Starting phenix.real_space_refine on Thu Feb 5 11:11:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1j_63573/02_2026/9m1j_63573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1j_63573/02_2026/9m1j_63573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m1j_63573/02_2026/9m1j_63573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1j_63573/02_2026/9m1j_63573.map" model { file = "/net/cci-nas-00/data/ceres_data/9m1j_63573/02_2026/9m1j_63573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1j_63573/02_2026/9m1j_63573.cif" } resolution = 2.14 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= 0.001 sd= 0.025 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 10570 2.51 5 N 2901 2.21 5 O 3113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16686 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 8744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8744 Classifications: {'peptide': 1116} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 1069} Chain breaks: 2 Chain: "E" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3062 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 17, 'TRANS': 368} Chain breaks: 1 Chain: "G" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1467 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain: "b" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3380 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.83, per 1000 atoms: 0.23 Number of scatterers: 16686 At special positions: 0 Unit cell: (147.703, 128.97, 169.318, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 3 15.00 Mg 1 11.99 O 3113 8.00 N 2901 7.00 C 10570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 748.9 milliseconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3970 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 9 sheets defined 59.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 43 through 46 removed outlier: 3.647A pdb=" N VAL D 46 " --> pdb=" O LEU D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 50 through 67 removed outlier: 3.879A pdb=" N TYR D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.591A pdb=" N LEU D 73 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 79 through 90 removed outlier: 3.845A pdb=" N ASP D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 113 Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 125 through 138 removed outlier: 4.126A pdb=" N GLU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Proline residue: D 131 - end of helix removed outlier: 3.569A pdb=" N VAL D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 removed outlier: 4.134A pdb=" N ARG D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 184 through 197 Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.990A pdb=" N ALA D 206 " --> pdb=" O LYS D 202 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D 215 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR D 216 " --> pdb=" O SER D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 239 Processing helix chain 'D' and resid 243 through 263 removed outlier: 3.737A pdb=" N VAL D 247 " --> pdb=" O THR D 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.932A pdb=" N CYS D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.663A pdb=" N GLY D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 309 removed outlier: 3.541A pdb=" N ARG D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 370 removed outlier: 3.695A pdb=" N LYS D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 removed outlier: 3.972A pdb=" N ARG D 377 " --> pdb=" O ASP D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 405 Processing helix chain 'D' and resid 412 through 430 removed outlier: 3.765A pdb=" N ARG D 429 " --> pdb=" O GLU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 435 No H-bonds generated for 'chain 'D' and resid 433 through 435' Processing helix chain 'D' and resid 436 through 448 removed outlier: 3.502A pdb=" N ALA D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 478 removed outlier: 4.265A pdb=" N ARG D 464 " --> pdb=" O GLY D 460 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP D 465 " --> pdb=" O THR D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 501 removed outlier: 3.529A pdb=" N VAL D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 488 " --> pdb=" O LYS D 484 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 489 " --> pdb=" O PRO D 485 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N SER D 492 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA D 493 " --> pdb=" O ALA D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 522 Processing helix chain 'D' and resid 526 through 534 Processing helix chain 'D' and resid 537 through 540 Processing helix chain 'D' and resid 541 through 546 removed outlier: 3.554A pdb=" N PHE D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 555 Processing helix chain 'D' and resid 556 through 559 Processing helix chain 'D' and resid 560 through 571 Processing helix chain 'D' and resid 576 through 592 removed outlier: 3.966A pdb=" N GLN D 592 " --> pdb=" O HIS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 601 Processing helix chain 'D' and resid 601 through 610 removed outlier: 3.674A pdb=" N ARG D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 639 removed outlier: 3.546A pdb=" N LEU D 623 " --> pdb=" O HIS D 619 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 656 Processing helix chain 'D' and resid 657 through 665 removed outlier: 3.502A pdb=" N GLN D 661 " --> pdb=" O GLN D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 690 removed outlier: 3.929A pdb=" N MET D 676 " --> pdb=" O GLY D 672 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 689 " --> pdb=" O GLU D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 713 removed outlier: 3.846A pdb=" N ASP D 701 " --> pdb=" O ASP D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 721 Processing helix chain 'D' and resid 