Starting phenix.real_space_refine on Thu Aug 6 08:33:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibz_52819/08_2026/9ibz_52819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibz_52819/08_2026/9ibz_52819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ibz_52819/08_2026/9ibz_52819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibz_52819/08_2026/9ibz_52819.map" model { file = "/net/cci-nas-00/data/ceres_data/9ibz_52819/08_2026/9ibz_52819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibz_52819/08_2026/9ibz_52819.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.186 sd= 0.913 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 44 5.49 5 S 81 5.16 5 C 8984 2.51 5 N 2530 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14339 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 959, 7645 Classifications: {'peptide': 959} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 62, 'TRANS': 896} Chain breaks: 6 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2976 Classifications: {'peptide': 368} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 350} Chain breaks: 3 Chain: "C" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2848 Classifications: {'peptide': 353} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 335} Chain breaks: 3 Chain: "P" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 438 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "T" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 402 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' CA': 2, 'DCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.22, per 1000 atoms: 0.22 Number of scatterers: 14339 At special positions: 0 Unit cell: (104.328, 107.64, 138.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 81 16.00 P 44 15.00 O 2698 8.00 N 2530 7.00 C 8984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 605.2 milliseconds 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3122 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 47.1% alpha, 11.6% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.732A pdb=" N GLN A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 118 through 142 Proline residue: A 132 - end of helix removed outlier: 3.842A pdb=" N ALA A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.571A pdb=" N LEU A 227 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.651A pdb=" N ASP A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.527A pdb=" N GLN A 264 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 370 through 400 removed outlier: 3.921A pdb=" N GLN A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 402 through 414 removed outlier: 3.989A pdb=" N LEU A 406 " --> pdb=" O HIS A 402 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 451 removed outlier: 3.628A pdb=" N ARG A 425 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 removed outlier: 3.504A pdb=" N SER A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLY A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 460 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR A 461 " --> pdb=" O GLY A 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 462 " --> pdb=" O GLU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 533 removed outlier: 4.198A pdb=" N LEU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.673A pdb=" N ASP A 538 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 3.877A pdb=" N LYS A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 557 " --> pdb=" O TRP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 629 through 644 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 748 through 754 Processing helix chain 'A' and resid 765 through 776 Processing helix chain 'A' and resid 776 through 788 removed outlier: 6.055A pdb=" N LYS A 784 " --> pdb=" O ARG A 780 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ARG A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 871 through 886 removed outlier: 3.700A pdb=" N ALA A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 900 Processing helix chain 'A' and resid 908 through 918 Processing helix chain 'A' and resid 920 through 934 Processing helix chain 'A' and resid 936 through 948 Processing helix chain 'A' and resid 952 through 968 removed outlier: 3.765A pdb=" N VAL A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 967 " --> pdb=" O MET A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1045 Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.682A pdb=" N GLU A1062 " --> pdb=" O ARG A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1101 removed outlier: 3.831A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1146 removed outlier: 3.562A pdb=" N LEU A1146 " --> pdb=" O PHE A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1156 Processing helix chain 'A' and resid 1197 through 1206 Processing helix chain 'B' and resid 67 through 76 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 100 through 119 Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.521A pdb=" N GLU B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 247 through 266 removed outlier: 3.787A pdb=" N ASP B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 342 through 354 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 424 through 435 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'B' and resid 470 through 482 removed outlier: 3.959A pdb=" N ALA B 482 " --> pdb=" O TYR B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 