Starting phenix.real_space_refine on Sat Sep 12 03:58:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uen_20754/09_2026/6uen_20754.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uen_20754/09_2026/6uen_20754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uen_20754/09_2026/6uen_20754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uen_20754/09_2026/6uen_20754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uen_20754/09_2026/6uen_20754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uen_20754/09_2026/6uen_20754.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 8726 2.51 5 N 2342 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13705 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1392, 11352 Classifications: {'peptide': 1392} Link IDs: {'PTRANS': 47, 'TRANS': 1344} Chain breaks: 2 Chain: "B" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 460 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 423 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "D" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Time building chain proxies: 3.09, per 1000 atoms: 0.23 Number of scatterers: 13705 At special positions: 0 Unit cell: (109.398, 140.422, 102.867, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2562 8.00 N 2342 7.00 C 8726 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: 1.17 Conformation dependent library (CDL) restraints added in 651.1 milliseconds 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3250 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 62.0% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 3.887A pdb=" N TYR A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 4.041A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.576A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.669A pdb=" N GLN A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.580A pdb=" N PHE A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 120 removed outlier: 3.840A pdb=" N GLN A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.818A pdb=" N LEU A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 228 removed outlier: 3.711A pdb=" N ILE A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 327 through 335 removed outlier: 3.984A pdb=" N ILE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.129A pdb=" N ILE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 379 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.567A pdb=" N ASP A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS A 386 " --> pdb=" O LEU A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.331A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 4.155A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 424 through 429 removed outlier: 4.517A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.569A pdb=" N MET A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ALA A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 removed outlier: 4.023A pdb=" N TYR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 removed outlier: 4.105A pdb=" N LEU A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 removed outlier: 3.924A pdb=" N ILE A 536 " --> pdb=" O ASP A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 removed outlier: 5.403A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 553 " --> pdb=" O TRP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 604 removed outlier: 4.029A pdb=" N VAL A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 655 Processing helix chain 'A' and resid 709 through 724 removed outlier: 3.553A pdb=" N SER A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 737 removed outlier: 3.509A pdb=" N LEU A 735 " --> pdb=" O SER A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.557A pdb=" N ASN A 762 " --> pdb=" O ASP A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 801 removed outlier: 3.819A pdb=" N TRP A 785 " --> pdb=" O CYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 removed outlier: 3.784A pdb=" N LYS A 886 " --> pdb=" O ALA A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 919 Processing helix chain 'A' and resid 922 through 939 removed outlier: 3.786A pdb=" N TRP A 932 " --> pdb=" O PHE A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 1004 through 1017 Processing helix chain 'A' and resid 1034 through 1045 removed outlier: 3.562A pdb=" N THR A1045 " --> pdb=" O THR A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.507A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1111 removed outlier: 3.828A pdb=" N THR A1103 " --> pdb=" O HIS A1099 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU A1104 " --> pdb=" O TYR A1100 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET A1111 " --> pdb=" O LEU A1107 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1131 through 1142 removed outlier: 3.630A pdb=" N ILE A1141 " --> pdb=" O ILE A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1153 Processing helix chain 'A' and resid 1158 through 1180 removed outlier: 3.712A pdb=" N ILE A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU A1176 " --> pdb=" O ASN A1172 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE A1177 " --> pdb=" O ILE A1173 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A1178 " --> pdb=" O THR A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1212 removed outlier: 3.864A pdb=" N TRP A1211 " --> pdb=" O ARG A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 3.733A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1359 removed outlier: 3.916A pdb=" N THR A1358 " --> pdb=" O PRO A1354 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR A1359 " --> pdb=" O ALA A1355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1354 through 1359' Processing helix chain 'A' and resid 1365 through 1375 removed outlier: 3.677A pdb=" N ASN A1369 " --> pdb=" O THR A1365 