogen bonds : bond 0.03954 ( 1106) hydrogen bonds : angle 4.32062 ( 3197) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.926 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 499 MET cc_start: 0.8711 (tpp) cc_final: 0.8264 (tpt) REVERT: B 525 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8544 (tp-100) REVERT: B 595 GLU cc_start: 0.8566 (pt0) cc_final: 0.8318 (pt0) REVERT: B 596 MET cc_start: 0.9302 (mmt) cc_final: 0.8989 (mmp) REVERT: B 661 LEU cc_start: 0.9587 (mt) cc_final: 0.9359 (mt) REVERT: B 797 GLU cc_start: 0.9281 (tt0) cc_final: 0.8664 (tm-30) REVERT: B 798 ASP cc_start: 0.8750 (m-30) cc_final: 0.8360 (m-30) REVERT: B 1078 LEU cc_start: 0.8347 (tt) cc_final: 0.8075 (mt) REVERT: B 1112 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8263 (tm-30) REVERT: B 1114 TYR cc_start: 0.8933 (m-10) cc_final: 0.8554 (m-10) REVERT: C 91 MET cc_start: 0.8823 (mtm) cc_final: 0.8443 (ttp) REVERT: C 338 ILE cc_start: 0.9427 (tp) cc_final: 0.9179 (tp) REVERT: C 548 LEU cc_start: 0.8982 (tt) cc_final: 0.8740 (tt) REVERT: C 571 LEU cc_start: 0.9450 (mt) cc_final: 0.9129 (mt) REVERT: C 665 MET cc_start: 0.7098 (ttt) cc_final: 0.6497 (ttm) REVERT: C 668 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7681 (mtt-85) REVERT: C 685 TYR cc_start: 0.8484 (t80) cc_final: 0.7612 (t80) REVERT: C 714 TYR cc_start: 0.8884 (t80) cc_final: 0.8035 (t80) REVERT: C 790 ASP cc_start: 0.8362 (t0) cc_final: 0.7983 (t0) REVERT: C 851 MET cc_start: 0.8621 (mtt) cc_final: 0.8415 (mtp) REVERT: C 1102 MET cc_start: 0.9267 (ttm) cc_final: 0.8951 (tmm) REVERT: D 393 ILE cc_start: 0.8068 (pt) cc_final: 0.7763 (pt) REVERT: D 407 MET cc_start: 0.8878 (mtm) cc_final: 0.8455 (tmm) REVERT: D 484 ILE cc_start: 0.8330 (mm) cc_final: 0.7664 (tp) REVERT: D 488 ASP cc_start: 0.8259 (t0) cc_final: 0.7972 (t0) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.1595 time to fit residues: 69.2083 Evaluate side-chains 194 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 90 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 260 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS B1035 GLN B1072 HIS B1133 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.070985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.055988 restraints weight = 111389.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057571 restraints weight = 64346.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058658 restraints weight = 43518.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.059390 restraints weight = 33041.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059869 restraints weight = 27235.568| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24774 Z= 0.214 Angle : 0.639 11.182 33908 Z= 0.324 Chirality : 0.041 0.170 3729 Planarity : 0.004 0.045 4219 Dihedral : 15.275 89.537 3843 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.12 % Allowed : 1.90 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2837 helix: 1.18 (0.14), residues: 1429 sheet: -0.15 (0.30), residues: 287 loop : -1.19 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 255 TYR 0.026 0.002 TYR C 550 PHE 0.024 0.002 PHE B 64 TRP 0.017 0.002 TRP B 652 HIS 0.007 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00470 (24774) covalent geometry : angle 0.63898 (33908) hydrogen bonds : bond 0.03804 ( 1106) hydrogen bonds : angle 4.25190 ( 3197) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 0.920 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 499 MET cc_start: 0.8735 (tpp) cc_final: 0.8291 (tpt) REVERT: B 525 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8418 (tp-100) REVERT: B 591 LEU cc_start: 0.8802 (mp) cc_final: 0.8592 (tt) REVERT: B 596 MET cc_start: 0.9413 (mmm) cc_final: 0.9189 (mmp) REVERT: B 661 LEU cc_start: 0.9541 (mt) cc_final: 0.9320 (mt) REVERT: B 727 MET cc_start: 0.8114 (mtt) cc_final: 0.7755 (mtt) REVERT: B 797 GLU cc_start: 0.9292 (tt0) cc_final: 0.8546 (tm-30) REVERT: B 1078 LEU cc_start: 0.8292 (tt) cc_final: 