76 Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 100 through 120 Processing helix chain 'C' and resid 185 through 192 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 247 through 266 removed outlier: 4.063A pdb=" N PHE C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 315 removed outlier: 3.960A pdb=" N MET C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.700A pdb=" N LYS C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS C 323 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.607A pdb=" N PHE C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 409 removed outlier: 3.849A pdb=" N GLN C 397 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL C 398 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 435 Processing helix chain 'C' and resid 445 through 449 Processing helix chain 'C' and resid 470 through 482 removed outlier: 3.530A pdb=" N ALA C 482 " --> pdb=" O TYR C 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.865A pdb=" N TRP A 158 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS A 207 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 205 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 203 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 181 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLN A 247 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 420 Processing sheet with id=AA3, first strand: chain 'A' and resid 726 through 729 removed outlier: 6.720A pdb=" N LEU A 586 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1107 through 1109 removed outlier: 6.269A pdb=" N PHE A1107 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU A1118 " --> pdb=" O PHE A1107 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A1109 " --> pdb=" O ARG A1116 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP A1164 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A1196 " --> pdb=" O VAL A1161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 127 removed outlier: 6.092A pdb=" N PHE B 126 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N ILE B 211 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 301 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 133 through 134 Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AA8, first strand: chain 'B' and resid 413 through 415 removed outlier: 7.230A pdb=" N VAL B 383 " --> pdb=" O TRP B 414 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 443 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 133 through 134 removed outlier: 3.592A pdb=" N LYS C 180 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 206 through 216 removed outlier: 3.802A pdb=" N TYR C 206 " --> pdb=" O PHE C 242 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 300 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU C 299 " --> pdb=" O TYR C 291 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR C 291 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 301 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR C 290 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 413 through 415 removed outlier: 6.968A pdb=" N VAL C 383 " --> pdb=" O TRP C 414 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA C 384 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL C 443 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP C 386 " --> pdb=" O VAL C 443 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 466 " --> pdb=" O ILE C 453 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4098 1.33 - 1.45: 2628 1.45 - 1.57: 7845 1.57 - 1.69: 85 1.69 - 1.81: 128 Bond restraints: 14784 Sorted by residual: bond pdb=" O3B DCP A1301 " pdb=" PG DCP A1301 " ideal model delta sigma weight residual 1.746 1.609 0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C3' DC P 6 " pdb=" C2' DC P 6 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" O3A DCP A1301 " pdb=" PB DCP A1301 " ideal model delta sigma weight residual 1.672 1.609 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C3' DT T 29 " pdb=" C2' DT T 29 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.38e+00 bond pdb=" C1' DT T 19 " pdb=" N1 DT T 19 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.15e+00 ... (remaining 14779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 20053 2.44 - 4.88: 151 4.88 - 7.31: 5 7.31 - 9.75: 0 9.75 - 12.19: 1 Bond angle restraints: 20210 Sorted by residual: angle pdb=" N3 DT T 24 " pdb=" C4 DT T 24 " pdb=" O4 DT T 24 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT P 14 " pdb=" C4 DT P 14 " pdb=" O4 DT P 14 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT P 9 " pdb=" C4 DT P 9 " pdb=" O4 DT P 9 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT T 29 " pdb=" C4 DT T 29 " pdb=" O4 DT T 29 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.80e+01 ... (remaining 20205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 7962 15.68 - 31.37: 492 31.37 - 47.05: 167 47.05 - 62.74: 87 62.74 - 78.42: 2 Dihedral angle restraints: 8710 sinusoidal: 3872 harmonic: 4838 Sorted by residual: dihedral pdb=" CA HIS B 77 " pdb=" C HIS B 77 " pdb=" N PHE B 78 " pdb=" CA PHE B 78 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA VAL A 179 " pdb=" C VAL A 179 " pdb=" N PHE A 180 " pdb=" CA PHE A 180 " ideal model delta harmonic sigma weight residual -180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" N MET C 346 " pdb=" CA MET C 346 " pdb=" CB MET C 346 " pdb=" CG