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE A1371 " --> pdb=" O PRO A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1404 removed outlier: 3.758A pdb=" N ILE A1389 " --> pdb=" O PHE A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1443 removed outlier: 3.599A pdb=" N GLN A1443 " --> pdb=" O VAL A1439 " (cutoff:3.500A) Processing helix chain 'A' and resid 1452 through 1460 removed outlier: 4.089A pdb=" N PHE A1460 " --> pdb=" O TYR A1456 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.630A pdb=" N SER B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 removed outlier: 3.807A pdb=" N ILE B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.774A pdb=" N ALA C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 182 removed outlier: 4.726A pdb=" N ASP C 164 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG C 167 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 171 through 202 removed outlier: 3.507A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 191 " --> pdb=" O MET D 187 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 removed outlier: 3.596A pdb=" N LEU E 152 " --> pdb=" O MET E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.527A pdb=" N MET E 177 " --> pdb=" O LEU E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 199 removed outlier: 3.512A pdb=" N ALA E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 210 removed outlier: 3.740A pdb=" N ALA E 207 " --> pdb=" O SER E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.670A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N VAL A 263 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA4, first strand: chain 'A' and resid 803 through 808 Processing sheet with id=AA5, first strand: chain 'A' and resid 867 through 869 removed outlier: 4.879A pdb=" N GLN A 867 " --> pdb=" O GLN A 874 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN A 874 " --> pdb=" O GLN A 867 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 869 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1229 through 1231 removed outlier: 3.533A pdb=" N ILE A1413 " --> pdb=" O ASP A1229 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1272 Processing sheet with id=AA8, first strand: chain 'E' and resid 158 through 159 removed outlier: 3.836A pdb=" N GLY E 158 " --> pdb=" O ARG E 167 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2118 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: 2.48 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4468 1.34 - 1.46: 2345 1.46 - 1.58: 7007 1.58 - 1.69: 0 1.69 - 1.81: 127 Bond restraints: 13947 Sorted by residual: bond pdb=" C GLY A 430 " pdb=" N HIS A 431 " ideal model delta sigma weight residual 1.331 1.301 0.030 2.07e-02 2.33e+03 2.11e+00 bond pdb=" CB ILE A 428 " pdb=" CG2 ILE A 428 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU A 131 " pdb=" CD1 LEU A 131 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB ILE A 787 " pdb=" CG2 ILE A 787 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00 bond pdb=" CB LEU A 313 " pdb=" CG LEU A 313 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 13942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 18147 1.51 - 3.01: 583 3.01 - 4.52: 94 4.52 - 6.02: 14 6.02 - 7.53: 6 Bond angle restraints: 18844 Sorted by residual: angle pdb=" C MET A 628 " pdb=" N PHE A 629 " pdb=" CA PHE A 629 " ideal model delta sigma weight residual 122.74 117.49 5.25 1.82e+00 3.02e-01 8.33e+00 angle pdb=" CA TRP A 287 " pdb=" CB TRP A 287 " pdb=" CG TRP A 287 " ideal model delta sigma weight residual 113.60 119.01 -5.41 1.90e+00 2.77e-01 8.11e+00 angle pdb=" N GLN A 831 " pdb=" CA GLN A 831 " pdb=" C GLN A 831 " ideal model delta sigma weight residual 113.72 109.61 4.11 1.52e+00 4.33e-01 7.32e+00 angle pdb=" N GLN A 831 " pdb=" CA GLN A 831 " pdb=" CB GLN A 831 " ideal model delta sigma weight residual 113.65 109.91 3.74 1.47e+00 4.63e-01 6.48e+00 angle pdb=" C ASN A1113 " pdb=" N ILE A1114 " pdb=" CA ILE A1114 " ideal model delta sigma weight residual 120.69 124.18 -3.49 1.46e+00 4.69e-01 5.70e+00 ... (remaining 18839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7639 17.92 - 35.84: 758 35.84 - 53.76: 118 53.76 - 71.68: 18 71.68 - 89.60: 11 Dihedral angle restraints: 8544 sinusoidal: 3538 harmonic: 5006 Sorted by residual: dihedral pdb=" CA PHE A 244 " pdb=" C PHE A 244 " pdb=" N ILE A 245 " pdb=" CA ILE A 245 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA ASN A1139 " pdb=" C ASN A1139 " pdb=" N LEU A1140 " pdb=" CA LEU A1140 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLN A 831 " pdb=" C GLN A 831 " pdb=" N ALA A 832 " pdb=" CA ALA A 832 " ideal model delta harmonic sigma weight residual 180.00 162.58 17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1419 0.037 - 0.074: 566 0.074 - 0.112: 157 0.112 - 0.149: 30 0.149 - 0.186: 3 Chirality restraints: 2175 Sorted by residual: chirality pdb=" CB VAL A 379 " pdb=" CA VAL A 379 " pdb=" CG1 VAL A 379 " pdb=" CG2 VAL A 379 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CB THR A 745 " pdb=" CA THR A 745 " pdb=" OG1 THR A 745 " pdb=" CG2 THR A 745 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE A 817 " pdb=" N ILE A 817 " pdb=" C ILE A 817 " pdb=" CB ILE A 817 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2172 not shown) Planarity restraints: 2381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 632 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 633 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1001 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A1002 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1002 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1002 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 737 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 738 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 738 