0.8039 (mt) REVERT: B 1112 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 1114 TYR cc_start: 0.8951 (m-10) cc_final: 0.8563 (m-10) REVERT: C 2 LEU cc_start: 0.7720 (tt) cc_final: 0.7356 (tt) REVERT: C 91 MET cc_start: 0.8826 (mtm) cc_final: 0.8420 (ttp) REVERT: C 571 LEU cc_start: 0.9438 (mt) cc_final: 0.9080 (mt) REVERT: C 647 GLN cc_start: 0.8169 (pm20) cc_final: 0.7384 (tm-30) REVERT: C 665 MET cc_start: 0.7089 (ttt) cc_final: 0.6339 (ttm) REVERT: C 668 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7830 (mtt-85) REVERT: C 685 TYR cc_start: 0.8449 (t80) cc_final: 0.7437 (t80) REVERT: C 714 TYR cc_start: 0.8823 (t80) cc_final: 0.7896 (t80) REVERT: C 785 THR cc_start: 0.8817 (p) cc_final: 0.8494 (p) REVERT: C 790 ASP cc_start: 0.8384 (t0) cc_final: 0.8105 (t0) REVERT: D 393 ILE cc_start: 0.7978 (pt) cc_final: 0.7694 (pt) REVERT: D 484 ILE cc_start: 0.8272 (mm) cc_final: 0.7778 (tp) REVERT: D 488 ASP cc_start: 0.8429 (t0) cc_final: 0.8141 (t0) REVERT: D 545 GLU cc_start: 0.8123 (tt0) cc_final: 0.7270 (pm20) outliers start: 3 outliers final: 0 residues processed: 260 average time/residue: 0.1537 time to fit residues: 65.8405 Evaluate side-chains 185 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 43 optimal weight: 9.9990 chunk 206 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 769 HIS ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN C1096 GLN ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.070263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055372 restraints weight = 112743.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.056961 restraints weight = 64933.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.058012 restraints weight = 43989.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.058753 restraints weight = 33433.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.059244 restraints weight = 27423.281| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24774 Z= 0.223 Angle : 0.662 10.826 33908 Z= 0.336 Chirality : 0.042 0.167 3729 Planarity : 0.004 0.059 4219 Dihedral : 15.388 89.339 3843 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.16), residues: 2837 helix: 1.09 (0.14), residues: 1430 sheet: -0.19 (0.30), residues: 287 loop : -1.15 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG B 259 TYR 0.016 0.002 TYR C 190 PHE 0.024 0.002 PHE C 68 TRP 0.042 0.002 TRP C 248 HIS 0.007 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00493 (24774) covalent geometry : angle 0.66194 (33908) hydrogen bonds : bond 0.03954 ( 1106) hydrogen bonds : angle 4.40650 ( 3197) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.938 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 499 MET cc_start: 0.8772 (tpp) cc_final: 0.8239 (tpt) REVERT: B 520 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8511 (tm-30) REVERT: B 525 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8423 (tp-100) REVERT: B 797 GLU cc_start: 0.9310 (tt0) cc_final: 0.8525 (tm-30) REVERT: B 1112 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8326 (tm-30) REVERT: B 1114 TYR cc_start: 0.8953 (m-10) cc_final: 0.8581 (m-10) REVERT: C 91 MET cc_start: 0.8820 (mtm) cc_final: 0.8540 (ttm) REVERT: C 665 MET cc_start: 0.7282 (ttt) cc_final: 0.6655 (ttt) REVERT: C 668 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7821 (mtt-85) REVERT: C 714 TYR cc_start: 0.8826 (t80) cc_final: 0.7835 (t80) REVERT: C 790 ASP cc_start: 0.8515 (t0) cc_final: 0.8216 (t0) REVERT: D 100 MET cc_start: 0.8963 (mpp) cc_final: 0.8521 (mpp) REVERT: D 324 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8273 (pp20) REVERT: D 484 ILE cc_start: 0.8285 (mm) cc_final: 0.7779 (tp) REVERT: D 488 ASP cc_start: 0.8355 (t0) cc_final: 0.8046 (t0) REVERT: D 545 GLU cc_start: 0.8077 (tt0) cc_final: 0.7389 (mp0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1580 time to fit residues: 62.0382 Evaluate side-chains 179 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 72 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 166 optimal weight: 0.0870 chunk 21 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS B1133 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.071328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056495 restraints weight = 111715.