MET C 346 " ideal model delta sinusoidal sigma weight residual -60.00 -116.38 56.38 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1724 0.045 - 0.090: 342 0.090 - 0.136: 98 0.136 - 0.181: 2 0.181 - 0.226: 1 Chirality restraints: 2167 Sorted by residual: chirality pdb=" C1' DCP A1301 " pdb=" C2' DCP A1301 " pdb=" N1 DCP A1301 " pdb=" O4' DCP A1301 " both_signs ideal model delta sigma weight residual False 2.25 2.48 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' DC T 18 " pdb=" C4' DC T 18 " pdb=" O3' DC T 18 " pdb=" C2' DC T 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE A 722 " pdb=" N ILE A 722 " pdb=" C ILE A 722 " pdb=" CB ILE A 722 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 2164 not shown) Planarity restraints: 2453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 118 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.48e+00 pdb=" C LEU A 118 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 118 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP A 119 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 116 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR C 116 " 0.030 2.00e-02 2.50e+03 pdb=" O THR C 116 " -0.011 2.00e-02 2.50e+03 pdb=" N SER C 117 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 55 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.49e+00 pdb=" N PRO A 56 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 56 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 56 " -0.022 5.00e-02 4.00e+02 ... (remaining 2450 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1853 2.75 - 3.29: 13474 3.29 - 3.83: 24038 3.83 - 4.36: 28679 4.36 - 4.90: 48859 Nonbonded interactions: 116903 Sorted by model distance: nonbonded pdb=" OE1 GLU A 873 " pdb=" OH TYR A 933 " model vdw 2.216 3.040 nonbonded pdb=" NE1 TRP B 263 " pdb=" OE1 GLU B 301 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN B 318 " pdb=" OG SER B 320 " model vdw 2.266 3.040 nonbonded pdb=" NH2 ARG A 292 " pdb=" OD1 ASN A 336 " model vdw 2.312 3.120 nonbonded pdb=" OD1 ASP A 451 " pdb=" NZ LYS B 373 " model vdw 2.315 3.120 ... (remaining 116898 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 66 through 137 or resid 178 through 218 or resid 230 throu \ gh 354 or resid 369 through 482)) selection = (chain 'C' and (resid 66 through 137 or resid 178 through 482)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 14784 Z= 0.226 Angle : 0.496 12.188 20210 Z= 0.318 Chirality : 0.039 0.226 2167 Planarity : 0.004 0.039 2453 Dihedral : 12.810 78.422 5588 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.68 % Allowed : 3.49 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1650 helix: 1.30 (0.21), residues: 670 sheet: -0.67 (0.37), residues: 196 loop : -0.25 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 931 TYR 0.013 0.001 TYR A1086 PHE 0.014 0.001 PHE C 254 TRP 0.008 0.001 TRP B 241 HIS 0.003 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.23 (14784) covalent geometry : angle 0.49593 / 0.32 (20210) hydrogen bonds : bond 0.17187 / 11.43 ( 652) hydrogen bonds : angle 6.42926 / 4.54 ( 1797) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 341 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.7530 (tt0) cc_final: 0.7224 (tp30) REVERT: A 221 GLN cc_start: 0.8422 (mt0) cc_final: 0.8097 (mm-40) REVERT: A 357 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6544 (mm-30) REVERT: A 466 TRP cc_start: 0.8500 (m-90) cc_final: 0.8080 (m-90) REVERT: A 562 ASP cc_start: 0.8883 (m-30) cc_final: 0.8416 (p0) REVERT: A 630 TYR cc_start: 0.8493 (p90) cc_final: 0.8089 (p90) REVERT: A 1086 TYR cc_start: 0.8085 (t80) cc_final: 0.7846 (t80) REVERT: A 1090 MET cc_start: 0.8437 (mtt) cc_final: 0.8203 (mtp) REVERT: A 1094 MET cc_start: 0.8618 (mmm) cc_final: 0.8380 (mmm) REVERT: A 1169 LYS cc_start: 0.8925 (tttt) cc_final: 0.8515 (ttmt) REVERT: A 1184 MET cc_start: 0.8443 (mmm) cc_final: 0.8126 (mmm) REVERT: A 1210 GLU cc_start: 0.8577 (tt0) cc_final: 0.8235 (pm20) REVERT: B 113 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8045 (mm-30) REVERT: B 180 LYS cc_start: 0.7890 (ptmt) cc_final: 0.7390 (mmtm) REVERT: B 181 LEU cc_start: 0.8101 (mt) cc_final: 0.7883 (mp) REVERT: B 203 ARG cc_start: 0.8276 (ttm110) cc_final: 0.8000 (mtm110) REVERT: B 268 MET cc_start: 0.8225 (mmm) cc_final: 0.8024 (mmm) REVERT: B 280 ASP cc_start: 0.8002 (t0) cc_final: 0.7366 (t0) REVERT: B 308 ASP cc_start: 0.6937 (p0) cc_final: 0.6516 (p0) REVERT: B 321 LYS cc_start: 0.7937 (mttt) cc_final: 0.7611 (mtmt) REVERT: B 394 GLU cc_start: 0.7283 (tp30) cc_final: 0.6935 (tp30) REVERT: B 408 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8316 (mp0) REVERT: B 419 GLU cc_start: 0.7903 (tt0) cc_final: 0.7091 (pt0) REVERT: B 435 MET cc_start: 0.8488 (mtp) cc_final: 0.8236 (mtp) REVERT: C 90 SER cc_start: 0.8425 (m) cc_final: 0.8211 (p) REVERT: C 180 LYS cc_start: 0.8323 (tttt) cc_final: 0.8012 (tttp) REVERT: C 248 SER cc_start: 0.8206 (p) cc_final: 0.7999 (t) REVERT: C 285 LYS cc_start: 0.7665 (ptmt) cc_final: 0.7446 (tptm) REVERT: C 287 ASN cc_start: 0.7907 (m-40) cc_final: 0.7386 (m-40) REVERT: C 301 GLU cc_start: 0.7748 (tt0) cc_final: 0.7512 (tp30) REVERT: C 391 PRO cc_start: 0.8341 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: C 396 ARG cc_start: 0.6742 (tpp-160) cc_final: 0.6519 (mpt180) REVERT: C 457 SER cc_start: 0.6867 (m) cc_final: 0.6424 (p) REVERT: C 462 MET cc_start: 0.7912 (mmt) cc_final: 0.7597 (mmm) REVERT: C 465 MET cc_start: 0.7723 (mtt) cc_final: 0.7255 (mtp) REVERT: C 477 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8117 (ttmm) outliers start: 10 outliers final: 6 residues processed: 349 average time/residue: 0.1369 time to fit residues: 67.6769 Evaluate side-chains 231 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 213 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 149 optimal weight: 5.