Starting phenix.real_space_refine on Thu Jul 31 15:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uen_20754/07_2025/6uen_20754.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uen_20754/07_2025/6uen_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uen_20754/07_2025/6uen_20754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uen_20754/07_2025/6uen_20754.map" model { file = "/net/cci-nas-00/data/ceres_data/6uen_20754/07_2025/6uen_20754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uen_20754/07_2025/6uen_20754.cif" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.69, per 1000 atoms: 0.56 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: 3.68 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.48 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: 4.65 Time building geometry restraints manager: 4.33 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: 0.180 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: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 33.210 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 9.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP A 480 HIS 0.007 0.001 HIS A 255 PHE 0.020 0.002 PHE A 25 TYR 0.018 0.002 TYR A 998 ARG 0.004 0.001 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.14268 ( 730) hydrogen bonds : angle 5.98136 ( 2118) covalent geometry : bond 0.00560 (13947) covalent geometry : angle 0.65390 (18844) *********************** 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 : 1.652 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7093 (m-80) cc_final: 0.6079 (m-10) REVERT: A 197 MET cc_start: 0.9018 (mtp) cc_final: 0.8653 (mtm) REVERT: A 438 GLN cc_start: 0.8104 (mp10) cc_final: 0.7666 (tm-30) REVERT: A 580 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7786 (mtt90) REVERT: A 721 ASP cc_start: 0.8232 (t0) cc_final: 0.7810 (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: 0.9083 (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: 0.6947 (t0) REVERT: B 161 SER cc_start: 0.8324 (p) cc_final: 0.8079 (p) REVERT: B 175 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6635 (mt-10) REVERT: C 141 LYS cc_start: 0.7335 (mttp) cc_final: 0.7021 (mttp) REVERT: D 150 HIS cc_start: 0.6946 (m-70) cc_final: 0.6585 (m-70) REVERT: D 195 MET cc_start: 0.6872 (ttm) cc_final: 0.6272 (ttm) REVERT: E 148 MET cc_start: 0.7261 (ttt) cc_final: 0.7010 (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: 0.2730 time to fit residues: 116.8636 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 : 1.572 ------------------------------------------------------------------------------- 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 141 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 199 HIS A 215 ASN 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 A1022 HIS ** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS E 150 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.116326 restraints weight = 20066.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117580 restraints weight = 15446.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118870 restraints weight = 11988.917| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13947 Z= 0.184 Angle : 0.595 7.612 18844 Z= 0.314 Chirality : 0.041 0.161 2175 Planarity : 0.004 0.059 2381 Dihedral : 4.748 37.364 1849 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.87 % Allowed : 14.50 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1682 helix: 0.39 (0.16), residues: 964 sheet: -0.72 (0.53), residues: 79 loop : -1.96 (0.22), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 932 HIS 0.006 0.001 HIS A 853 PHE 0.019 0.002 PHE A1328 TYR 0.017 0.001 TYR A 998 ARG 0.004 0.000 ARG A1339 Details of bonding type rmsd hydrogen bonds : bond 0.05660 ( 730) hydrogen bonds : angle 4.53059 ( 2118) covalent geometry : bond 0.00430 (13947) covalent geometry : angle 0.59491 (18844) *********************** 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 286 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6998 (m-80) cc_final: 0.6000 (m-10) REVERT: A 197 MET cc_start: 0.8913 (mtp) cc_final: 0.8462 (mtm) REVERT: A 374 ASN cc_start: 0.8481 (t0) cc_final: 0.7883 (m110) REVERT: A 511 ARG cc_start: 0.7143 (ptt90) cc_final: 0.6870 (ptt90) REVERT: A 568 HIS cc_start: 0.7309 (t70) cc_final: 0.6807 (m-70) REVERT: A 580 ARG