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 738 " -0.022 5.00e-02 4.00e+02 ... (remaining 2378 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 220 2.67 - 3.23: 13904 3.23 - 3.78: 19770 3.78 - 4.34: 26248 4.34 - 4.90: 44239 Nonbonded interactions: 104381 Sorted by model distance: nonbonded pdb=" OH TYR A 606 " pdb=" O SER A 728 " model vdw 2.112 3.040 nonbonded pdb=" OH TYR A 917 " pdb=" O ARG A 995 " model vdw 2.116 3.040 nonbonded pdb=" O TYR A 752 " pdb=" NE2 GLN A 766 " model vdw 2.195 3.120 nonbonded pdb=" O ARG A 555 " pdb=" NE2 GLN A 563 " model vdw 2.219 3.120 nonbonded pdb=" OG1 THR B 160 " pdb=" OD1 ASP E 168 " model vdw 2.241 3.040 ... (remaining 104376 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 128 through 182) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 0.039 13947 Z= 0.240 Angle : 0.654 7.531 18844 Z= 0.361 Chirality : 0.043 0.186 2175 Planarity : 0.004 0.052 2381 Dihedral : 14.230 89.605 5294 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.13 % Allowed : 7.35 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.28 (0.18), residues: 1682 helix: -0.96 (0.15), residues: 947 sheet: -0.92 (0.59), residues: 59 loop : -2.28 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 889 TYR 0.018 0.002 TYR A 998 PHE 0.020 0.002 PHE A 25 TRP 0.018 0.002 TRP A 480 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (13947) covalent geometry : angle 0.65390 / 0.36 (18844) hydrogen bonds : bond 0.14268 / 9.03 ( 730) hydrogen bonds : angle 5.98136 / 4.25 ( 2118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 297 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7093 (m-80) cc_final: 0.6080 (m-10) REVERT: A 197 MET cc_start: 0.9018 (mtp) cc_final: 0.8652 (mtm) REVERT: A 438 GLN cc_start: 0.8103 (mp10) cc_final: 0.7667 (tm-30) REVERT: A 580 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7786 (mtt90) REVERT: A 721 ASP cc_start: 0.8230 (t0) cc_final: 0.7805 (t0) REVERT: A 824 MET cc_start: 0.5857 (mmm) cc_final: 0.5484 (mpp) REVERT: A 887 VAL cc_start: 0.9311 (m) cc_final: 0.9062 (p) REVERT: A 959 LEU cc_start: 0.9128 (mt) cc_final: 0.8870 (mp) REVERT: A 1017 SER cc_start: 0.9082 (m) cc_final: 0.8852 (p) REVERT: A 1169 MET cc_start: 0.8778 (mtm) cc_final: 0.8384 (mtm) REVERT: A 1290 ASP cc_start: 0.7293 (t70) cc_final: 0.6946 (t0) REVERT: B 161 SER cc_start: 0.8324 (p) cc_final: 0.8083 (p) REVERT: B 175 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6649 (mt-10) REVERT: C 141 LYS cc_start: 0.7336 (mttp) cc_final: 0.7022 (mttp) REVERT: C 177 MET cc_start: 0.5497 (mtp) cc_final: 0.5294 (mmm) REVERT: D 150 HIS cc_start: 0.6946 (m-70) cc_final: 0.6584 (m-70) REVERT: E 148 MET cc_start: 0.7261 (ttt) cc_final: 0.7009 (ttm) REVERT: E 175 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6440 (mm-30) outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.1220 time to fit residues: 53.0996 Evaluate side-chains 236 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 235 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 743 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 199 HIS A 228 ASN A 363 ASN A 381 HIS A 556 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 773 HIS A 930 ASN A 980 ASN B 150 HIS C 150 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.150761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119831 restraints weight = 20054.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121598 restraints weight = 14616.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122526 restraints weight = 11039.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122716 restraints weight = 9628.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123717 restraints weight = 8849.902| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13947 Z= 0.122 Angle : 0.534 8.192 18844 Z= 0.282 Chirality : 0.039 0.146 2175 Planarity : 0.004 0.058 2381 Dihedral : 4.484 35.415 1849 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.42 % Allowed : 13.53 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.48 (0.20), residues: 1682 helix: 0.66 (0.16), residues: 968 sheet: -0.28 (0.56), residues: 73 loop : -1.85 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.012 0.001 TYR A 998 PHE 0.014 0.001 PHE A1328 TRP 0.015 0.001 TRP A 287 HIS 0.006 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13947) covalent geometry : angle 0.53371 / 0.28 (18844) hydrogen bonds : bond 0.04725 / 3.12 ( 730) hydrogen bonds : angle 4.26950 / 3.02 ( 2118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.556 Fit side-chains REVERT: A 13 TYR cc_start: 0.6975 (m-80) cc_final: 0.6015 (m-10) REVERT: A 92 MET cc_start: 0.8867 (mmp) cc_final: 0.8180 (mmp) REVERT: A 197 MET cc_start: 0.8633 (mtp) cc_final: 0.8399 (mtm) REVERT: A 360 MET cc_start: 0.8500 (tmm) cc_final: 0.8207 (ppp) REVERT: A 374 ASN cc_start: 0.8489 (t0) cc_final: 0.7990 (m110) REVERT: A 427 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7374 (mmm160) REVERT: A 512 ASP cc_start: 0.8277 (m-30) cc_final: 0.8069 (m-30) REVERT: A 568 HIS cc_start: 0.7281 (t70) cc_final: 0.6783 (m-70) REVERT: A 580 ARG cc_start: 0.8166 (mtt180) cc_final: 0.7750 (mtt90) REVERT: A 816 ASP cc_start: 0.7425 (p0) cc_final: 0.7128 (p0) REVERT: A 900 ASP cc_start: 0.7501 (m-30) cc_final: 0.7300 (m-30) REVERT: A 1226 TYR cc_start: 0.9068 (t80) cc_final: 0.8838 (t80) REVERT: A 1290 ASP cc_start: 0.7568 (t70) cc_final: 0.7183 (t0) REVERT: A 1359 THR cc_start: 0.9116 (p) cc_final: 0.8708 (p) REVERT: B 148 MET cc_start: 0.8398 (ttm) cc_final: 0.8004 (mtp) REVERT: B 161 SER cc_start: 0.8461 (p) cc_final: 0.8238 (p) REVERT: C 167 ARG cc_start: 0.6040 (ptm-80) cc_final: 0.5617 (ptt180) REVERT: D 145 ILE cc_start: 0.7640 (mt) cc_final: 0.7426 (mt) REVERT: D 150 HIS cc_start: 0.6886 (m-70) cc_final: 0.6388 (m-70) REVERT: E 142 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6588 (mt) REVERT: E 146 LEU cc_start: 0.8247 (tt) cc_final: 0.8044 (mm) REVERT: E 148 MET cc_start: 0.7174 (ttt) cc_final: 0.6940 (ttm) REVERT: E 175 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6283 (pm20) REVERT: E 180 LYS cc_start: 0.6347 (mtpp) cc_final: 0.5918 (mttt) REVERT: E 191 ARG cc_start: 0.7129 (ptm160) cc_final: 0.6689 (tmm-80) REVERT: E 206 MET cc_start: 0.6535 (tpt) cc_final: 0.6078 (tpt) outliers start: 22 outliers final: 11 residues processed: 288 average time/residue: 0.1076 time to fit residues: 47.3974 Evaluate side-chains 254 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 949 ASN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 147 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 58 optimal weight: 9.9990 chunk 121 optimal weight: 0.0270 chunk 14 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 153 optimal weight: 30.0000 chunk 81 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 HIS A 215 ASN A 448 ASN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS E 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120839 restraints weight = 20354.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122783 restraints weight = 14192.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124054 restraints weight = 10780.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.124269 restraints weight = 8919.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124529 restraints weight = 8540.385| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13947 Z= 0.115 Angle : 0.507 9.159 18844 Z= 0.265 Chirality : 0.038 0.136 2175 Planarity : 0.003 0.058 2381 Dihedral : 4.250 34.448 1849 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.32 % Allowed : 15.40 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.20), residues: 1682 helix: 1.29 (0.17), residues: 967 sheet: -0.15 (0.58), residues: 72 loop : -1.61 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 462 TYR 0.011 0.001 TYR A 998 PHE 0.011 0.001 PHE A1328 TRP 0.012 0.001 TRP A 287 HIS 0.006 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13947) covalent geometry : angle 0.50657 / 0.27 (18844) hydrogen bonds : bond 0.04218 / 2.80 ( 730) hydrogen bonds : angle 3.97282 / 2.82 ( 2118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6950 (m-80) cc_final: 0.6013 (m-10) REVERT: A 197 MET cc_start: 0.8715 (mtp) cc_final: 0.8502 (mtm) REVERT: A 204 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7759 (tt) REVERT: A 340 MET cc_start: 0.7518 (mtp) cc_final: 0.7300 (mtt) REVERT: A 360 MET cc_start: 0.8503 (tmm) cc_final: 0.8140 (ppp) REVERT: A 374 ASN cc_start: 0.8278 (t0) cc_final: 0.8047 (m110) REVERT: A 512 ASP cc_start: 0.8446 (m-30) cc_final: 0.8187 (m-30) REVERT: A 568 HIS cc_start: 0.7285 (t70) cc_final: 0.6832 (m-70) REVERT: A 580 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7734 (mtt90) REVERT: A 607 LEU cc_start: 0.8969 (mt) cc_final: 0.8740 (mp) REVERT: A 619 LYS cc_start: 0.7212 (ttmt) cc_final: 0.6534 (tttm) REVERT: A 722 GLU cc_start: 0.8519 (tp30) cc_final: 0.7895 (mm-30) REVERT: A 816 ASP cc_start: 0.7496 (p0) cc_final: 0.7176 (p0) REVERT: A 1046 PHE cc_start: 0.7863 (p90) cc_final: 0.7630 (p90) REVERT: A 1290 ASP cc_start: 0.7657 (t70) cc_final: 0.7306 (t0) REVERT: A 1430 ASP cc_start: 0.8352 (m-30) cc_final: 0.8117 (m-30) REVERT: B 174 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7366 (mmt90) REVERT: C 167 ARG cc_start: 0.6344 (ptm-80) cc_final: 0.5985 (ptt180) REVERT: D 150 HIS cc_start: 0.7167 (m-70) cc_final: 0.6647 (m-70) REVERT: E 142 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6669 (mt) REVERT: E 146 LEU cc_start: 0.8290 (tt) cc_final: 0.8083 (mm) REVERT: E 148 MET cc_start: 0.7396 (ttt) cc_final: 0.6999 (ttm) REVERT: E 163 ARG cc_start: 0.7902 (ptp90) cc_final: 0.7655 (ptp-170) REVERT: E 175 GLU cc_start: 0.6640 (mm-30) cc_final: 0.6218 (pm20) REVERT: E 180 LYS cc_start: 0.6716 (mtpp) cc_final: 0.6173 (mttt) REVERT: E 187 MET cc_start: 0.7952 (ppp) cc_final: 0.7424 (ppp) REVERT: E 191 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6959 (tmm-80) outliers start: 36 outliers final: 20 residues processed: 289 average time/residue: 0.1092 time to fit residues: 48.0203 Evaluate side-chains 264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 116 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 HIS ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS E 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121814 restraints weight = 20196.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.124496 restraints weight = 13951.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125841 restraints weight = 10269.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125931 restraints weight = 8497.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126105 restraints weight = 8225.440| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13947 Z= 0.101 Angle : 0.494 8.492 18844 Z= 0.257 Chirality : 0.038 0.156 2175 Planarity : 0.003 0.054 2381 Dihedral : 4.082 31.514 1849 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.45 % Allowed : 17.27 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.21), residues: 1682 helix: 1.60 (0.17), residues: 971 sheet: -0.07 (0.59), residues: 72 loop : -1.48 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 174 TYR 0.011 0.001 TYR A 917 PHE 0.010 0.001 PHE A 87 TRP 0.011 0.001 TRP A 287 HIS 0.013 0.001 HIS E 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (13947) covalent geometry : angle 0.49437 / 0.26 (18844) hydrogen bonds : bond 0.03777 / 2.51 ( 730) hydrogen bonds : angle 3.83556 / 2.71 ( 2118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6947 (m-80) cc_final: 0.5981 (m-10) REVERT: A 197 MET cc_start: 0.8714 (mtp) cc_final: 0.8468 (mtm) REVERT: A 360 MET cc_start: 0.8433 (tmm) cc_final: 0.8042 (ppp) REVERT: A 374 ASN cc_start: 