722 through 740 Processing helix chain 'D' and resid 749 through 762 Processing helix chain 'D' and resid 763 through 766 Processing helix chain 'D' and resid 768 through 780 removed outlier: 3.520A pdb=" N ARG D 772 " --> pdb=" O GLU D 768 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 777 " --> pdb=" O CYS D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 784 through 788 removed outlier: 3.700A pdb=" N LYS D 788 " --> pdb=" O PHE D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 803 removed outlier: 3.652A pdb=" N VAL D 794 " --> pdb=" O ARG D 790 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 801 " --> pdb=" O GLY D 797 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS D 803 " --> pdb=" O ARG D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.737A pdb=" N GLY D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 removed outlier: 3.652A pdb=" N ALA D 851 " --> pdb=" O GLN D 847 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS D 855 " --> pdb=" O ALA D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 856 through 858 No H-bonds generated for 'chain 'D' and resid 856 through 858' Processing helix chain 'D' and resid 867 through 889 removed outlier: 3.974A pdb=" N VAL D 871 " --> pdb=" O VAL D 867 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 884 " --> pdb=" O MET D 880 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 885 " --> pdb=" O ASP D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 890 through 894 Processing helix chain 'D' and resid 895 through 911 removed outlier: 3.528A pdb=" N CYS D 899 " --> pdb=" O GLU D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 930 Processing helix chain 'D' and resid 941 through 949 Processing helix chain 'D' and resid 961 through 964 Processing helix chain 'D' and resid 965 through 970 Processing helix chain 'D' and resid 971 through 975 removed outlier: 3.510A pdb=" N GLY D 974 " --> pdb=" O GLN D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 980 through 991 removed outlier: 3.782A pdb=" N VAL D 988 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing helix chain 'D' and resid 994 through 1010 removed outlier: 3.634A pdb=" N PHE D1006 " --> pdb=" O THR D1002 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D1007 " --> pdb=" O GLN D1003 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR D1008 " --> pdb=" O SER D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1015 through 1033 Processing helix chain 'D' and resid 1039 through 1052 removed outlier: 3.547A pdb=" N THR D1052 " --> pdb=" O ASP D1048 " (cutoff:3.500A) Processing helix chain 'D' and resid 1065 through 1079 removed outlier: 3.571A pdb=" N VAL D1069 " --> pdb=" O HIS D1065 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D1077 " --> pdb=" O ALA D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1098 Processing helix chain 'D' and resid 1099 through 1101 No H-bonds generated for 'chain 'D' and resid 1099 through 1101' Processing helix chain 'D' and resid 1103 through 1118 removed outlier: 3.583A pdb=" N ARG D1107 " --> pdb=" O GLY D1103 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS D1118 " --> pdb=" O CYS D1114 " (cutoff:3.500A) Processing helix chain 'D' and resid 1121 through 1139 Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 4.098A pdb=" N ASP D1149 " --> pdb=" O ALA D1145 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU D1150 " --> pdb=" O ASP D1146 " (cutoff:3.500A) Processing helix chain 'D' and resid 1163 through 1178 removed outlier: 3.709A pdb=" N GLN D1170 " --> pdb=" O VAL D1166 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 Processing helix chain 'E' and resid 167 through 178 removed outlier: 4.436A pdb=" N VAL E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 268 through 273 removed outlier: 4.342A pdb=" N LEU E 272 " --> pdb=" O ASN E 268 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE E 273 " --> pdb=" O GLN E 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 268 through 273' Processing helix chain 'E' and resid 274 through 276 No H-bonds generated for 'chain 'E' and resid 274 through 276' Processing helix chain 'E' and resid 322 through 329 removed outlier: 3.682A pdb=" N ASN E 326 " --> pdb=" O TRP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 362 Processing helix chain 'E' and resid 374 through 396 removed outlier: 5.109A pdb=" N ASN E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU E 392 " --> pdb=" O ALA E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 415 Processing helix chain 'E' and resid 417 through 425 Processing helix chain 'E' and resid 470 through 483 removed outlier: 3.553A pdb=" N VAL E 474 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 489 removed outlier: 3.545A pdb=" N ASP E 488 " --> pdb=" O PRO E 485 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU E 489 " --> pdb=" O VAL E 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 485 through 489' Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 28 through 35 removed outlier: 4.191A pdb=" N ILE G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.584A pdb=" N ARG G 78 " --> pdb=" O ARG G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 110 removed outlier: 3.850A pdb=" N CYS G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 165 through 178 removed outlier: 3.887A pdb=" N LEU G 172 " --> pdb=" O GLY G 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 29 removed outlier: 3.575A pdb=" N ASP b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 44 removed outlier: 3.894A pdb=" N GLN b 43 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU b 44 " --> pdb=" O ASP b 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 40 through 44' Processing helix chain 'b' and resid 69 through 78 removed outlier: 4.529A pdb=" N MET b 73 " --> pdb=" O GLU b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 88 No H-bonds generated for 'chain 'b' and resid 86 through 