cc_start: 0.8234 (mtt180) cc_final: 0.7803 (mtt90) REVERT: A 721 ASP cc_start: 0.7982 (t0) cc_final: 0.7551 (t0) REVERT: A 959 LEU cc_start: 0.9214 (mt) cc_final: 0.9006 (mp) REVERT: A 1226 TYR cc_start: 0.9116 (t80) cc_final: 0.8900 (t80) REVERT: A 1290 ASP cc_start: 0.7616 (t70) cc_final: 0.7203 (t0) REVERT: A 1319 LEU cc_start: 0.8599 (mt) cc_final: 0.8339 (mt) REVERT: A 1348 GLU cc_start: 0.7878 (mp0) cc_final: 0.7244 (mp0) REVERT: A 1404 ASN cc_start: 0.8322 (t0) cc_final: 0.7955 (t0) REVERT: B 148 MET cc_start: 0.8386 (ttm) cc_final: 0.7961 (ttp) REVERT: B 161 SER cc_start: 0.8518 (p) cc_final: 0.8272 (p) REVERT: C 141 LYS cc_start: 0.7250 (mttp) cc_final: 0.6985 (mttt) REVERT: C 167 ARG cc_start: 0.6168 (ptm-80) cc_final: 0.5681 (ptt180) REVERT: D 150 HIS cc_start: 0.6999 (m-70) cc_final: 0.6543 (m-70) REVERT: E 142 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6528 (mt) REVERT: E 146 LEU cc_start: 0.8331 (tt) cc_final: 0.8082 (mm) REVERT: E 148 MET cc_start: 0.7268 (ttt) cc_final: 0.7046 (ttm) REVERT: E 175 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6406 (pm20) REVERT: E 180 LYS cc_start: 0.6420 (mtpp) cc_final: 0.6076 (mttt) REVERT: E 191 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6865 (tmm-80) outliers start: 29 outliers final: 18 residues processed: 268 average time/residue: 0.2386 time to fit residues: 96.0028 Evaluate side-chains 251 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 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 743 ILE Chi-restraints excluded: chain A residue 894 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 B residue 178 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 176 GLU 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 111 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 chunk 109 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 58 optimal weight: 0.0170 chunk 130 optimal weight: 30.0000 chunk 52 optimal weight: 0.5980 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 766 GLN B 150 HIS C 150 HIS ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.152799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121170 restraints weight = 20087.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.124714 restraints weight = 14282.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.125438 restraints weight = 10484.364| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13947 Z= 0.105 Angle : 0.500 8.063 18844 Z= 0.264 Chirality : 0.038 0.135 2175 Planarity : 0.003 0.055 2381 Dihedral : 4.268 32.969 1849 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.06 % Allowed : 15.79 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.20), residues: 1682 helix: 1.24 (0.17), residues: 972 sheet: -0.16 (0.57), residues: 74 loop : -1.69 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 287 HIS 0.020 0.001 HIS E 150 PHE 0.010 0.001 PHE A 802 TYR 0.009 0.001 TYR A 998 ARG 0.004 0.000 ARG A 462 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 730) hydrogen bonds : angle 3.95821 ( 2118) covalent geometry : bond 0.00217 (13947) covalent geometry : angle 0.50021 (18844) *********************** 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 311 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 1.452 Fit side-chains REVERT: A 13 TYR cc_start: 0.6958 (m-80) cc_final: 0.6005 (m-10) REVERT: A 197 MET cc_start: 0.8663 (mtp) cc_final: 0.8437 (mtm) REVERT: A 204 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7661 (tt) REVERT: A 568 HIS cc_start: 0.7282 (t70) cc_final: 0.6817 (m-70) REVERT: A 580 ARG cc_start: 0.8135 (mtt180) cc_final: 0.7726 (mtt90) REVERT: A 816 ASP cc_start: 0.7484 (p0) cc_final: 0.7151 (p0) REVERT: A 914 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 1242 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8734 (tp) REVERT: A 1269 GLU cc_start: 0.7519 (pt0) cc_final: 0.7178 (pt0) REVERT: A 1290 ASP cc_start: 0.7598 (t70) cc_final: 0.7270 (t0) REVERT: A 1348 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: A 1458 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7542 (mp0) REVERT: B 148 MET cc_start: 0.8252 (ttm) cc_final: 0.7781 (mtp) REVERT: C 167 ARG cc_start: 0.6226 (ptm-80) cc_final: 0.5893 (ptt180) REVERT: D 150 HIS cc_start: 0.7118 (m-70) cc_final: 0.6572 (m-70) REVERT: E 142 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6649 (mt) REVERT: E 148 MET cc_start: 0.7572 (ttt) cc_final: 0.7273 (ttm) REVERT: E 175 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6193 (pm20) REVERT: E 180 LYS cc_start: 0.6498 (mtpp) cc_final: 0.6037 (mttt) REVERT: E 187 MET cc_start: 0.7928 (ppp) cc_final: 0.7335 (ppp) REVERT: E 191 ARG cc_start: 0.7041 (ptm160) cc_final: 0.6581 (tmm-80) outliers start: 32 outliers final: 15 residues processed: 291 average time/residue: 0.2432 time to fit residues: 106.7128 Evaluate side-chains 258 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 457 SER Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1279 GLN Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1396 MET 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 E residue 142 LEU Chi-restraints excluded: chain E residue 160 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 167 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 604 GLN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN A 913 GLN C 150 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116947 restraints weight = 20190.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.119206 restraints weight = 14598.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120068 restraints weight = 10141.454| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13947 Z= 0.228 Angle : 0.615 8.833 18844 Z= 0.319 Chirality : 0.042 0.162 2175 Planarity : 0.004 0.060 2381 Dihedral : 4.551 38.495 1849 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.16 % Allowed : 18.30 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1682 helix: 1.11 (0.17), residues: 965 sheet: -0.17 (0.58), residues: 74 loop : -1.66 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 480 HIS 0.007 0.001 HIS A 612 PHE 0.020 0.002 PHE A 25 TYR 0.019 0.002 TYR A 998 ARG 0.005 0.001 ARG A 492 Details of bonding type rmsd hydrogen bonds : bond 0.05591 ( 730) hydrogen bonds : angle 4.25552 ( 2118) covalent geometry : bond 0.00542 (13947) covalent geometry : angle 0.61512 (18844) *********************** 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 287 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 1.582 Fit side-chains REVERT: A 13 TYR cc_start: 0.6904 (m-80) cc_final: 0.5954 (m-10) REVERT: A 197 MET cc_start: 0.9036 (mtp) cc_final: 0.8675 (mtm) REVERT: A 204 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8101 (tt) REVERT: A 438 GLN cc_start: 0.8116 (mp10) cc_final: 0.7556 (tm-30) REVERT: A 568 HIS cc_start: 0.7292 (t70) cc_final: 0.6861 (m-70) REVERT: A 580 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7743 (mtt90) REVERT: A 619 LYS cc_start: 0.7376 (ttmt) cc_final: 0.6632 (tttm) REVERT: A 646 MET cc_start: 0.8706 (mmm) cc_final: 0.8349 (mmm) REVERT: A 918 ARG cc_start: 0.7920 (mtt90) cc_final: 0.7503 (mtt90) REVERT: A 1182 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7697 (pp) REVERT: A 1194 MET cc_start: 0.6951 (pmm) cc_final: 0.6710 (pmm) REVERT: A 1242 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8752 (tp) REVERT: A 1319 LEU cc_start: 0.8524 (mt) cc_final: 0.8268 (mt) REVERT: A 1404 ASN cc_start: 0.8137 (t0) cc_final: 0.7806 (t0) REVERT: C 167 ARG cc_start: 0.6506 (ptm-80) cc_final: 0.5979 (ptt180) REVERT: E 148 MET cc_start: 0.7754 (ttt) cc_final: 0.7463 (ttm) REVERT: E 175 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6179 (pm20) REVERT: E 180 LYS cc_start: 0.6584 (mtpp) cc_final: 0.6198 (mttt) REVERT: E 191 ARG cc_start: 0.7290 (ptm160) cc_final: 0.6930 (tmm-80) outliers start: 49 outliers final: 28 residues processed: 261 average time/residue: 0.2370 time to fit residues: 92.7825 Evaluate side-chains 258 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP 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 204 LEU Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 LEU 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 696 SER 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 948 ASN Chi-restraints excluded: chain A residue 949 ASN 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 B residue 183 THR 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 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 138 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 612 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS D 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.146496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115310 restraints weight = 20554.