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.058101 restraints weight = 64130.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.059172 restraints weight = 43321.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.059895 restraints weight = 32783.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.060377 restraints weight = 27002.143| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 24774 Z= 0.159 Angle : 0.615 9.709 33908 Z= 0.312 Chirality : 0.040 0.171 3729 Planarity : 0.004 0.071 4219 Dihedral : 15.337 88.864 3843 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 2837 helix: 1.27 (0.14), residues: 1423 sheet: -0.16 (0.30), residues: 289 loop : -1.04 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 662 TYR 0.037 0.001 TYR C 550 PHE 0.022 0.001 PHE B 64 TRP 0.037 0.001 TRP B 236 HIS 0.009 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00356 (24774) covalent geometry : angle 0.61459 (33908) hydrogen bonds : bond 0.03628 ( 1106) hydrogen bonds : angle 4.26835 ( 3197) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.912 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 499 MET cc_start: 0.8706 (tpp) cc_final: 0.8203 (tpt) REVERT: B 503 LEU cc_start: 0.8950 (tt) cc_final: 0.8214 (pt) REVERT: B 504 MET cc_start: 0.7003 (ttm) cc_final: 0.6317 (ttm) REVERT: B 525 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8454 (tp-100) REVERT: B 604 MET cc_start: 0.8385 (ttt) cc_final: 0.7252 (ttp) REVERT: B 661 LEU cc_start: 0.9547 (mt) cc_final: 0.9315 (mt) REVERT: B 727 MET cc_start: 0.8260 (mtt) cc_final: 0.7976 (mtt) REVERT: B 797 GLU cc_start: 0.9260 (tt0) cc_final: 0.8514 (tm-30) REVERT: B 1066 ILE cc_start: 0.9279 (mt) cc_final: 0.7929 (mt) REVERT: B 1078 LEU cc_start: 0.8205 (tt) cc_final: 0.7949 (mt) REVERT: B 1112 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 1114 TYR cc_start: 0.8916 (m-10) cc_final: 0.8493 (m-10) REVERT: B 1171 MET cc_start: 0.8381 (ppp) cc_final: 0.8105 (ppp) REVERT: C 91 MET cc_start: 0.8778 (mtm) cc_final: 0.8430 (ttp) REVERT: C 342 ILE cc_start: 0.9565 (tt) cc_final: 0.9326 (tp) REVERT: C 571 LEU cc_start: 0.9423 (mt) cc_final: 0.9027 (mt) REVERT: C 647 GLN cc_start: 0.8130 (pm20) cc_final: 0.7209 (tm-30) REVERT: C 665 MET cc_start: 0.7694 (ttt) cc_final: 0.7355 (ttm) REVERT: C 685 TYR cc_start: 0.8339 (t80) cc_final: 0.7635 (t80) REVERT: C 714 TYR cc_start: 0.8770 (t80) cc_final: 0.7874 (t80) REVERT: C 785 THR cc_start: 0.8745 (p) cc_final: 0.8542 (p) REVERT: C 790 ASP cc_start: 0.8408 (t0) cc_final: 0.8194 (t0) REVERT: D 275 ASP cc_start: 0.8788 (p0) cc_final: 0.8499 (p0) REVERT: D 324 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8217 (pp20) REVERT: D 484 ILE cc_start: 0.8351 (mm) cc_final: 0.7833 (tp) REVERT: D 488 ASP cc_start: 0.8378 (t0) cc_final: 0.7998 (t0) REVERT: D 545 GLU cc_start: 0.8050 (tt0) cc_final: 0.7399 (mp0) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1472 time to fit residues: 58.7691 Evaluate side-chains 187 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 104 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 263 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 241 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 0.0030 chunk 129 optimal weight: 5.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 792 GLN ** D 542 GLN ** 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 = 0.3478 r_free = 0.3478 target = 0.071164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056348 restraints weight = 112198.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.057945 restraints weight = 64769.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.059015 restraints weight = 43828.