88' Processing helix chain 'b' and resid 100 through 106 Processing helix chain 'b' and resid 112 through 126 removed outlier: 3.553A pdb=" N VAL b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 159 removed outlier: 3.840A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR b 149 " --> pdb=" O SER b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 193 removed outlier: 3.756A pdb=" N GLN b 191 " --> pdb=" O LEU b 187 " (cutoff:3.500A) Processing helix chain 'b' and resid 204 through 212 Processing helix chain 'b' and resid 221 through 237 removed outlier: 3.949A pdb=" N LEU b 225 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU b 228 " --> pdb=" O ASP b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 258 Processing helix chain 'b' and resid 285 through 294 Processing helix chain 'b' and resid 295 through 299 removed outlier: 3.534A pdb=" N ASN b 298 " --> pdb=" O ASP b 295 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET b 299 " --> pdb=" O ALA b 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 295 through 299' Processing helix chain 'b' and resid 304 through 308 Processing helix chain 'b' and resid 322 through 334 removed outlier: 3.776A pdb=" N GLN b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 390 removed outlier: 4.264A pdb=" N LEU b 377 " --> pdb=" O ALA b 373 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN b 384 " --> pdb=" O ARG b 380 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET b 388 " --> pdb=" O GLN b 384 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG b 390 " --> pdb=" O THR b 386 " (cutoff:3.500A) Processing helix chain 'b' and resid 395 through 400 Processing helix chain 'b' and resid 404 through 427 removed outlier: 4.362A pdb=" N PHE b 408 " --> pdb=" O ASP b 404 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR b 409 " --> pdb=" O GLU b 405 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 22 through 23 removed outlier: 7.331A pdb=" N LEU G 120 " --> pdb=" O CYS G 153 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLN G 155 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE G 122 " --> pdb=" O GLN G 155 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU G 87 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N PHE G 123 " --> pdb=" O LEU G 87 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP G 89 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASN G 125 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL G 91 " --> pdb=" O ASN G 125 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU G 19 " --> pdb=" O TRP G 65 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL G 67 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N MET G 21 " --> pdb=" O VAL G 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 452 through 454 removed outlier: 3.839A pdb=" N CYS D 457 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 131 through 133 removed outlier: 6.561A pdb=" N VAL E 158 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU E 234 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 281 through 283 removed outlier: 3.622A pdb=" N LEU E 282 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER E 338 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 462 through 466 removed outlier: 3.509A pdb=" N LEU E 465 " --> pdb=" O LEU E 446 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N LEU E 523 " --> pdb=" O THR E 447 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS E 449 " --> pdb=" O LEU E 523 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL E 525 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS E 451 " --> pdb=" O VAL E 525 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU E 491 " --> pdb=" O LEU E 505 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 90 through 91 removed outlier: 8.975A pdb=" N VAL b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU b 3 " --> pdb=" O LEU b 130 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY b 132 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL b 5 " --> pdb=" O GLY b 132 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ASN b 165 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE b 167 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU b 135 " --> pdb=" O PHE b 167 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU b 198 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR b 200 " --> pdb=" O THR b 166 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE b 265 " --> pdb=" O SER b 371 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER b 371 " --> pdb=" O PHE b 265 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR b 312 " --> pdb=" O ASN b 370 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N LYS b 350 " --> pdb=" O LEU b 311 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL b 313 " --> pdb=" O LYS b 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 90 through 91 removed outlier: 8.975A pdb=" N VAL b 91 " --> pdb=" O ALA b 63 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU b 65 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU b 3 " --> pdb=" O LEU b 130 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY b 132 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL b 5 " --> pdb=" O GLY b 132 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ASN b 165 " --> pdb=" O GLN b 131 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE b 133 " --> pdb=" O ASN b 165 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE b 167 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU b 135 " --> pdb=" O PHE b 167 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU b 198 " --> pdb=" O MET b 164 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR b 200 " --> pdb=" O THR b 166 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR b 199 " --> pdb=" O PHE b 266 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE b 265 " --> pdb=" O SER b 371 