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116600 restraints weight = 14723.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117685 restraints weight = 11297.454| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13947 Z= 0.206 Angle : 0.607 7.195 18844 Z= 0.315 Chirality : 0.042 0.155 2175 Planarity : 0.004 0.061 2381 Dihedral : 4.596 37.270 1849 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.16 % Allowed : 19.52 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1682 helix: 1.15 (0.16), residues: 968 sheet: -0.58 (0.55), residues: 80 loop : -1.65 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 932 HIS 0.007 0.001 HIS A 612 PHE 0.017 0.002 PHE A 25 TYR 0.017 0.002 TYR A 998 ARG 0.004 0.000 ARG B 174 Details of bonding type rmsd hydrogen bonds : bond 0.05509 ( 730) hydrogen bonds : angle 4.22553 ( 2118) covalent geometry : bond 0.00491 (13947) covalent geometry : angle 0.60680 (18844) *********************** 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 284 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 235 time to evaluate : 1.481 Fit side-chains REVERT: A 13 TYR cc_start: 0.6908 (m-80) cc_final: 0.5920 (m-10) REVERT: A 197 MET cc_start: 0.9013 (mtp) cc_final: 0.8635 (mtm) REVERT: A 204 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 438 GLN cc_start: 0.8109 (mp10) cc_final: 0.7567 (tm-30) REVERT: A 453 TYR cc_start: 0.8272 (m-80) cc_final: 0.7874 (m-10) REVERT: A 460 MET cc_start: 0.8271 (mtm) cc_final: 0.7999 (mtm) REVERT: A 580 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7771 (mtt90) REVERT: A 619 LYS cc_start: 0.7356 (ttmt) cc_final: 0.6611 (tttm) REVERT: A 700 ASP cc_start: 0.8449 (t0) cc_final: 0.8195 (t0) REVERT: A 804 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8431 (tt) REVERT: A 918 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7513 (mtt90) REVERT: A 1182 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 1309 MET cc_start: 0.8587 (tpp) cc_final: 0.8083 (mmt) REVERT: A 1319 LEU cc_start: 0.8534 (mt) cc_final: 0.8263 (mt) REVERT: A 1348 GLU cc_start: 0.8086 (mp0) cc_final: 0.7850 (mp0) REVERT: A 1404 ASN cc_start: 0.8172 (t0) cc_final: 0.7861 (t0) REVERT: E 175 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6066 (pm20) REVERT: E 180 LYS cc_start: 0.6746 (mtpp) cc_final: 0.6205 (mttt) REVERT: E 191 ARG cc_start: 0.7334 (ptm160) cc_final: 0.6935 (tmm-80) outliers start: 49 outliers final: 34 residues processed: 260 average time/residue: 0.2487 time to fit residues: 97.4561 Evaluate side-chains 263 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.470 ------------------------------------------------------------------------------- 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 473 PHE Chi-restraints excluded: chain A residue 483 LEU 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 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 815 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 949 ASN 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 1296 ASP 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 B residue 183 THR Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 150 HIS Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 130 optimal weight: 30.0000 chunk 114 optimal weight: 0.0770 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A 609 ASN C 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116995 restraints weight = 20656.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117792 restraints weight = 13816.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118966 restraints weight = 11468.496| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13947 Z= 0.151 Angle : 0.563 14.173 18844 Z= 0.291 Chirality : 0.040 0.160 2175 Planarity : 0.004 0.060 2381 Dihedral : 4.433 37.090 1849 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.22 % Allowed : 20.75 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1682 helix: 1.36 (0.17), residues: 969 sheet: -0.47 (0.55), residues: 80 loop : -1.59 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.011 0.001 HIS D 150 PHE 0.012 0.002 PHE A 25 TYR 0.014 0.001 TYR A 998 ARG 0.007 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04834 ( 730) hydrogen bonds : angle 4.04887 ( 2118) covalent geometry : bond 0.00349 (13947) covalent