0.8256 (t0) cc_final: 0.8041 (m110) REVERT: A 453 TYR cc_start: 0.8104 (m-80) cc_final: 0.7586 (m-10) REVERT: A 460 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7760 (mtm) REVERT: A 512 ASP cc_start: 0.8367 (m-30) cc_final: 0.8084 (m-30) REVERT: A 568 HIS cc_start: 0.7259 (t70) cc_final: 0.6818 (m-70) REVERT: A 580 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7697 (mtt90) REVERT: A 619 LYS cc_start: 0.7018 (ttmt) cc_final: 0.6302 (tttm) REVERT: A 646 MET cc_start: 0.8625 (mmm) cc_final: 0.8196 (mmm) REVERT: A 816 ASP cc_start: 0.7453 (p0) cc_final: 0.7160 (p0) REVERT: A 1309 MET cc_start: 0.8548 (tpp) cc_final: 0.8287 (mmt) REVERT: A 1359 THR cc_start: 0.9296 (p) cc_final: 0.8853 (p) REVERT: C 137 ARG cc_start: 0.6878 (mtp180) cc_final: 0.6592 (mtp85) REVERT: C 167 ARG cc_start: 0.6244 (ptm-80) cc_final: 0.5770 (ptt180) REVERT: E 148 MET cc_start: 0.7504 (ttt) cc_final: 0.7244 (ttm) REVERT: E 175 GLU cc_start: 0.6548 (mm-30) cc_final: 0.5716 (pm20) REVERT: E 180 LYS cc_start: 0.6589 (mtpp) cc_final: 0.6049 (mttt) REVERT: E 187 MET cc_start: 0.8062 (ppp) cc_final: 0.7590 (ppp) REVERT: E 191 ARG cc_start: 0.7288 (ptm160) cc_final: 0.6871 (tmm-80) outliers start: 38 outliers final: 23 residues processed: 276 average time/residue: 0.1029 time to fit residues: 43.8115 Evaluate side-chains 264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 93 optimal weight: 0.0030 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 448 ASN A 604 GLN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN C 150 HIS D 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.153729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.122400 restraints weight = 20179.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.124771 restraints weight = 13880.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125701 restraints weight = 10394.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.125798 restraints weight = 9133.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.127152 restraints weight = 8587.499| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13947 Z= 0.106 Angle : 0.511 14.527 18844 Z= 0.261 Chirality : 0.038 0.260 2175 Planarity : 0.003 0.053 2381 Dihedral : 4.007 31.796 1849 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.77 % Allowed : 18.36 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.21), residues: 1682 helix: 1.73 (0.17), residues: 972 sheet: -0.09 (0.54), residues: 83 loop : -1.40 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 174 TYR 0.012 0.001 TYR A 917 PHE 0.010 0.001 PHE A 424 TRP 0.010 0.001 TRP A 287 HIS 0.012 0.001 HIS E 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (13947) covalent geometry : angle 0.51084 / 0.26 (18844) hydrogen bonds : bond 0.03805 / 2.52 ( 730) hydrogen bonds : angle 3.76050 / 2.66 ( 2118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6726 (m-80) cc_final: 0.5702 (m-10) REVERT: A 197 MET cc_start: 0.8693 (mtp) cc_final: 0.8491 (mtm) REVERT: A 204 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7938 (tt) REVERT: A 360 MET cc_start: 0.8429 (tmm) cc_final: 0.8014 (ppp) REVERT: A 453 TYR cc_start: 0.8138 (m-80) cc_final: 0.7642 (m-10) REVERT: A 568 HIS cc_start: 0.7155 (t70) cc_final: 0.6721 (m-70) REVERT: A 580 ARG cc_start: 0.8159 (mtt180) cc_final: 0.7660 (mtt90) REVERT: A 619 LYS cc_start: 0.6997 (ttmt) cc_final: 0.6291 (tttm) REVERT: A 816 ASP cc_start: 0.7486 (p0) cc_final: 0.7203 (p0) REVERT: A 898 LEU cc_start: 0.7471 (tp) cc_final: 0.7145 (tt) REVERT: A 1168 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.7034 (ttp) REVERT: A 1182 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7730 (pp) REVERT: A 1309 MET cc_start: 0.8690 (tpp) cc_final: 0.8329 (mmt) REVERT: A 1359 THR cc_start: 0.9149 (p) cc_final: 0.8681 (p) REVERT: A 1436 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8865 (tt) REVERT: A 1449 ASP cc_start: 0.8513 (t0) cc_final: 0.7966 (t0) REVERT: B 152 LEU cc_start: 0.8596 (tt) cc_final: 0.8328 (tp) REVERT: C 137 ARG cc_start: 0.6957 (mtp180) cc_final: 0.6621 (mtp85) REVERT: C 141 LYS cc_start: 0.7004 (mtpt) cc_final: 0.6746 (mttt) REVERT: C 167 ARG cc_start: 0.6288 (ptm-80) cc_final: 0.5868 (ptt180) REVERT: E 148 MET cc_start: 0.7897 (ttt) cc_final: 0.7587 (ttm) REVERT: E 150 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7815 (m-70) REVERT: E 175 GLU cc_start: 0.6755 (mm-30) cc_final: 0.5891 (pm20) REVERT: E 180 LYS cc_start: 0.6559 (mtpp) cc_final: 0.6019 (mttt) REVERT: E 187 MET cc_start: 0.8040 (ppp) cc_final: 0.7610 (ppp) REVERT: E 191 ARG cc_start: 0.7164 (ptm160) cc_final: 0.6885 (tmm-80) outliers start: 43 outliers final: 26 residues processed: 276 average time/residue: 0.1065 time to fit residues: 45.0333 Evaluate side-chains 267 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1179 ILE Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 150 HIS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 28 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.118853 restraints weight = 20332.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.119679 restraints weight = 14025.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.120730 restraints weight = 11389.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121021 restraints weight = 9790.