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N SER b 371 " --> pdb=" O PHE b 265 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY b 369 " --> pdb=" O MET b 267 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR b 312 " --> pdb=" O ASN b 370 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N CYS b 354 " --> pdb=" O ALA b 315 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE b 317 " --> pdb=" O CYS b 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 51 through 53 Processing sheet with id=AA9, first strand: chain 'b' and resid 169 through 170 831 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4076 1.33 - 1.45: 3146 1.45 - 1.57: 9633 1.57 - 1.69: 5 1.69 - 1.81: 146 Bond restraints: 17006 Sorted by residual: bond pdb=" C ARG b 121 " pdb=" N LYS b 122 " ideal model delta sigma weight residual 1.335 1.280 0.055 1.38e-02 5.25e+03 1.60e+01 bond pdb=" C ALA D 594 " pdb=" O ALA D 594 " ideal model delta sigma weight residual 1.238 1.288 -0.050 1.28e-02 6.10e+03 1.53e+01 bond pdb=" C GLU D 267 " pdb=" N ASP D 268 " ideal model delta sigma weight residual 1.333 1.280 0.053 1.37e-02 5.33e+03 1.49e+01 bond pdb=" N GLU D 130 " pdb=" CA GLU D 130 " ideal model delta sigma weight residual 1.462 1.488 -0.026 7.70e-03 1.69e+04 1.16e+01 bond pdb=" N VAL D 358 " pdb=" CA VAL D 358 " ideal model delta sigma weight residual 1.461 1.500 -0.039 1.19e-02 7.06e+03 1.09e+01 ... (remaining 17001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 22979 3.79 - 7.58: 54 7.58 - 11.37: 8 11.37 - 15.16: 0 15.16 - 18.95: 2 Bond angle restraints: 23043 Sorted by residual: angle pdb=" PB GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sigma weight residual 120.50 139.45 -18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" PA GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PB GTP b1500 " ideal model delta sigma weight residual 120.50 139.35 -18.85 3.00e+00 1.11e-01 3.95e+01 angle pdb=" N LEU b 68 " pdb=" CA LEU b 68 " pdb=" C LEU b 68 " ideal model delta sigma weight residual 113.17 107.20 5.97 1.26e+00 6.30e-01 2.24e+01 angle pdb=" O LYS D 634 " pdb=" C LYS D 634 " pdb=" N LEU D 635 " ideal model delta sigma weight residual 122.12 117.50 4.62 1.06e+00 8.90e-01 1.90e+01 angle pdb=" C SER D1082 " pdb=" N LYS D1083 " pdb=" CA LYS D1083 " ideal model delta sigma weight residual 122.37 115.77 6.60 1.54e+00 4.22e-01 1.83e+01 ... (remaining 23038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 10052 32.52 - 65.03: 225 65.03 - 97.55: 20 97.55 - 130.07: 0 130.07 - 162.59: 4 Dihedral angle restraints: 10301 sinusoidal: 4169 harmonic: 6132 Sorted by residual: dihedral pdb=" O3A GTP b1500 " pdb=" O3B GTP b1500 " pdb=" PB GTP b1500 " pdb=" PG GTP b1500 " ideal model delta sinusoidal sigma weight residual 303.79 141.21 162.59 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C8 GTP b1500 " pdb=" C1' GTP b1500 " pdb=" N9 GTP b1500 " pdb=" O4' GTP b1500 " ideal model delta sinusoidal sigma weight residual 104.59 -51.13 155.72 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O3B GTP b1500 " pdb=" O3A GTP b1500 " pdb=" PB GTP b1500 " pdb=" PA GTP b1500 " ideal model delta sinusoidal sigma weight residual -68.92 83.49 -152.41 1 2.00e+01 2.50e-03 4.53e+01 ... (remaining 10298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1846 0.042 - 0.083: 433 0.083 - 0.125: 239 0.125 - 0.166: 77 0.166 - 0.208: 38 Chirality restraints: 2633 Sorted by residual: chirality pdb=" C3' GTP b1500 " pdb=" C2' GTP b1500 " pdb=" C4' GTP b1500 " pdb=" O3' GTP b1500 " both_signs ideal model delta sigma weight residual False -2.47 -2.68 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE G 32 " pdb=" N ILE G 32 " pdb=" C ILE G 32 " pdb=" CB ILE G 32 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE b 163 " pdb=" N ILE b 163 " pdb=" C ILE b 163 " pdb=" CB ILE b 163 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 2630 not shown) Planarity restraints: 2964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D1076 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.72e+00 pdb=" C LYS D1076 " 0.038 2.00e-02 2.50e+03 pdb=" O LYS D1076 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS D1077 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 127 " -0.008 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C ALA D 127 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA D 127 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP D 128 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 603 " 0.022 5.00e-02 4.00e+02 3.29e-02 1.74e+00 pdb=" N PRO D 604 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 604 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 604 " 0.019 5.00e-02 4.00e+02 ... (remaining 2961 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 6776 2.94 - 3.43: 16610 3.43 - 3.92: 27446 3.92 - 4.41: 29848 4.41 - 4.90: 50178 Nonbonded interactions: 130858 Sorted by model distance: nonbonded pdb=" OE1 GLN b 15 " pdb=" O6 GTP b1500 " model vdw 2.447 3.040 nonbonded pdb=" O VAL b 76 " pdb=" N GLY b 79 " model vdw 2.461 3.120 nonbonded pdb=" OG1 THR b 143 " pdb=" O3G GTP b1500 " model vdw 2.468 3.040 nonbonded pdb=" O2B GTP b1500 " pdb="MG MG b1501 " model vdw 2.475 2.170 nonbonded pdb=" N ILE E 450 " pdb=" O LEU E 461 " model vdw 2.505 3.120 ... (remaining 130853 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 individual isotropic 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: 5.