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.059748 restraints weight = 33161.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060199 restraints weight = 27231.724| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24774 Z= 0.164 Angle : 0.620 9.480 33908 Z= 0.314 Chirality : 0.041 0.204 3729 Planarity : 0.004 0.055 4219 Dihedral : 15.307 87.886 3843 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.16), residues: 2837 helix: 1.31 (0.14), residues: 1424 sheet: -0.15 (0.30), residues: 289 loop : -0.99 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 259 TYR 0.015 0.001 TYR D 108 PHE 0.018 0.001 PHE B 64 TRP 0.029 0.001 TRP B 236 HIS 0.009 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00368 (24774) covalent geometry : angle 0.61973 (33908) hydrogen bonds : bond 0.03643 ( 1106) hydrogen bonds : angle 4.26631 ( 3197) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.992 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 384 ASP cc_start: 0.8830 (t70) cc_final: 0.8540 (t0) REVERT: B 503 LEU cc_start: 0.8954 (tt) cc_final: 0.8233 (pt) REVERT: B 504 MET cc_start: 0.7220 (ttm) cc_final: 0.6785 (ttm) REVERT: B 525 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8508 (tp-100) REVERT: B 661 LEU cc_start: 0.9587 (mt) cc_final: 0.9348 (mt) REVERT: B 727 MET cc_start: 0.8354 (mtt) cc_final: 0.8036 (mtt) REVERT: B 797 GLU cc_start: 0.9231 (tt0) cc_final: 0.8502 (tm-30) REVERT: B 1112 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 1114 TYR cc_start: 0.8913 (m-10) cc_final: 0.8529 (m-10) REVERT: C 91 MET cc_start: 0.8778 (mtm) cc_final: 0.8394 (ttp) REVERT: C 342 ILE cc_start: 0.9548 (tt) cc_final: 0.9314 (tp) REVERT: C 396 MET cc_start: 0.8686 (tpp) cc_final: 0.8484 (tpp) REVERT: C 571 LEU cc_start: 0.9425 (mt) cc_final: 0.9034 (mt) REVERT: C 647 GLN cc_start: 0.8159 (pm20) cc_final: 0.7353 (tm-30) REVERT: C 685 TYR cc_start: 0.8332 (t80) cc_final: 0.7640 (t80) REVERT: C 714 TYR cc_start: 0.8746 (t80) cc_final: 0.7854 (t80) REVERT: C 787 MET cc_start: 0.7658 (mpp) cc_final: 0.7188 (mpp) REVERT: C 1080 MET cc_start: 0.8975 (ptm) cc_final: 0.8078 (tmm) REVERT: D 324 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8208 (pp20) REVERT: D 484 ILE cc_start: 0.8353 (mm) cc_final: 0.7857 (tp) REVERT: D 488 ASP cc_start: 0.8442 (t0) cc_final: 0.8116 (t0) REVERT: D 545 GLU cc_start: 0.8100 (tt0) cc_final: 0.7445 (mp0) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1513 time to fit residues: 60.8369 Evaluate side-chains 183 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 130 optimal weight: 0.3980 chunk 127 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 134 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 248 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN B 956 HIS B1133 HIS C 38 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.073101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058264 restraints weight = 110877.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059904 restraints weight = 63758.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.061022 restraints weight = 43155.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.061773 restraints weight = 32600.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.062227 restraints weight = 26710.939| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24774 Z= 0.115 Angle : 0.607 9.230 33908 Z= 0.305 Chirality : 0.040 0.236 3729 Planarity : 0.004 0.045 4219 Dihedral : 15.177 89.041 3843 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.16), residues: 2837 helix: 1.44 (0.14), residues: 1420 sheet: -0.02 (0.30), residues: 282 loop : -0.95 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 259 TYR 0.025 0.001 TYR C 550 PHE 0.016 0.001 PHE C 68 TRP 0.057 0.001 TRP C1045 HIS 0.010 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00257 (24774) covalent geometry : angle 0.60695 (33908) hydrogen bonds : bond 0.03463 ( 1106) hydrogen bonds : angle 4.12457 ( 3197) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.929 