geometry : angle 0.56251 (18844) *********************** 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 296 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 1.529 Fit side-chains REVERT: A 13 TYR cc_start: 0.6903 (m-80) cc_final: 0.5892 (m-10) REVERT: A 197 MET cc_start: 0.8991 (mtp) cc_final: 0.8636 (mtm) REVERT: A 204 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 249 TYR cc_start: 0.7954 (m-80) cc_final: 0.7673 (m-80) REVERT: A 438 GLN cc_start: 0.8083 (mp10) cc_final: 0.7542 (tm-30) REVERT: A 453 TYR cc_start: 0.8339 (m-80) cc_final: 0.7935 (m-10) REVERT: A 580 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7740 (mtt90) REVERT: A 619 LYS cc_start: 0.7248 (ttmt) cc_final: 0.6450 (tttm) REVERT: A 816 ASP cc_start: 0.7511 (p0) cc_final: 0.7135 (p0) REVERT: A 1182 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7699 (pp) REVERT: A 1194 MET cc_start: 0.7265 (pmm) cc_final: 0.7062 (pmm) REVERT: A 1226 TYR cc_start: 0.8925 (t80) cc_final: 0.8679 (t80) REVERT: A 1242 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8802 (tp) REVERT: A 1309 MET cc_start: 0.8595 (tpp) cc_final: 0.8106 (mmt) REVERT: A 1319 LEU cc_start: 0.8507 (mt) cc_final: 0.8291 (mt) REVERT: A 1404 ASN cc_start: 0.8209 (t0) cc_final: 0.7885 (t0) REVERT: A 1436 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8874 (tt) REVERT: A 1449 ASP cc_start: 0.8611 (t0) cc_final: 0.8083 (t0) REVERT: B 161 SER cc_start: 0.9184 (t) cc_final: 0.8838 (p) REVERT: C 141 LYS cc_start: 0.7287 (mtpt) cc_final: 0.6891 (mttt) REVERT: C 148 MET cc_start: 0.4648 (mtt) cc_final: 0.4412 (mtt) REVERT: D 150 HIS cc_start: 0.6855 (m170) cc_final: 0.6647 (m-70) REVERT: E 148 MET cc_start: 0.8069 (ttm) cc_final: 0.7772 (ttm) REVERT: E 150 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7588 (t-90) REVERT: E 175 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6285 (pm20) REVERT: E 180 LYS cc_start: 0.6542 (mtpp) cc_final: 0.6053 (mttt) REVERT: E 191 ARG cc_start: 0.7405 (ptm160) cc_final: 0.7064 (tmm-80) outliers start: 50 outliers final: 36 residues processed: 271 average time/residue: 0.2533 time to fit residues: 103.3057 Evaluate side-chains 270 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 204 LEU Chi-restraints excluded: chain A residue 341 SER 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 457 SER Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 483 LEU 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 696 SER 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 815 ILE Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 1087 THR 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 1279 GLN Chi-restraints excluded: chain A residue 1296 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 85 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 111 optimal weight: 0.0170 chunk 62 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 561 HIS C 150 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.151478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119958 restraints weight = 20244.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122946 restraints weight = 14147.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.124263 restraints weight = 10344.327| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13947 Z= 0.112 Angle : 0.540 14.776 18844 Z= 0.275 Chirality : 0.038 0.136 2175 Planarity : 0.003 0.055 2381 Dihedral : 4.174 34.991 1849 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.09 % Allowed : 21.01 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1682 helix: 1.63 (0.17), residues: 974 sheet: -0.05 (0.58), residues: 74 loop : -1.53 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 287 HIS 0.004 0.001 HIS A 853 PHE 0.011 0.001 PHE A 87 TYR 0.012 0.001 TYR A 917 ARG 0.006 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 730) hydrogen bonds : angle 3.88274 ( 2118) covalent geometry : bond 0.00248 (13947) covalent geometry : angle 0.54008 (18844) *********************** 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 299 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 1.501 Fit side-chains REVERT: A 13 TYR cc_start: 0.6942 (m-80) cc_final: 0.5963 (m-10) REVERT: A 197 MET cc_start: 0.8715 (mtp) cc_final: 0.8486 (mtm) REVERT: A 204 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 249 TYR cc_start: 0.7947 (m-80) cc_final: 0.7725 (m-80) REVERT: A 438 GLN cc_start: 0.8056 (mp10) cc_final: 0.7420 (tm-30) REVERT: A 453 TYR cc_start: 0.8212 (m-80) cc_final: 0.7864 (m-10) REVERT: A 568 HIS cc_start: 0.6989 (t70) cc_final: 0.6686 (m-70) REVERT: A 619 LYS cc_start: 0.7040 (ttmt) cc_final: 0.6348 (tttm) REVERT: A 816 ASP cc_start: 0.7488 (p0) cc_final: 0.7136 (p0) REVERT: A 898 LEU cc_start: 0.7527 (tp) cc_final: 0.7295 (tt) REVERT: A 1182 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7654 (pp) REVERT: A 1226 TYR cc_start: 0.9010 (t80) cc_final: 0.8767 (t80) REVERT: A 1242 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8776 (tp) REVERT: A 1309 MET cc_start: 0.8545 (tpp) cc_final: 0.8218 (mmt) REVERT: A 1436 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8870 (tt) REVERT: A 1449 ASP cc_start: 0.8502 (t0) cc_final: 0.7951 (t0) REVERT: B 161 SER cc_start: 0.9225 (t) cc_final: 0.8776 (p) REVERT: C 141 LYS cc_start: 0.7303 (mtpt) cc_final: 0.6905 (mttt) REVERT: C 167 ARG cc_start: 0.6479 (ptm-80) cc_final: 0.5854 (ptt180) REVERT: E 148 MET cc_start: 0.7883 (ttm) cc_final: 0.7577 (ttm) REVERT: E 175 GLU cc_start: 0.6639 (mm-30) cc_final: 0.5956 (pm20) REVERT: E 180 LYS cc_start: 0.6483 (mtpp) cc_final: 0.6014 (mttt) REVERT: E 191 ARG cc_start: 0.7336 (ptm160) cc_final: 0.6988 (tmm-80) outliers start: 48 outliers final: 28 residues processed: 276 average time/residue: 0.2348 time to fit residues: 99.4941 Evaluate side-chains 265 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.501 ------------------------------------------------------------------------------- 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 190 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 506 LEU 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 613 VAL Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 696 SER 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 872 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 1087 THR 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 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 1436 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain E residue 160 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 612 HIS ** 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 = 0.3715 r_free = 0.3715 target = 0.148166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116054 restraints weight = 20357.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119055 restraints weight = 13967.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.120500 restraints weight = 9819.080| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13947 Z= 0.173 Angle : 0.586 14.071 18844 Z= 0.302 Chirality : 0.040 0.162 2175 Planarity : 0.004 0.059 2381 Dihedral : 4.335 36.907 1849 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.22 % Allowed : 21.13 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1682 helix: 1.49 (0.17), residues: 971 sheet: 0.02 (0.60), residues: 70 loop : -1.51 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.005 0.001 HIS A 612 PHE 0.015 0.002 PHE A 25 TYR 0.015 0.001 TYR A 998 ARG 0.006 0.000 ARG B 174 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 730) hydrogen bonds : angle 4.02400 ( 2118) covalent geometry : bond 0.00407 (13947) covalent geometry : angle 0.58586 (18844) *********************** 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 282 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 232 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6882 (m-80) cc_final: 0.5886 (m-10) REVERT: A 197 MET cc_start: 0.9030 (mtp) cc_final: 0.8676 (mtm) REVERT: A 204 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8025 (tt) REVERT: A 438 GLN cc_start: 0.8112 (mp10) cc_final: 0.7409 (tm-30) REVERT: A 568 HIS cc_start: 0.6999 (t70) cc_final: 0.6692 (m-70) REVERT: A 580 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7702 (mtt90) REVERT: A 619 LYS cc_start: 0.7182 (ttmt) cc_final: 0.6381 (tttm) REVERT: A 646 MET cc_start: 0.8672 (mmm) cc_final: 0.8344 (mmm) REVERT: A 1182 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7757 (pp) REVERT: A 1242 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8792 (tp) REVERT: A 1319 LEU cc_start: 0.8702 (mt) cc_final: 0.8472 (mt) REVERT: A 1436 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8863 (tt) REVERT: A 1449 ASP cc_start: 0.8550 (t0) cc_final: 