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.700 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 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 : 0.006 0.055 17006 Z= 0.427 Angle : 0.775 18.952 23043 Z= 0.549 Chirality : 0.053 0.208 2633 Planarity : 0.003 0.033 2964 Dihedral : 13.966 162.587 6331 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -1.82 (0.17), residues: 2103 helix: -0.28 (0.15), residues: 1094 sheet: -1.01 (0.43), residues: 146 loop : -2.45 (0.18), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 618 TYR 0.005 0.000 TYR b 159 PHE 0.012 0.001 PHE D1059 TRP 0.009 0.000 TRP D 472 HIS 0.002 0.000 HIS D 619 Details of bonding type rmsd covalent geometry : bond 0.00561 (17006) covalent geometry : angle 0.77546 (23043) hydrogen bonds : bond 0.18657 ( 811) hydrogen bonds : angle 5.95198 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 576 ASP cc_start: 0.6299 (t0) cc_final: 0.6068 (t70) REVERT: D 1104 ASP cc_start: 0.6787 (m-30) cc_final: 0.6520 (m-30) REVERT: b 3 GLU cc_start: 0.7658 (mp0) cc_final: 0.7348 (mp0) REVERT: b 161 ASP cc_start: 0.6420 (p0) cc_final: 0.6218 (p0) outliers start: 0 outliers final: 1 residues processed: 525 average time/residue: 0.6427 time to fit residues: 370.8968 Evaluate side-chains 425 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0970 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN D 70 GLN D 140 ASN D 263 HIS D 302 GLN D 505 ASN D 515 GLN D 544 ASN D 723 GLN D 920 HIS D 938 HIS D1028 GLN D1036 ASN D1049 HIS D1172 ASN E 364 GLN E 369 ASN E 444 GLN G 51 ASN G 150 HIS G 155 GLN b 8 GLN b 99 ASN ** b 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 131 GLN b 195 ASN b 279 GLN b 292 GLN b 329 GLN b 332 ASN b 335 ASN b 396 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.185439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.151280 restraints weight = 19460.887| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.47 r_work: 0.3740 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3604 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17006 Z= 0.150 Angle : 0.560 7.341 23043 Z= 0.294 Chirality : 0.042 0.153 2633 Planarity : 0.004 0.043 2964 Dihedral : 6.116 138.994 2306 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.57 % Allowed : 11.99 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -0.01 (0.18), residues: 2103 helix: 1.09 (0.16), residues: 1140 sheet: -0.60 (0.40), residues: 177 loop : -1.49 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 390 TYR 0.020 0.002 TYR D 107 PHE 0.020 0.002 PHE D 775 TRP 0.014 0.002 TRP D 147 HIS 0.012 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00308 (17006) covalent geometry : angle 0.56046 (23043) hydrogen bonds : bond 0.06423 ( 811) hydrogen bonds : angle 3.82779 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 469 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 302 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: E 451 LYS cc_start: 0.8165 (mttt) cc_final: 0.7940 (mttt) REVERT: b 27 GLU cc_start: 0.7981 (tt0) cc_final: 0.7108 (tt0) REVERT: b 46 ARG cc_start: 0.7838 (mmm-85) cc_final: 0.7507 (mtm-85) REVERT: b 197 ASP cc_start: 0.8150 (m-30) cc_final: 0.7937 (m-30) REVERT: b 321 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8397 (pmm) outliers start: 47 outliers final: 15 residues processed: 489 average time/residue: 0.7202 time to fit residues: 385.2911 Evaluate side-chains 459 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 442 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 678 GLN Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1061 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1176 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 196 THR Chi-restraints excluded: chain b residue 321 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 4 optimal weight: 0.8980 chunk 120 optimal weight: 0.0670 chunk 128 optimal weight: 0.3980 chunk 146 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 115 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 172 optimal weight: 0.0970 chunk 137 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 70 GLN D 140 ASN D 302 GLN D1131 GLN b 100 ASN b 131 GLN b 134 GLN b 291 GLN b 292 GLN b 396 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151004 restraints weight = 19987.105| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.65 r_work: 0.3742 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17006 Z= 0.101 Angle : 0.464 8.345 23043 Z= 0.237 Chirality : 0.038 0.152 2633 Planarity : 0.003 0.060 2964 Dihedral : 5.627 138.313 2304 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.75 % Allowed : 16.37 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.77 (0.19), residues: 2103 helix: 1.65 (0.16), residues: 1150 sheet: -0.15 (0.40), residues: 184 loop : -1.09 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 824 TYR 0.012 0.001 TYR D 107 PHE 0.019 0.001 PHE b 367 TRP 0.010 0.001 TRP D 472 HIS 0.005 0.001 HIS b 396 Details of bonding type rmsd covalent geometry : bond 0.00200 (17006) covalent geometry : angle 0.46355 (23043) hydrogen bonds : bond 0.04427 ( 811) hydrogen bonds : angle 3.41990 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 443 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 451 LYS cc_start: 0.8188 (mttt) cc_final: 0.7963 (mttt) REVERT: E 492 SER cc_start: 0.8230 (t) cc_final: 0.7902 (t) REVERT: b 3 GLU cc_start: 0.7878 (mp0) cc_final: 0.7643 (mp0) REVERT: b 27 GLU cc_start: 0.7716 (tt0) cc_final: 0.7225 (tt0) REVERT: b 46 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7470 (mtm-85) REVERT: b 197 ASP cc_start: 0.8087 (m-30) cc_final: 0.7837 (m-30) outliers start: 32 outliers final: 15 residues processed: 458 average time/residue: 0.7776 time to fit residues: 389.7995 Evaluate side-chains 449 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 434 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 295 ASP Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 118 optimal weight: 0.1980 chunk 197 optimal weight: 0.4980 chunk 183 optimal weight: 0.6980 chunk 207 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 28 optimal weight: 0.0770 chunk 176 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 HIS D 140 ASN D 640 ASN E 455 GLN E 458 GLN b 131 GLN b 165 ASN b 292 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.184709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.150045 restraints weight = 