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 66 GLU cc_start: 0.9078 (tt0) cc_final: 0.8780 (tp30) REVERT: B 384 ASP cc_start: 0.8897 (t70) cc_final: 0.8633 (t0) REVERT: B 499 MET cc_start: 0.8513 (tpp) cc_final: 0.8100 (tpt) REVERT: B 503 LEU cc_start: 0.8995 (tt) cc_final: 0.8347 (pt) REVERT: B 504 MET cc_start: 0.7105 (ttm) cc_final: 0.6830 (ttm) REVERT: B 525 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8497 (tp-100) REVERT: B 727 MET cc_start: 0.8259 (mtt) cc_final: 0.7932 (mtt) REVERT: B 797 GLU cc_start: 0.9142 (tt0) cc_final: 0.8416 (tm-30) REVERT: B 798 ASP cc_start: 0.8563 (m-30) cc_final: 0.8142 (m-30) REVERT: B 1066 ILE cc_start: 0.9247 (mt) cc_final: 0.7727 (mt) REVERT: B 1112 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8475 (tm-30) REVERT: B 1114 TYR cc_start: 0.8878 (m-10) cc_final: 0.8486 (m-10) REVERT: C 91 MET cc_start: 0.8816 (mtm) cc_final: 0.8419 (ttp) REVERT: C 548 LEU cc_start: 0.8861 (tt) cc_final: 0.8640 (tt) REVERT: C 571 LEU cc_start: 0.9424 (mt) cc_final: 0.9029 (mt) REVERT: C 647 GLN cc_start: 0.8115 (pm20) cc_final: 0.7394 (tm-30) REVERT: C 680 MET cc_start: 0.9063 (mmm) cc_final: 0.8727 (mmm) REVERT: C 685 TYR cc_start: 0.8243 (t80) cc_final: 0.7709 (t80) REVERT: C 714 TYR cc_start: 0.8703 (t80) cc_final: 0.7929 (t80) REVERT: C 749 GLN cc_start: 0.8426 (tp40) cc_final: 0.7849 (tp40) REVERT: C 785 THR cc_start: 0.8748 (p) cc_final: 0.8302 (p) REVERT: C 834 LEU cc_start: 0.9469 (tp) cc_final: 0.9170 (tp) REVERT: C 1040 GLU cc_start: 0.8229 (pm20) cc_final: 0.7209 (pm20) REVERT: C 1080 MET cc_start: 0.8982 (ptm) cc_final: 0.8646 (ptm) REVERT: D 275 ASP cc_start: 0.8720 (p0) cc_final: 0.8471 (p0) REVERT: D 324 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8112 (pp20) REVERT: D 353 CYS cc_start: 0.7990 (p) cc_final: 0.7651 (m) REVERT: D 488 ASP cc_start: 0.8467 (t0) cc_final: 0.8171 (t0) REVERT: D 545 GLU cc_start: 0.8027 (tt0) cc_final: 0.7211 (pm20) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1546 time to fit residues: 68.0422 Evaluate side-chains 191 residues out of total 2415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 286 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 135 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 108 optimal weight: 20.0000 chunk 277 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 202 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 485 GLN ** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 HIS ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** 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 = 0.3517 r_free = 0.3517 target = 0.072889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.058002 restraints weight = 110547.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059620 restraints weight = 63823.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060736 restraints weight = 43294.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.061501 restraints weight = 32706.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.062012 restraints weight = 26780.315| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24774 Z= 0.126 Angle : 0.610 10.596 33908 Z= 0.306 Chirality : 0.040 0.204 3729 Planarity : 0.004 0.044 4219 Dihedral : 15.116 89.888 3843 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.04 % Allowed : 0.25 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2837 helix: 1.50 (0.14), residues: 1424 sheet: -0.03 (0.30), residues: 288 loop : -0.88 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 259 TYR 0.027 0.001 TYR C 550 PHE 0.028 0.001 PHE B 428 TRP 0.036 0.001 TRP C1045 HIS 0.009 0.001 HIS B 956 Details of bonding type rmsd covalent geometry : bond 0.00285 (24774) covalent geometry : angle 0.60973 (33908) hydrogen bonds : bond 0.03464 ( 1106) hydrogen bonds : angle 4.12708 ( 3197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3602.12 seconds wall clock time: 63 minutes 15.00 seconds (3795.00 seconds total)