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 HIS ** A1076 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN B 305 ASN B 409 ASN B 422 GLN C 187 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.129193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099447 restraints weight = 24213.093| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.81 r_work: 0.3378 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14784 Z= 0.155 Angle : 0.562 7.452 20210 Z= 0.299 Chirality : 0.040 0.159 2167 Planarity : 0.004 0.046 2453 Dihedral : 14.477 59.862 2298 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.26 % Allowed : 8.56 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.21), residues: 1650 helix: 1.46 (0.20), residues: 673 sheet: -0.70 (0.37), residues: 202 loop : -0.13 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 369 TYR 0.025 0.002 TYR C 432 PHE 0.020 0.002 PHE A 939 TRP 0.014 0.001 TRP A 726 HIS 0.005 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14784) covalent geometry : angle 0.56242 / 0.30 (20210) hydrogen bonds : bond 0.04462 / 2.96 ( 652) hydrogen bonds : angle 4.96754 / 3.52 ( 1797) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7377 (ttp-110) REVERT: A 168 GLU cc_start: 0.7416 (tt0) cc_final: 0.7003 (tp30) REVERT: A 221 GLN cc_start: 0.8391 (mt0) cc_final: 0.8162 (mm-40) REVERT: A 357 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6553 (mm-30) REVERT: A 466 TRP cc_start: 0.8446 (m-90) cc_final: 0.8003 (m-90) REVERT: A 562 ASP cc_start: 0.8836 (m-30) cc_final: 0.8463 (p0) REVERT: A 638 ARG cc_start: 0.7102 (mtm-85) cc_final: 0.6701 (mtm-85) REVERT: A 726 TRP cc_start: 0.7503 (m-90) cc_final: 0.6876 (m-90) REVERT: A 1086 TYR cc_start: 0.8153 (t80) cc_final: 0.7904 (t80) REVERT: A 1090 MET cc_start: 0.8525 (mtt) cc_final: 0.8293 (mtp) REVERT: A 1169 LYS cc_start: 0.8963 (tttt) cc_final: 0.8601 (ttmt) REVERT: A 1184 MET cc_start: 0.8521 (mmm) cc_final: 0.8168 (mmm) REVERT: A 1210 GLU cc_start: 0.8667 (tt0) cc_final: 0.8299 (pm20) REVERT: B 180 LYS cc_start: 0.7973 (ptmt) cc_final: 0.7486 (mptt) REVERT: B 203 ARG cc_start: 0.8406 (ttm110) cc_final: 0.8110 (mtm110) REVERT: B 280 ASP cc_start: 0.7900 (t0) cc_final: 0.7361 (t0) REVERT: B 285 LYS cc_start: 0.8560 (mttp) cc_final: 0.8147 (mttm) REVERT: B 308 ASP cc_start: 0.7043 (p0) cc_final: 0.6633 (p0) REVERT: B 321 LYS cc_start: 0.7965 (mttt) cc_final: 0.7707 (mtmt) REVERT: B 394 GLU cc_start: 0.7301 (tp30) cc_final: 0.7012 (tp30) REVERT: B 408 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8446 (mp0) REVERT: C 180 LYS cc_start: 0.8367 (tttt) cc_final: 0.8126 (tttp) REVERT: C 248 SER cc_start: 0.8307 (p) cc_final: 0.8073 (t) REVERT: C 301 GLU cc_start: 0.7990 (tt0) cc_final: 0.7578 (tp30) REVERT: C 396 ARG cc_start: 0.6883 (tpp-160) cc_final: 0.6546 (mpt180) REVERT: C 457 SER cc_start: 0.6964 (m) cc_final: 0.6489 (p) REVERT: C 462 MET cc_start: 0.7928 (mmt) cc_final: 0.7595 (mmm) REVERT: C 465 MET cc_start: 0.7787 (mtt) cc_final: 0.7256 (mtp) REVERT: C 477 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8024 (ttmm) outliers start: 33 outliers final: 24 residues processed: 262 average time/residue: 0.1374 time to fit residues: 51.4669 Evaluate side-chains 240 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 931 ARG Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain C residue 108 LYS Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 446 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 156 optimal weight: 0.0980 chunk 132 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 949 HIS A1076 ASN A1080 GLN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.128552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098634 restraints weight = 24512.109| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.84 r_work: 0.3357 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14784 Z= 0.155 Angle : 0.534 7.285 20210 Z= 0.283 Chirality : 0.040 0.196 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.556 59.971 2295 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.74 % Allowed : 9.45 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.21), residues: 1650 helix: 1.57 (0.20), residues: 667 sheet: -0.94 (0.35), residues: 212 loop : -0.06 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 534 TYR 0.036 0.002 TYR C 432 PHE 0.019 0.001 PHE A 939 TRP 0.014 0.001 TRP B 241 HIS 0.005 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (14784) covalent geometry : angle 0.53388 / 0.28 (20210) hydrogen bonds : bond 0.03890 / 2.62 ( 652) hydrogen bonds : angle 4.65676 / 3.30 ( 1797) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7565 (ptt-90) REVERT: A 168 GLU cc_start: 0.7381 (tt0) cc_final: 0.6888 (tp30) REVERT: A 176 ARG cc_start: 0.8519 (mtp-110) cc_final: 0.8316 (mtp85) REVERT: A 221 GLN cc_start: 0.8431 (mt0) cc_final: 0.8190 (mm-40) REVERT: A 357 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6466 (mm-30) REVERT: A 1086 TYR cc_start: 0.8160 (t80) cc_final: 0.7864 (t80) REVERT: A 1090 MET cc_start: 0.8508 (mtt) cc_final: 0.8298 (mtp) REVERT: A 1169 LYS cc_start: 0.8959 (tttt) cc_final: 0.8600 (ttmt) REVERT: A 1184 MET cc_start: 0.8497 (mmm) cc_final: 0.8186 (mmm) REVERT: A 1210 GLU cc_start: 0.8683 (tt0) cc_final: 0.8287 (pm20) REVERT: B 180 LYS cc_start: 0.7897 (ptmt) cc_final: 0.7508 (mmtm) REVERT: B 203 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8009 (mtm110) REVERT: B 280 ASP cc_start: 0.7960 (t0) cc_final: 0.7499 (t0) REVERT: B 285 LYS cc_start: 0.8553 (mttp) cc_final: 0.8135 (mttm) REVERT: B 308 ASP cc_start: 0.6963 (p0) cc_final: 0.6585 (p0) REVERT: B 321 LYS cc_start: 0.7955 (mttt) cc_final: 0.7699 (mtmt) REVERT: B 394 GLU cc_start: 0.7161 (tp30) cc_final: 0.6955 (tp30) REVERT: B 408 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8396 (mp0) REVERT: B 446 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.7883 (p) REVERT: C 180 LYS cc_start: 0.8365 (tttt) cc_final: 0.8125 (tttp) REVERT: C 199 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8075 (mt) REVERT: C 253 ASP cc_start: 0.7808 (m-30) cc_final: 0.7605 (m-30) REVERT: C 301 GLU cc_start: 0.8030 (tt0) cc_final: 0.7622 (tp30) REVERT: C 396 ARG cc_start: 0.6996 (tpp-160) cc_final: 0.6676 (mpt180) REVERT: C 421 MET cc_start: 0.8017 (ppp) cc_final: 0.7626 (ppp) REVERT: C 457 SER cc_start: 0.7015 (m) cc_final: 0.6586 (p) REVERT: C 462 MET cc_start: 0.7941 (mmt) cc_final: 0.7603 (mmm) REVERT: C 465 MET cc_start: 0.7799 (mtt) cc_final: 0.7261 (mtp) REVERT: C 477 LYS cc_start: 0.8444 (ttpt) cc_final: 0.7998 (ttmm) outliers start: 40 outliers final: 29 residues processed: 252 average time/residue: 0.1305 time to fit residues: 47.1708 Evaluate side-chains 243 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 966 VAL Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 9.9990 chunk 169 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 949 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.128885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.099039 restraints weight = 24220.881| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.91 r_work: 0.3373 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14784 Z= 0.129 Angle : 0.518 10.874 20210 Z= 0.273 Chirality : 0.039 0.187 2167 Planarity : 0.004 0.048 2453 Dihedral : 14.479 59.870 2291 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.81 % Allowed : 10.68 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1650 helix: 1.67 (0.20), residues: 669 sheet: -0.93 (0.34), residues: 211 loop : -0.04 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 638 TYR 0.025 0.001 TYR C 432 PHE 0.020 0.001 PHE A 939 TRP 0.015 0.001 TRP B 241 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (14784) covalent geometry : angle 0.51798 / 0.27 (20210) hydrogen bonds : bond 0.03564 / 2.41 ( 652) hydrogen bonds : angle 4.47927 / 3.17 ( 1797) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7455 (tttp) cc_final: 0.6996 (ptpt) REVERT: A 112 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7647 (ptt-90) REVERT: A 168 GLU cc_start: 0.7364 (tt0) cc_final: 0.6894 (tp30) REVERT: A 221 GLN cc_start: 0.8425 (mt0) cc_final: 0.8193 (mm-40) REVERT: A 357 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6454 (mm-30) REVERT: A 466 TRP cc_start: 0.8305 (m-90) cc_final: 0.8044 (m-90) REVERT: A 638 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: A 726 TRP cc_start: 0.7431 (m-90) cc_final: 0.6841 (m-90) REVERT: A 1032 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: A 1086 TYR cc_start: 0.8169 (t80) cc_final: 0.7916 (t80) REVERT: A 1169 LYS cc_start: 0.9002 (tttt) cc_final: 0.8648 (ttmt) REVERT: A 1184 MET cc_start: 0.8503 (mmm) cc_final: 0.8192 (mmm) REVERT: A 1210 GLU cc_start: 0.8655 (tt0) cc_final: 0.8300 (pm20) REVERT: B 180 LYS cc_start: 0.7956 (ptmt) cc_final: 0.7528 (mmtm) REVERT: B 203 ARG cc_start: 0.8418 (ttm110) cc_final: 0.8015 (mtm110) REVERT: B 280 ASP cc_start: 0.7941 (t0) cc_final: 0.7286 (t0) REVERT: B 285 LYS cc_start: 0.8519 (mttp) cc_final: 0.8128 (mttm) REVERT: B 308 ASP cc_start: 0.6954 (p0) cc_final: 0.6638 (p0) REVERT: B 321 LYS cc_start: 0.7974 (mttt) cc_final: 0.7720 (mtmt) REVERT: B 394 GLU cc_start: 0.7237 (tp30) cc_final: 0.7006 (tp30) REVERT: B 408 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8392 (mp0) REVERT: C 180 LYS cc_start: 0.8384 (tttt) cc_final: 0.8168 (tttp) REVERT: C 253 ASP cc_start: 0.7787 (m-30) cc_final: 0.7554 (m-30) REVERT: C 301 GLU cc_start: 0.8034 (tt0) cc_final: 0.7644 (tp30) REVERT: C 396 ARG cc_start: 0.7057 (tpp-160) cc_final: 0.6694 (mpt180) REVERT: C 421 MET cc_start: 0.8063 (ppp) cc_final: 0.7537 (ppp) REVERT: C 457 SER cc_start: 0.6991 (m) cc_final: 0.6577 (p) REVERT: C 462 MET cc_start: 0.7972 (mmt) cc_final: 0.7638 (mmm) REVERT: C 465 MET cc_start: 0.7775 (mtt) cc_final: 0.7250 (mtp) REVERT: C 477 LYS cc_start: 0.8426 (ttpt) cc_final: 0.7968 (ttmm) outliers start: 41 outliers final: 29 residues processed: 246 average time/residue: 0.1283 time to fit residues: 45.2718 Evaluate side-chains 242 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 810 ASP Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 HIS A 527 HIS A 949 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 287 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.129428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.098309 restraints weight = 24543.112| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.98 