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122690 restraints weight = 8936.439| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13947 Z= 0.155 Angle : 0.548 13.551 18844 Z= 0.286 Chirality : 0.040 0.147 2175 Planarity : 0.004 0.057 2381 Dihedral : 4.205 36.813 1849 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.03 % Allowed : 19.46 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.20), residues: 1682 helix: 1.59 (0.17), residues: 974 sheet: 0.04 (0.58), residues: 72 loop : -1.44 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.015 0.001 TYR A 998 PHE 0.015 0.002 PHE A 25 TRP 0.011 0.002 TRP A 480 HIS 0.022 0.001 HIS D 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (13947) covalent geometry : angle 0.54818 / 0.29 (18844) hydrogen bonds : bond 0.04658 / 3.11 ( 730) hydrogen bonds : angle 3.92866 / 2.78 ( 2118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6770 (m-80) cc_final: 0.5702 (m-10) REVERT: A 197 MET cc_start: 0.8792 (mtp) cc_final: 0.8540 (mtm) REVERT: A 204 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 360 MET cc_start: 0.8515 (tmm) cc_final: 0.8092 (ppp) REVERT: A 453 TYR cc_start: 0.8299 (m-80) cc_final: 0.7933 (m-10) REVERT: A 514 ILE cc_start: 0.8645 (mt) cc_final: 0.8438 (mt) REVERT: A 568 HIS cc_start: 0.7183 (t70) cc_final: 0.6743 (m-70) REVERT: A 580 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7703 (mtt90) REVERT: A 646 MET cc_start: 0.8675 (mmm) cc_final: 0.8352 (mmm) REVERT: A 700 ASP cc_start: 0.8475 (t0) cc_final: 0.8236 (t0) REVERT: A 804 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8308 (tt) REVERT: A 816 ASP cc_start: 0.7501 (p0) cc_final: 0.7171 (p0) REVERT: A 898 LEU cc_start: 0.7453 (tp) cc_final: 0.7087 (tt) REVERT: A 1109 ASP cc_start: 0.6985 (m-30) cc_final: 0.6692 (m-30) REVERT: A 1168 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7125 (ttp) REVERT: A 1182 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7778 (pp) REVERT: A 1309 MET cc_start: 0.8789 (tpp) cc_final: 0.8397 (mmt) REVERT: A 1359 THR cc_start: 0.9200 (p) cc_final: 0.8806 (p) REVERT: A 1436 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8921 (tt) REVERT: A 1449 ASP cc_start: 0.8539 (t0) cc_final: 0.7987 (t0) REVERT: B 152 LEU cc_start: 0.8633 (tt) cc_final: 0.8421 (tp) REVERT: B 161 SER cc_start: 0.9185 (t) cc_final: 0.8860 (p) REVERT: C 141 LYS cc_start: 0.7328 (mtpt) cc_final: 0.6963 (mttt) REVERT: C 167 ARG cc_start: 0.6305 (ptm-80) cc_final: 0.5794 (ptt180) REVERT: E 148 MET cc_start: 0.8042 (ttt) cc_final: 0.7622 (ttm) REVERT: E 163 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7673 (ptp-170) REVERT: E 175 GLU cc_start: 0.6674 (mm-30) cc_final: 0.5716 (pm20) REVERT: E 180 LYS cc_start: 0.6577 (mtpp) cc_final: 0.6002 (mttt) REVERT: E 191 ARG cc_start: 0.7204 (ptm160) cc_final: 0.6921 (tmm-80) outliers start: 47 outliers final: 31 residues processed: 265 average time/residue: 0.1065 time to fit residues: 43.5770 Evaluate side-chains 264 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 145 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 125 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 67.73 > 50:) chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 96 optimal weight: 0.0770 chunk 20 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 609 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.150288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.119554 restraints weight = 20346.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120525 restraints weight = 14212.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.121488 restraints weight = 11748.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121935 restraints weight = 9995.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.122409 restraints weight = 9046.423| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13947 Z= 0.143 Angle : 0.545 14.685 18844 Z= 0.283 Chirality : 0.039 0.140 2175 Planarity : 0.003 0.056 2381 Dihedral : 4.192 37.119 1849 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.16 % Allowed : 20.10 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.20), residues: 1682 helix: 1.63 (0.17), residues: 975 sheet: -0.18 (0.57), residues: 76 loop : -1.40 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.014 0.001 TYR A 998 PHE 0.013 0.001 PHE A 25 TRP 0.011 0.001 TRP A 932 HIS 0.004 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13947) covalent geometry : angle 0.54465 / 0.28 (18844) hydrogen bonds : bond 0.04458 / 2.98 ( 730) hydrogen bonds : angle 3.90950 / 2.76 ( 2118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7056 (m-80) cc_final: 0.5866 (m-10) REVERT: A 197 MET cc_start: 0.8773 (mtp) cc_final: 0.8524 (mtm) REVERT: A 204 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7872 (tt) REVERT: A 360 MET cc_start: 0.8492 (tmm) cc_final: 0.8062 (ppp) REVERT: A 510 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7445 (tm-30) REVERT: A 568 HIS cc_start: 0.7049 (t70) cc_final: 0.6735 (m-70) REVERT: A 580 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7694 (mtt90) REVERT: A 646 MET cc_start: 0.8692 (mmm) cc_final: 0.8319 (mmm) REVERT: A 700 ASP cc_start: 0.8376 (t0) cc_final: 0.8038 (t0) REVERT: A 804 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8286 (tt) REVERT: A 816 ASP cc_start: 0.7366 (p0) cc_final: 0.7056 (p0) REVERT: A 898 LEU cc_start: 0.7414 (tp) cc_final: 0.7108 (tt) REVERT: A 1109 ASP cc_start: 0.6903 (m-30) cc_final: 0.6580 (m-30) REVERT: A 1168 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7116 (ttp) REVERT: A 1182 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7589 (pp) REVERT: A 1242 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8693 (tp) REVERT: A 1309 MET cc_start: 0.8786 (tpp) cc_final: 0.8403 (mmt) REVERT: A 1436 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8943 (tt) REVERT: A 1449 ASP cc_start: 0.8533 (t0) cc_final: 0.7984 (t0) REVERT: B 152 LEU cc_start: 0.8735 (tt) cc_final: 0.8489 (tp) REVERT: C 141 LYS cc_start: 0.7232 (mtpt) cc_final: 0.6898 (mttt) REVERT: C 149 LEU cc_start: 0.8693 (mt) cc_final: 0.8401 (mm) REVERT: C 167 ARG cc_start: 0.6294 (ptm-80) cc_final: 0.5836 (ptt180) REVERT: E 163 ARG cc_start: 0.7955 (ptp90) cc_final: 0.7750 (ptp-110) REVERT: E 175 GLU cc_start: 0.6668 (mm-30) cc_final: 0.5701 (pm20) REVERT: E 180 LYS cc_start: 0.6508 (mtpp) cc_final: 0.6014 (mttt) REVERT: E 191 ARG cc_start: 0.7189 (ptm160) cc_final: 0.6967 (tmm-80) REVERT: E 193 GLU cc_start: 0.7372 (tp30) cc_final: 0.7136 (tp30) outliers start: 49 outliers final: 34 residues processed: 262 average time/residue: 0.1050 time to fit residues: 42.4315 Evaluate side-chains 267 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 144 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 154 optimal weight: 0.0670 overall best weight: 3.