19712.484| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 1.23 r_work: 0.3767 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17006 Z= 0.101 Angle : 0.462 8.760 23043 Z= 0.235 Chirality : 0.038 0.138 2633 Planarity : 0.003 0.051 2964 Dihedral : 5.518 138.836 2304 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.81 % Allowed : 16.76 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.24 (0.19), residues: 2103 helix: 1.98 (0.16), residues: 1147 sheet: 0.10 (0.40), residues: 182 loop : -0.78 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 480 TYR 0.012 0.001 TYR E 493 PHE 0.018 0.001 PHE b 270 TRP 0.010 0.001 TRP D 472 HIS 0.006 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00199 (17006) covalent geometry : angle 0.46150 (23043) hydrogen bonds : bond 0.04354 ( 811) hydrogen bonds : angle 3.30925 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 425 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 448 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8124 (pt) REVERT: b 27 GLU cc_start: 0.7698 (tt0) cc_final: 0.7181 (tt0) REVERT: b 46 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7473 (mtm-85) outliers start: 33 outliers final: 19 residues processed: 440 average time/residue: 0.7922 time to fit residues: 380.3920 Evaluate side-chains 441 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 421 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1147 VAL Chi-restraints excluded: chain D residue 1176 ASP Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 448 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 126 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 105 optimal weight: 0.0770 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN D 640 ASN D 792 GLN G 63 ASN b 52 ASN b 131 GLN b 165 ASN b 291 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.145042 restraints weight = 19274.973| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.49 r_work: 0.3652 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17006 Z= 0.143 Angle : 0.536 10.626 23043 Z= 0.278 Chirality : 0.041 0.147 2633 Planarity : 0.004 0.049 2964 Dihedral : 5.906 141.917 2304 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.52 % Allowed : 16.48 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.22 (0.19), residues: 2103 helix: 1.92 (0.16), residues: 1144 sheet: 0.17 (0.40), residues: 176 loop : -0.71 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 213 TYR 0.014 0.001 TYR D 107 PHE 0.017 0.002 PHE b 367 TRP 0.011 0.001 TRP b 344 HIS 0.009 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00298 (17006) covalent geometry : angle 0.53605 (23043) hydrogen bonds : bond 0.06415 ( 811) hydrogen bonds : angle 3.60546 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 431 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 202 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7686 (tmtt) REVERT: E 507 ASN cc_start: 0.8662 (t0) cc_final: 0.7655 (t0) REVERT: b 3 GLU cc_start: 0.7894 (mp0) cc_final: 0.7664 (mp0) REVERT: b 27 GLU cc_start: 0.7945 (tt0) cc_final: 0.7382 (tt0) REVERT: b 46 ARG cc_start: 0.7834 (mmm-85) cc_final: 0.7546 (mtm-85) REVERT: b 73 MET cc_start: 0.8112 (mmp) cc_final: 0.7827 (mmm) outliers start: 46 outliers final: 30 residues processed: 449 average time/residue: 0.7809 time to fit residues: 384.5798 Evaluate side-chains 460 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 429 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1061 THR Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1176 ASP Chi-restraints excluded: chain D residue 1177 LEU Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain b residue 45 ASP Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 196 THR Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Chi-restraints excluded: chain b residue 386 THR Chi-restraints excluded: chain b residue 392 LYS Chi-restraints excluded: chain b residue 412 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 133 optimal weight: 8.9990 chunk 153 optimal weight: 0.0770 chunk 126 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN D 289 ASN D1108 GLN b 131 GLN b 165 ASN b 291 GLN b 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.178357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143441 restraints weight = 19185.892| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.48 r_work: 0.3622 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17006 Z= 0.157 Angle : 0.566 10.591 23043 Z= 0.294 Chirality : 0.043 0.150 2633 Planarity : 0.004 0.045 2964 Dihedral : 6.074 141.865 2304 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.30 % Allowed : 17.25 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.20 (0.19), residues: 2103 helix: 1.86 (0.16), residues: 1141 sheet: 0.24 (0.39), residues: 176 loop : -0.65 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1107 TYR 0.014 0.002 TYR D 107 PHE 0.018 0.002 PHE D 228 TRP 0.012 0.002 TRP b 344 HIS 0.010 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00335 (17006) covalent geometry : angle 0.56589 (23043) hydrogen bonds : bond 0.06876 ( 811) hydrogen bonds : angle 3.71141 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 431 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 202 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7644 (tmtt) REVERT: D 285 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8111 (mt) REVERT: E 507 ASN cc_start: 0.8716 (t0) cc_final: 0.7777 (t0) REVERT: b 3 GLU cc_start: 0.7930 (mp0) cc_final: 0.7698 (mp0) REVERT: b 27 GLU cc_start: 0.8035 (tt0) cc_final: 0.7527 (tt0) REVERT: b 46 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7565 (mtm-85) REVERT: b 73 MET cc_start: 0.8021 (mmp) cc_final: 0.7777 (mmm) REVERT: b 233 MET cc_start: 0.9111 (mtp) cc_final: 0.8850 (mtm) REVERT: b 332 ASN cc_start: 0.8074 (OUTLIER) cc_final: 0.7457 (m-40) REVERT: b 340 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6808 (p90) outliers start: 42 outliers final: 25 