0.8007 (t0) REVERT: C 141 LYS cc_start: 0.7235 (mtpt) cc_final: 0.6892 (mttt) REVERT: C 170 MET cc_start: 0.6264 (tpp) cc_final: 0.6051 (tpp) REVERT: E 175 GLU cc_start: 0.6660 (mm-30) cc_final: 0.5946 (pm20) REVERT: E 180 LYS cc_start: 0.6521 (mtpp) cc_final: 0.6017 (mttt) outliers start: 50 outliers final: 37 residues processed: 258 average time/residue: 0.2496 time to fit residues: 96.0127 Evaluate side-chains 265 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 341 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 506 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 512 ASP 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 613 VAL Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 696 SER 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 872 THR Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain A residue 904 SER 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 1436 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 183 THR 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 160 THR Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122479 restraints weight = 20064.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.123254 restraints weight = 14149.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123954 restraints weight = 11803.726| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13947 Z= 0.111 Angle : 0.551 15.707 18844 Z= 0.280 Chirality : 0.038 0.133 2175 Planarity : 0.003 0.057 2381 Dihedral : 4.116 33.971 1849 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.45 % Allowed : 22.36 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1682 helix: 1.71 (0.17), residues: 976 sheet: -0.04 (0.55), residues: 81 loop : -1.43 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 287 HIS 0.004 0.001 HIS C 150 PHE 0.011 0.001 PHE A 424 TYR 0.012 0.001 TYR A 917 ARG 0.005 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 730) hydrogen bonds : angle 3.82394 ( 2118) covalent geometry : bond 0.00245 (13947) covalent geometry : angle 0.55079 (18844) *********************** 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 279 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6950 (m-80) cc_final: 0.5872 (m-10) REVERT: A 197 MET cc_start: 0.8739 (mtp) cc_final: 0.8511 (mtm) REVERT: A 204 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 438 GLN cc_start: 0.8093 (mp10) cc_final: 0.7562 (tm-30) REVERT: A 568 HIS cc_start: 0.6936 (t70) cc_final: 0.6602 (m-70) REVERT: A 580 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7686 (mtt90) REVERT: A 619 LYS cc_start: 0.6943 (ttmt) cc_final: 0.6156 (tttm) REVERT: A 646 MET cc_start: 0.8631 (mmm) cc_final: 0.8292 (mmm) REVERT: A 816 ASP cc_start: 0.7516 (p0) cc_final: 0.7169 (p0) REVERT: A 1182 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7816 (pp) REVERT: A 1242 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8790 (tp) REVERT: A 1309 MET cc_start: 0.8754 (tpp) cc_final: 0.8423 (mmt) REVERT: A 1436 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 1449 ASP cc_start: 0.8535 (t0) cc_final: 0.7994 (t0) REVERT: C 149 LEU cc_start: 0.8432 (mm) cc_final: 0.8127 (mm) REVERT: D 170 MET cc_start: 0.5702 (mmt) cc_final: 0.5468 (mtt) REVERT: E 175 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6044 (pm20) REVERT: E 180 LYS cc_start: 0.6473 (mtpp) cc_final: 0.5993 (mttt) REVERT: E 191 ARG cc_start: 0.7747 (tmm-80) cc_final: 0.6921 (ptm160) outliers start: 38 outliers final: 28 residues processed: 260 average time/residue: 0.2324 time to fit residues: 91.7027 Evaluate side-chains 268 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 236 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 341 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 506 LEU 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 613 VAL Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 696 SER 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 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 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 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 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 81 optimal weight: 0.0970 chunk 139 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122039 restraints weight = 20175.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.122979 restraints weight = 14829.