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 107 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116754 restraints weight = 20262.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.117944 restraints weight = 13995.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118624 restraints weight = 11163.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119043 restraints weight = 9938.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119951 restraints weight = 8926.542| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13947 Z= 0.193 Angle : 0.597 14.042 18844 Z= 0.310 Chirality : 0.041 0.147 2175 Planarity : 0.004 0.061 2381 Dihedral : 4.392 36.946 1849 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.22 % Allowed : 20.68 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.20), residues: 1682 helix: 1.45 (0.16), residues: 974 sheet: -0.16 (0.58), residues: 76 loop : -1.47 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.017 0.002 TYR A 998 PHE 0.018 0.002 PHE A 25 TRP 0.014 0.002 TRP A 480 HIS 0.006 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (13947) covalent geometry : angle 0.59659 / 0.31 (18844) hydrogen bonds : bond 0.05254 / 3.51 ( 730) hydrogen bonds : angle 4.09833 / 2.89 ( 2118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6503 (m-80) cc_final: 0.5418 (m-10) REVERT: A 197 MET cc_start: 0.9015 (mtp) cc_final: 0.8669 (mtm) REVERT: A 204 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 438 GLN cc_start: 0.8120 (mp10) cc_final: 0.7441 (tm-30) REVERT: A 453 TYR cc_start: 0.8313 (m-80) cc_final: 0.7989 (m-10) REVERT: A 460 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7899 (mtm) REVERT: A 568 HIS cc_start: 0.7022 (t70) cc_final: 0.6700 (m-70) REVERT: A 580 ARG cc_start: 0.8283 (mtt180) cc_final: 0.7745 (mtt90) REVERT: A 646 MET cc_start: 0.8713 (mmm) cc_final: 0.8345 (mmm) REVERT: A 804 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (tt) REVERT: A 816 ASP cc_start: 0.7496 (p0) cc_final: 0.7173 (p0) REVERT: A 1058 MET cc_start: 0.7999 (ttp) cc_final: 0.7781 (ttm) REVERT: A 1109 ASP cc_start: 0.7002 (m-30) cc_final: 0.6673 (m-30) REVERT: A 1168 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7187 (ttp) REVERT: A 1182 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7709 (pp) REVERT: A 1242 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8783 (tp) REVERT: A 1309 MET cc_start: 0.8815 (tpp) cc_final: 0.8429 (mmt) REVERT: A 1319 LEU cc_start: 0.8402 (mt) cc_final: 0.8178 (mt) REVERT: A 1436 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8928 (tt) REVERT: A 1449 ASP cc_start: 0.8574 (t0) cc_final: 0.8041 (t0) REVERT: C 141 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6925 (mttt) REVERT: E 175 GLU cc_start: 0.6755 (mm-30) cc_final: 0.5963 (pm20) REVERT: E 180 LYS cc_start: 0.6544 (mtpp) cc_final: 0.6031 (mttt) REVERT: E 191 ARG cc_start: 0.7027 (ptm160) cc_final: 0.6787 (tmm-80) REVERT: E 193 GLU cc_start: 0.7393 (tp30) cc_final: 0.7172 (tp30) outliers start: 50 outliers final: 38 residues processed: 256 average time/residue: 0.1075 time to fit residues: 42.2943 Evaluate side-chains 266 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1336 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 358 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1387 ASN C 150 HIS D 150 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.152970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121435 restraints weight = 20083.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124520 restraints weight = 13949.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125687 restraints weight = 9947.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125899 restraints weight = 8125.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.126024 restraints weight = 8203.849| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13947 Z= 0.107 Angle : 0.531 15.737 18844 Z= 0.273 Chirality : 0.038 0.159 2175 Planarity : 0.003 0.055 2381 Dihedral : 4.056 31.937 1849 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.58 % Allowed : 21.84 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.21), residues: 1682 helix: 1.78 (0.17), residues: 971 sheet: 0.01 (0.56), residues: 82 loop : -1.32 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 174 TYR 0.011 0.001 TYR A 330 PHE 0.011 0.001 PHE A 424 TRP 0.015 0.001 TRP A 287 HIS 0.004 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13947) covalent geometry : angle 0.53066 / 0.27 (18844) hydrogen bonds : bond 0.03768 / 2.52 ( 730) hydrogen bonds : angle 3.77697 / 2.66 ( 2118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6950 (m-80) cc_final: 0.5714 (m-10) REVERT: A 197 MET cc_start: 0.8673 (mtp) cc_final: 0.8468 (mtm) REVERT: A 204 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 329 PHE cc_start: 0.8718 (m-80) cc_final: 0.8459 (m-10) REVERT: A 568 HIS cc_start: 0.6920 (t70) cc_final: 0.6597 (m-70) REVERT: A 646 MET cc_start: 0.8660 (mmm) cc_final: 0.8303 (mmm) REVERT: A 804 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8217 (tt) REVERT: A 816 ASP cc_start: 0.7337 (p0) cc_final: 0.7023 (p0) REVERT: A 898 LEU cc_start: 0.7403 (tp) cc_final: 0.7165 (tt) REVERT: A 1109 ASP cc_start: 0.6716 (m-30) cc_final: 0.6379 (m-30) REVERT: A 1168 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6897 (ttp) REVERT: A 1182 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7756 (pp) REVERT: A 1242 