residues processed: 454 average time/residue: 0.7750 time to fit residues: 384.5114 Evaluate side-chains 460 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 431 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1061 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1176 ASP Chi-restraints excluded: chain D residue 1177 LEU Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 196 THR Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 332 ASN Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 340 TYR Chi-restraints excluded: chain b residue 367 PHE Chi-restraints excluded: chain b residue 392 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 209 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 66 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN D1108 GLN b 6 HIS b 100 ASN b 131 GLN ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 291 GLN b 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.179342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.144081 restraints weight = 19225.173| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.33 r_work: 0.3680 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17006 Z= 0.133 Angle : 0.533 9.817 23043 Z= 0.275 Chirality : 0.041 0.206 2633 Planarity : 0.004 0.068 2964 Dihedral : 5.921 140.919 2304 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.30 % Allowed : 17.91 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.37 (0.19), residues: 2103 helix: 1.98 (0.16), residues: 1142 sheet: 0.41 (0.39), residues: 176 loop : -0.57 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1107 TYR 0.013 0.001 TYR D 107 PHE 0.017 0.002 PHE D 775 TRP 0.012 0.001 TRP b 344 HIS 0.008 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00276 (17006) covalent geometry : angle 0.53272 (23043) hydrogen bonds : bond 0.05959 ( 811) hydrogen bonds : angle 3.58920 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 433 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 119 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7659 (mp) REVERT: E 507 ASN cc_start: 0.8678 (t0) cc_final: 0.7741 (t0) REVERT: b 3 GLU cc_start: 0.7862 (mp0) cc_final: 0.7620 (mp0) REVERT: b 27 GLU cc_start: 0.7887 (tt0) cc_final: 0.7283 (tt0) REVERT: b 46 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7548 (mtm-85) REVERT: b 233 MET cc_start: 0.9077 (mtp) cc_final: 0.8803 (mtm) REVERT: b 332 ASN cc_start: 0.7864 (OUTLIER) cc_final: 0.7231 (m-40) outliers start: 42 outliers final: 25 residues processed: 457 average time/residue: 0.6773 time to fit residues: 339.0301 Evaluate side-chains 455 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 428 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 238 ARG Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 987 VAL Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1061 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 196 THR Chi-restraints excluded: chain b residue 332 ASN Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Chi-restraints excluded: chain b residue 386 THR Chi-restraints excluded: chain b residue 392 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 78 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN b 6 HIS ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 291 GLN b 332 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.179053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143951 restraints weight = 19253.812| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.22 r_work: 0.3682 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17006 Z= 0.136 Angle : 0.545 10.312 23043 Z= 0.280 Chirality : 0.042 0.243 2633 Planarity : 0.004 0.066 2964 Dihedral : 5.925 141.235 2304 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.08 % Allowed : 18.84 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.43 (0.19), residues: 2103 helix: 2.00 (0.16), residues: 1143 sheet: 0.51 (0.40), residues: 176 loop : -0.51 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1107 TYR 0.013 0.001 TYR D 107 PHE 0.017 0.002 PHE D 775 TRP 0.011 0.001 TRP b 344 HIS 0.008 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00284 (17006) covalent geometry : angle 0.54508 (23043) hydrogen bonds : bond 0.06035 ( 811) hydrogen bonds : angle 3.59788 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 430 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 119 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7678 (mp) REVERT: D 285 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8010 (mt) REVERT: E 507 ASN cc_start: 0.8683 (t0) cc_final: 0.7768 (t0) REVERT: b 27 GLU cc_start: 0.7883 (tt0) cc_final: 0.7386 (tt0) REVERT: b 46 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7563 (mtm-85) REVERT: b 233 MET cc_start: 0.9092 (mtp) cc_final: 0.8826 (mtm) outliers start: 38 outliers final: 24 residues processed: 450 average time/residue: 0.6989 time to fit residues: 344.1525 Evaluate side-chains 453 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 427 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 200 SER Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 987 VAL Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 291 GLN Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Chi-restraints excluded: chain b residue 392 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 194 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN D1065 HIS D1108 GLN E 444 GLN b 6 HIS ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 291 GLN b 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.177677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142501 restraints weight = 19052.324| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.53 r_work: 0.3610 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17006 Z= 0.157 Angle : 0.583 10.610 23043 Z= 0.301 Chirality : 0.043 0.252 2633 Planarity : 0.004 0.059 2964 Dihedral : 6.085 141.875 2304 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.41 % Allowed : 18.57 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.40 (0.19), residues: 2103 helix: 1.96 (0.16), residues: 1136 sheet: 0.57 (0.40), residues: 173 loop : -0.49 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D1107 TYR 0.016 0.002 TYR b 340 PHE 0.019 0.002 PHE D 775 TRP 0.012 0.002 TRP D 80 HIS 0.009 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00335 (17006) covalent geometry : angle 0.58285 (23043) hydrogen bonds : bond 0.06911 ( 811) hydrogen bonds : angle 3.72285 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 430 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 119 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7742 (mp) REVERT: D 285 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8066 (mt) REVERT: E 507 ASN cc_start: 0.8724 (t0) cc_final: 0.7809 (t0) REVERT: b 27 GLU cc_start: 0.8019 (tt0) cc_final: 0.7426 (tt0) REVERT: b 46 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7592 (mtm-85) REVERT: b 233 MET cc_start: 0.9123 (mtp) cc_final: 0.8859 (mtm) outliers start: 44 outliers final: 30 residues processed: 452 average time/residue: 0.6955 time to fit residues: 344.1012 Evaluate side-chains 459 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 427 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 763 GLU Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 987 VAL Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1061 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 61 LYS Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 196 THR Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Chi-restraints excluded: chain b residue 386 THR Chi-restraints excluded: chain b residue 392 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 1 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 156 optimal weight: 0.4980 chunk 172 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 113 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN E 252 GLN b 6 HIS ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 291 GLN b 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.143407 restraints weight = 18959.740| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.39 r_work: 0.3625 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17006 Z= 0.157 Angle : 0.587 10.634 23043 Z= 0.303 Chirality : 0.043 0.241 2633 Planarity : 0.004 0.063 2964 Dihedral : 6.109 141.728 2304 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.19 % Allowed : 19.00 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.40 (0.19), residues: 2103 helix: 1.96 (0.16), residues: 1135 sheet: 0.55 (0.40), residues: 173 loop : -0.47 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D1107 TYR 0.014 0.002 TYR D 107 PHE 0.019 0.002 PHE D 775 TRP 0.017 0.002 TRP b 344 HIS 0.009 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00337 (17006) covalent geometry : angle 0.58719 (23043) hydrogen bonds : bond 0.06742 ( 811) hydrogen bonds : angle 3.71135 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 429 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 119 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7719 (mp) REVERT: D 285 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8059 (mt) REVERT: E 507 ASN cc_start: 0.8698 (t0) cc_final: 0.7812 (t0) REVERT: G 1 MET cc_start: -0.1372 (ptm) cc_final: -0.1626 (ptm) REVERT: b 27 GLU cc_start: 0.8017 (tt0) cc_final: 0.7505 (tt0) REVERT: b 46 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7583 (mtm-85) REVERT: b 233 MET cc_start: 0.9117 (mtp) cc_final: 0.8840 (mtm) outliers start: 40 outliers final: 29 residues processed: 450 average time/residue: 0.6576 time to fit residues: 323.8112 Evaluate side-chains 459 residues out of total 1826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 428 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 685 GLU Chi-restraints excluded: chain D residue 698 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 987 VAL Chi-restraints excluded: chain D residue 1002 THR Chi-restraints excluded: chain D residue 1061 THR Chi-restraints excluded: chain D residue 1099 VAL Chi-restraints excluded: chain D residue 1105 VAL Chi-restraints excluded: chain D residue 1185 LEU Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain b residue 176 SER Chi-restraints excluded: chain b residue 196 THR Chi-restraints excluded: chain b residue 313 VAL Chi-restraints excluded: chain b residue 333 VAL Chi-restraints excluded: chain b residue 367 PHE Chi-restraints excluded: chain b residue 368 ILE Chi-restraints excluded: chain b residue 386 THR Chi-restraints excluded: chain b residue 392 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 201 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 HIS D 140 ASN D 592 GLN b 6 HIS ** b 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 291 GLN b 332 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.177768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143170 restraints weight = 19117.434| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.46 r_work: 0.3618 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17006 Z= 0.150 Angle : 0.579 10.477 23043 Z= 0.297 Chirality : 0.043 0.235 2633 Planarity : 0.004 0.062 2964 Dihedral : 6.075 141.378 2304 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.25 % Allowed : 18.89 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 2103 helix: 1.99 (0.16), residues: 1136 sheet: 0.51 (0.40), residues: 173 loop : -0.45 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1107 TYR 0.014 0.001 TYR D 107 PHE 0.018 0.002 PHE D 228 TRP 0.012 0.002 TRP b 344 HIS 0.009 0.001 HIS b 227 Details of bonding type rmsd covalent geometry : bond 0.00321 (17006) covalent geometry : angle 0.57859 (23043) hydrogen bonds : bond 0.06546 ( 811) hydrogen bonds : angle 3.69128 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13383.40 seconds wall clock time: 226 minutes 48.51 seconds (13608.51 seconds total)