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.124092 restraints weight = 12889.791| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2828 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= 0.114 Angle : 0.551 16.023 18844 Z= 0.279 Chirality : 0.038 0.141 2175 Planarity : 0.003 0.058 2381 Dihedral : 4.048 33.822 1849 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.26 % Allowed : 22.62 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1682 helix: 1.79 (0.17), residues: 974 sheet: -0.01 (0.54), residues: 84 loop : -1.39 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 287 HIS 0.004 0.001 HIS A 853 PHE 0.015 0.001 PHE A 87 TYR 0.012 0.001 TYR A 917 ARG 0.005 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 730) hydrogen bonds : angle 3.79294 ( 2118) covalent geometry : bond 0.00255 (13947) covalent geometry : angle 0.55112 (18844) ********************** 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 279 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 TYR cc_start: 0.6866 (m-80) cc_final: 0.5692 (m-10) REVERT: A 197 MET cc_start: 0.8923 (mtp) cc_final: 0.8522 (mtm) REVERT: A 204 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8020 (tt) REVERT: A 329 PHE cc_start: 0.8810 (m-80) cc_final: 0.8472 (m-10) REVERT: A 438 GLN cc_start: 0.8112 (mp10) cc_final: 0.7564 (tm-30) REVERT: A 453 TYR cc_start: 0.8152 (m-80) cc_final: 0.7943 (m-10) REVERT: A 568 HIS cc_start: 0.6921 (t70) cc_final: 0.6604 (m-70) REVERT: A 580 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7671 (mtt90) REVERT: A 619 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6097 (tttm) REVERT: A 646 MET cc_start: 0.8622 (mmm) cc_final: 0.8290 (mmm) REVERT: A 816 ASP cc_start: 0.7497 (p0) cc_final: 0.7194 (p0) REVERT: A 1182 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7811 (pp) REVERT: A 1242 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 1404 ASN cc_start: 0.7985 (t0) cc_final: 0.7624 (t0) REVERT: A 1436 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8842 (tt) REVERT: A 1449 ASP cc_start: 0.8494 (t0) cc_final: 0.7962 (t0) REVERT: B 152 LEU cc_start: 0.8699 (tt) cc_final: 0.8471 (tp) REVERT: C 149 LEU cc_start: 0.8378 (mm) cc_final: 0.8031 (mm) REVERT: E 175 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6026 (pm20) REVERT: E 180 LYS cc_start: 0.6443 (mtpp) cc_final: 0.5965 (mttt) REVERT: E 184 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7267 (mm-30) REVERT: E 191 ARG cc_start: 0.7913 (tmm-80) cc_final: 0.7087 (ptm160) outliers start: 35 outliers final: 26 residues processed: 263 average time/residue: 0.2426 time to fit residues: 96.4510 Evaluate side-chains 263 residues out of total 1552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 341 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 506 LEU 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 613 VAL Chi-restraints excluded: chain A residue 696 SER 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 904 SER 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 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 D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 20 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3749 r_free = 0.3749 target = 0.151002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120876 restraints weight = 20392.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.122114 restraints weight = 14355.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122966 restraints weight = 11881.826| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13947 Z= 0.125 Angle : 0.562 11.336 18844 Z= 0.286 Chirality : 0.039 0.137 2175 Planarity : 0.003 0.058 2381 Dihedral : 4.089 35.003 1849 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.38 % Allowed : 22.94 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1682 helix: 1.77 (0.17), residues: 974 sheet: -0.07 (0.54), residues: 84 loop : -1.38 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 932 HIS 0.004 0.001 HIS A 612 PHE 0.017 0.001 PHE A 87 TYR 0.012 0.001 TYR A 998 ARG 0.005 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 730) hydrogen bonds : angle 3.81229 ( 2118) covalent geometry : bond 0.00286 (13947) covalent geometry : angle 0.56217 (18844) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3989.79 seconds wall clock time: 70 minutes 18.26 seconds (4218.26 seconds total)