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8759 (tp) REVERT: A 1309 MET cc_start: 0.8769 (tpp) cc_final: 0.8390 (mmt) REVERT: A 1436 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 1449 ASP cc_start: 0.8500 (t0) cc_final: 0.7956 (t0) REVERT: B 152 LEU cc_start: 0.8685 (tt) cc_final: 0.8468 (tp) REVERT: C 141 LYS cc_start: 0.7173 (mtpt) cc_final: 0.6862 (mttt) REVERT: E 175 GLU cc_start: 0.6767 (mm-30) cc_final: 0.5875 (pm20) REVERT: E 180 LYS cc_start: 0.6404 (mtpp) cc_final: 0.5960 (mttt) REVERT: E 191 ARG cc_start: 0.7100 (ptm160) cc_final: 0.6877 (tmm-80) REVERT: E 206 MET cc_start: 0.7150 (tpt) cc_final: 0.6671 (tpt) REVERT: E 222 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8479 (mtmm) outliers start: 40 outliers final: 27 residues processed: 265 average time/residue: 0.1073 time to fit residues: 43.4276 Evaluate side-chains 263 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 230 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 chunk 117 optimal weight: 10.0000 chunk 149 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.153170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122377 restraints weight = 20252.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.123695 restraints weight = 14167.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.124359 restraints weight = 11634.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125004 restraints weight = 10206.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.125459 restraints weight = 9033.035| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13947 Z= 0.111 Angle : 0.555 15.300 18844 Z= 0.281 Chirality : 0.038 0.147 2175 Planarity : 0.003 0.056 2381 Dihedral : 4.008 31.866 1849 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.45 % Allowed : 21.97 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.89 (0.20), residues: 1682 helix: 1.78 (0.17), residues: 975 sheet: -0.04 (0.56), residues: 82 loop : -1.28 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 174 TYR 0.016 0.001 TYR A 917 PHE 0.011 0.001 PHE A 424 TRP 0.013 0.001 TRP A 287 HIS 0.004 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13947) covalent geometry : angle 0.55520 / 0.28 (18844) hydrogen bonds : bond 0.03802 / 2.54 ( 730) hydrogen bonds : angle 3.74755 / 2.64 ( 2118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3364 Ramachandran restraints generated. 1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6953 (m-80) cc_final: 0.5686 (m-10) REVERT: A 197 MET cc_start: 0.8717 (mtp) cc_final: 0.8492 (mtm) REVERT: A 204 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7914 (tt) REVERT: A 329 PHE cc_start: 0.8658 (m-80) cc_final: 0.8411 (m-10) REVERT: A 568 HIS cc_start: 0.6922 (t70) cc_final: 0.6596 (m-70) REVERT: A 580 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7639 (mtt90) REVERT: A 646 MET cc_start: 0.8664 (mmm) cc_final: 0.8314 (mmm) REVERT: A 804 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8230 (tt) REVERT: A 816 ASP cc_start: 0.7327 (p0) cc_final: 0.7029 (p0) REVERT: A 898 LEU cc_start: 0.7367 (tp) cc_final: 0.7161 (tt) REVERT: A 1109 ASP cc_start: 0.6844 (m-30) cc_final: 0.6489 (m-30) REVERT: A 1168 MET cc_start: 0.7239 (ttm) cc_final: 0.6895 (ttp) REVERT: A 1182 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7798 (pp) REVERT: A 1242 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8753 (tp) REVERT: A 1309 MET cc_start: 0.8752 (tpp) cc_final: 0.8378 (mmt) REVERT: A 1436 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8778 (tt) REVERT: A 1449 ASP cc_start: 0.8545 (t0) cc_final: 0.8001 (t0) REVERT: C 149 LEU cc_start: 0.8424 (mm) cc_final: 0.8068 (mm) REVERT: E 175 GLU cc_start: 0.6741 (mm-30) cc_final: 0.5900 (pm20) REVERT: E 180 LYS cc_start: 0.6324 (mtpp) cc_final: 0.5888 (mttt) outliers start: 38 outliers final: 30 residues processed: 256 average time/residue: 0.1070 time to fit residues: 41.6428 Evaluate side-chains 263 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 228 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1087 THR Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1368 ILE Chi-restraints excluded: chain A residue 1384 VAL Chi-restraints excluded: chain A residue 1396 MET Chi-restraints excluded: chain A residue 1436 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 150 HIS Chi-restraints excluded: chain E residue 171 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 20 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS D 150 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.154876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125322 restraints weight = 20152.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127838 restraints weight = 14384.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.128960 restraints weight = 10261.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129062 restraints weight = 8467.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129314 restraints weight = 8401.708| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13947 Z= 0.103 Angle : 0.543 15.192 18844 Z= 0.275 Chirality : 0.038 0.145 2175 Planarity : 0.003 0.054 2381 Dihedral : 3.906 28.411 1849 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.32 % Allowed : 22.42 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.21), residues: 1682 helix: 1.90 (0.17), residues: 969 sheet: -0.05 (0.55), residues: 82 loop : -1.21 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 918 TYR 0.015 0.001 TYR A 917 PHE 0.017 0.001 PHE A 868 TRP 0.014 0.001 TRP A 287 HIS 0.004 0.000 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13947) covalent geometry : angle 0.54287 / 0.28 (18844) hydrogen bonds : bond 0.03505 / 2.34 ( 730) hydrogen bonds : angle 3.67967 / 2.58 ( 2118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.26 seconds wall clock time: 37 minutes 10.58 seconds (2230.58 seconds total)