r_work: 0.3369 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14784 Z= 0.128 Angle : 0.510 9.006 20210 Z= 0.270 Chirality : 0.039 0.201 2167 Planarity : 0.004 0.048 2453 Dihedral : 14.448 59.935 2290 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.01 % Allowed : 10.61 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1650 helix: 1.76 (0.21), residues: 670 sheet: -0.83 (0.34), residues: 217 loop : -0.05 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 534 TYR 0.025 0.001 TYR C 432 PHE 0.030 0.001 PHE A 591 TRP 0.015 0.001 TRP B 241 HIS 0.004 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14784) covalent geometry : angle 0.51032 / 0.27 (20210) hydrogen bonds : bond 0.03412 / 2.31 ( 652) hydrogen bonds : angle 4.34464 / 3.07 ( 1797) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7468 (tttp) cc_final: 0.7001 (ptpt) REVERT: A 112 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7675 (ptt-90) REVERT: A 168 GLU cc_start: 0.7413 (tt0) cc_final: 0.6957 (tp30) REVERT: A 221 GLN cc_start: 0.8473 (mt0) cc_final: 0.8228 (mm-40) REVERT: A 357 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6509 (mm-30) REVERT: A 466 TRP cc_start: 0.8277 (m-90) cc_final: 0.8015 (m-90) REVERT: A 726 TRP cc_start: 0.7371 (m-90) cc_final: 0.6947 (m-90) REVERT: A 1032 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: A 1086 TYR cc_start: 0.8148 (t80) cc_final: 0.7900 (t80) REVERT: A 1169 LYS cc_start: 0.8966 (tttt) cc_final: 0.8620 (ttmt) REVERT: A 1184 MET cc_start: 0.8501 (mmm) cc_final: 0.8183 (mmm) REVERT: A 1210 GLU cc_start: 0.8645 (tt0) cc_final: 0.8285 (pm20) REVERT: B 180 LYS cc_start: 0.7930 (ptmt) cc_final: 0.7504 (mmtt) REVERT: B 203 ARG cc_start: 0.8392 (ttm110) cc_final: 0.7975 (mtm110) REVERT: B 280 ASP cc_start: 0.7805 (t0) cc_final: 0.7458 (t0) REVERT: B 285 LYS cc_start: 0.8506 (mttp) cc_final: 0.8104 (mttm) REVERT: B 308 ASP cc_start: 0.6970 (p0) cc_final: 0.6615 (p0) REVERT: B 321 LYS cc_start: 0.7967 (mttt) cc_final: 0.7731 (mtmt) REVERT: B 394 GLU cc_start: 0.7325 (tp30) cc_final: 0.7058 (tp30) REVERT: C 191 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7829 (mt-10) REVERT: C 253 ASP cc_start: 0.7783 (m-30) cc_final: 0.7546 (m-30) REVERT: C 301 GLU cc_start: 0.8070 (tt0) cc_final: 0.7646 (tp30) REVERT: C 396 ARG cc_start: 0.7111 (tpp-160) cc_final: 0.6748 (mpt180) REVERT: C 421 MET cc_start: 0.8100 (ppp) cc_final: 0.7529 (ppp) REVERT: C 457 SER cc_start: 0.6979 (m) cc_final: 0.6560 (p) REVERT: C 462 MET cc_start: 0.7970 (mmt) cc_final: 0.7642 (mmm) REVERT: C 465 MET cc_start: 0.7786 (mtt) cc_final: 0.7289 (mtp) REVERT: C 477 LYS cc_start: 0.8425 (ttpt) cc_final: 0.7967 (ttmm) outliers start: 44 outliers final: 30 residues processed: 249 average time/residue: 0.1362 time to fit residues: 48.7538 Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.128030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.096598 restraints weight = 24464.500| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.02 r_work: 0.3338 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14784 Z= 0.192 Angle : 0.545 8.592 20210 Z= 0.285 Chirality : 0.041 0.220 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.469 59.637 2290 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.87 % Allowed : 11.23 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1650 helix: 1.65 (0.20), residues: 676 sheet: -0.82 (0.34), residues: 222 loop : -0.14 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 325 TYR 0.022 0.002 TYR C 432 PHE 0.026 0.002 PHE A 591 TRP 0.014 0.001 TRP B 241 HIS 0.006 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (14784) covalent geometry : angle 0.54547 / 0.29 (20210) hydrogen bonds : bond 0.03629 / 2.44 ( 652) hydrogen bonds : angle 4.36406 / 3.10 ( 1797) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7642 (ptt-90) REVERT: A 168 GLU cc_start: 0.7427 (tt0) cc_final: 0.6936 (tp30) REVERT: A 221 GLN cc_start: 0.8482 (mt0) cc_final: 0.8179 (mm-40) REVERT: A 357 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6468 (mm-30) REVERT: A 466 TRP cc_start: 0.8361 (m-90) cc_final: 0.8034 (m-90) REVERT: A 539 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8535 (tt) REVERT: A 638 ARG cc_start: 0.7613 (mtm110) cc_final: 0.7362 (mtm110) REVERT: A 726 TRP cc_start: 0.7304 (m-90) cc_final: 0.6924 (m-90) REVERT: A 1032 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 1090 MET cc_start: 0.8294 (mtp) cc_final: 0.8020 (mtm) REVERT: A 1169 LYS cc_start: 0.8967 (tttt) cc_final: 0.8613 (ttmt) REVERT: A 1184 MET cc_start: 0.8500 (mmm) cc_final: 0.8171 (mmm) REVERT: A 1210 GLU cc_start: 0.8673 (tt0) cc_final: 0.8263 (pm20) REVERT: B 180 LYS cc_start: 0.7866 (ptmt) cc_final: 0.7531 (mmtm) REVERT: B 203 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7976 (mtm110) REVERT: B 280 ASP cc_start: 0.7856 (t0) cc_final: 0.7450 (t0) REVERT: B 285 LYS cc_start: 0.8491 (mttp) cc_final: 0.8073 (mttm) REVERT: B 308 ASP cc_start: 0.6900 (p0) cc_final: 0.6518 (p0) REVERT: B 321 LYS cc_start: 0.7930 (mttt) cc_final: 0.7698 (mtmt) REVERT: B 325 ARG cc_start: 0.7993 (mtm110) cc_final: 0.7697 (mtm110) REVERT: B 394 GLU cc_start: 0.7297 (tp30) cc_final: 0.6995 (tp30) REVERT: C 253 ASP cc_start: 0.7807 (m-30) cc_final: 0.7566 (m-30) REVERT: C 301 GLU cc_start: 0.8116 (tt0) cc_final: 0.7611 (tp30) REVERT: C 396 ARG cc_start: 0.7024 (tpp-160) cc_final: 0.6687 (mpt180) REVERT: C 421 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7493 (ppp) REVERT: C 457 SER cc_start: 0.6997 (m) cc_final: 0.6566 (p) REVERT: C 462 MET cc_start: 0.7958 (mmt) cc_final: 0.7628 (mmm) REVERT: C 465 MET cc_start: 0.7745 (mtt) cc_final: 0.7247 (mtp) REVERT: C 477 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7935 (ttmm) outliers start: 42 outliers final: 32 residues processed: 241 average time/residue: 0.1192 time to fit residues: 41.1184 Evaluate side-chains 242 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 32 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 949 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.131777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102551 restraints weight = 24116.839| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.74 r_work: 0.3475 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14784 Z= 0.125 Angle : 0.512 8.361 20210 Z= 0.270 Chirality : 0.039 0.208 2167 Planarity : 0.004 0.050 2453 Dihedral : 14.401 59.483 2290 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.74 % Allowed : 11.50 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.21), residues: 1650 helix: 1.71 (0.20), residues: 676 sheet: -0.70 (0.35), residues: 211 loop : -0.03 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.019 0.001 TYR B 315 PHE 0.021 0.001 PHE A 591 TRP 0.016 0.001 TRP B 241 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (14784) covalent geometry : angle 0.51246 / 0.27 (20210) hydrogen bonds : bond 0.03351 / 2.28 ( 652) hydrogen bonds : angle 4.27608 / 3.02 ( 1797) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7463 (tttp) cc_final: 0.6991 (ptpt) REVERT: A 112 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7634 (ptt-90) REVERT: A 168 GLU cc_start: 0.7368 (tt0) cc_final: 0.6876 (tp30) REVERT: A 221 GLN cc_start: 0.8402 (mt0) cc_final: 0.8145 (mm-40) REVERT: A 357 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6477 (mm-30) REVERT: A 466 TRP cc_start: 0.8325 (m-90) cc_final: 0.7985 (m-90) REVERT: A 539 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8479 (tt) REVERT: A 638 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7169 (mtm110) REVERT: A 726 TRP cc_start: 0.7277 (m-90) cc_final: 0.6896 (m-90) REVERT: A 1032 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: A 1169 LYS cc_start: 0.8923 (tttt) cc_final: 0.8576 (ttmt) REVERT: A 1184 MET cc_start: 0.8506 (mmm) cc_final: 0.8190 (mmm) REVERT: A 1210 GLU cc_start: 0.8643 (tt0) cc_final: 0.8276 (pm20) REVERT: B 180 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7521 (mmtm) REVERT: B 203 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7940 (mtm110) REVERT: B 280 ASP cc_start: 0.7862 (t0) cc_final: 0.7480 (t0) REVERT: B 285 LYS cc_start: 0.8466 (mttp) cc_final: 0.8040 (mttm) REVERT: B 308 ASP cc_start: 0.6902 (p0) cc_final: 0.6542 (p0) REVERT: B 321 LYS cc_start: 0.7930 (mttt) cc_final: 0.7704 (mtmt) REVERT: B 325 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7700 (mtm110) REVERT: B 394 GLU cc_start: 0.7302 (tp30) cc_final: 0.7005 (tp30) REVERT: B 408 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8294 (mp0) REVERT: C 301 GLU cc_start: 0.8089 (tt0) cc_final: 0.7589 (tp30) REVERT: C 396 ARG cc_start: 0.7080 (tpp-160) cc_final: 0.6735 (mpt180) REVERT: C 421 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7524 (ppp) REVERT: C 457 SER cc_start: 0.7007 (m) cc_final: 0.6572 (p) REVERT: C 462 MET cc_start: 0.7927 (mmt) cc_final: 0.7599 (mmm) REVERT: C 465 MET cc_start: 0.7688 (mtt) cc_final: 0.7200 (mtp) REVERT: C 477 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7903 (ttmm) outliers start: 40 outliers final: 31 residues processed: 241 average time/residue: 0.1270 time to fit residues: 44.1029 Evaluate side-chains 243 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 712 HIS Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 0.0010 chunk 115 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.103384 restraints weight = 23982.122| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.77 r_work: 0.3470 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14784 Z= 0.119 Angle : 0.510 7.837 20210 Z= 0.268 Chirality : 0.039 0.215 2167 Planarity : 0.004 0.050 2453 Dihedral : 14.327 59.831 2290 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.60 % Allowed : 12.05 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.21), residues: 1650 helix: 1.73 (0.21), residues: 683 sheet: -0.66 (0.35), residues: 211 loop : -0.03 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.019 0.001 TYR B 315 PHE 0.019 0.001 PHE A 939 TRP 0.016 0.001 TRP B 241 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (14784) covalent geometry : angle 0.50983 / 0.27 (20210) hydrogen bonds : bond 0.03197 / 2.18 ( 652) hydrogen bonds : angle 4.18165 / 2.95 ( 1797) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7460 (tttp) cc_final: 0.6989 (ptpt) REVERT: A 112 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7624 (ptt-90) REVERT: A 168 GLU cc_start: 0.7432 (tt0) cc_final: 0.6898 (tp30) REVERT: A 221 GLN cc_start: 0.8414 (mt0) cc_final: 0.8161 (mm-40) REVERT: A 357 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6469 (mm-30) REVERT: A 466 TRP cc_start: 0.8292 (m-90) cc_final: 0.7934 (m-90) REVERT: A 539 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8519 (tt) REVERT: A 638 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7348 (mtm110) REVERT: A 726 TRP cc_start: 0.7260 (m-90) cc_final: 0.6859 (m-90) REVERT: A 1032 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: A 1169 LYS cc_start: 0.8933 (tttt) cc_final: 0.8597 (ttmt) REVERT: A 1184 MET cc_start: 0.8505 (mmm) cc_final: 0.8187 (mmm) REVERT: A 1210 GLU cc_start: 0.8650 (tt0) cc_final: 0.8275 (pm20) REVERT: B 180 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7531 (mmtm) REVERT: B 191 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7554 (tm-30) REVERT: B 203 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7935 (mtm110) REVERT: B 280 ASP cc_start: 0.7855 (t0) cc_final: 0.7480 (t0) REVERT: B 285 LYS cc_start: 0.8482 (mttp) cc_final: 0.8033 (mttm) REVERT: B 308 ASP cc_start: 0.6878 (p0) cc_final: 0.6529 (p0) REVERT: B 321 LYS cc_start: 0.7922 (mttt) cc_final: 0.7697 (mtmt) REVERT: B 394 GLU cc_start: 0.7345 (tp30) cc_final: 0.7033 (tp30) REVERT: C 301 GLU cc_start: 0.8088 (tt0) cc_final: 0.7601 (tp30) REVERT: C 396 ARG cc_start: 0.7049 (tpp-160) cc_final: 0.6709 (mpt180) REVERT: C 421 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7571 (ppp) REVERT: C 457 SER cc_start: 0.7013 (m) cc_final: 0.6581 (p) REVERT: C 462 MET cc_start: 0.7918 (mmt) cc_final: 0.7592 (mmm) REVERT: C 465 MET cc_start: 0.7640 (mtt) cc_final: 0.7174 (mtp) REVERT: C 477 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7933 (ttmm) outliers start: 38 outliers final: 28 residues processed: 238 average time/residue: 0.1267 time to fit residues: 43.1136 Evaluate side-chains 239 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 287 ASN Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 144 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 124 optimal weight: 0.0970 chunk 32 optimal weight: 0.2980 chunk 139 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 781 ASN ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.133593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103698 restraints weight = 24322.149| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.89 r_work: 0.3482 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14784 Z= 0.112 Angle : 0.504 7.739 20210 Z= 0.266 Chirality : 0.038 0.219 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.293 59.446 2290 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.40 % Allowed : 12.25 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1650 helix: 1.76 (0.21), residues: 683 sheet: -0.73 (0.34), residues: 220 loop : -0.01 (0.24), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 325 TYR 0.018 0.001 TYR B 315 PHE 0.022 0.001 PHE A 591 TRP 0.015 0.001 TRP B 241 HIS 0.003 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14784) covalent geometry : angle 0.50394 / 0.27 (20210) hydrogen bonds : bond 0.03131 / 2.14 ( 652) hydrogen bonds : angle 4.15570 / 2.92 ( 1797) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7460 (tttp) cc_final: 0.6985 (ptpt) REVERT: A 112 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7634 (ptt-90) REVERT: A 168 GLU cc_start: 0.7445 (tt0) cc_final: 0.6921 (tp30) REVERT: A 221 GLN cc_start: 0.8415 (mt0) cc_final: 0.8159 (mm-40) REVERT: A 357 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6455 (mm-30) REVERT: A 466 TRP cc_start: 0.8267 (m-90) cc_final: 0.7896 (m-90) REVERT: A 539 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (tt) REVERT: A 638 ARG cc_start: 0.7606 (mtm110) cc_final: 0.7337 (mtm110) REVERT: A 726 TRP cc_start: 0.7283 (m-90) cc_final: 0.6930 (m-90) REVERT: A 1032 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: A 1094 MET cc_start: 0.8474 (mmm) cc_final: 0.8249 (mmm) REVERT: A 1169 LYS cc_start: 0.8931 (tttt) cc_final: 0.8590 (ttmt) REVERT: A 1184 MET cc_start: 0.8492 (mmm) cc_final: 0.8166 (mmm) REVERT: A 1210 GLU cc_start: 0.8646 (tt0) cc_final: 0.8272 (pm20) REVERT: B 180 LYS cc_start: 0.7869 (ptmt) cc_final: 0.7529 (mmtm) REVERT: B 191 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7607 (tm-30) REVERT: B 203 ARG cc_start: 0.8343 (ttm110) cc_final: 0.8024 (mtm110) REVERT: B 280 ASP cc_start: 0.7851 (t0) cc_final: 0.7475 (t0) REVERT: B 285 LYS cc_start: 0.8468 (mttp) cc_final: 0.8010 (mttm) REVERT: B 308 ASP cc_start: 0.6868 (p0) cc_final: 0.6518 (p0) REVERT: B 321 LYS cc_start: 0.7918 (mttt) cc_final: 0.7685 (mtmt) REVERT: B 394 GLU cc_start: 0.7349 (tp30) cc_final: 0.7032 (tp30) REVERT: C 122 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7986 (mmt180) REVERT: C 216 HIS cc_start: 0.7121 (m170) cc_final: 0.6578 (m-70) REVERT: C 301 GLU cc_start: 0.8101 (tt0) cc_final: 0.7580 (tp30) REVERT: C 396 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6722 (mpt180) REVERT: C 421 MET cc_start: 0.8187 (ppp) cc_final: 0.7600 (ppp) REVERT: C 457 SER cc_start: 0.7014 (m) cc_final: 0.6577 (p) REVERT: C 462 MET cc_start: 0.7908 (mmt) cc_final: 0.7581 (mmm) REVERT: C 465 MET cc_start: 0.7644 (mtt) cc_final: 0.7211 (mtp) REVERT: C 477 LYS cc_start: 0.8353 (ttpt) cc_final: 0.7922 (ttmm) outliers start: 35 outliers final: 28 residues processed: 236 average time/residue: 0.1279 time to fit residues: 42.8552 Evaluate side-chains 239 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 208 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.131540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.101951 restraints weight = 24047.734| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.80 r_work: 0.3460 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14784 Z= 0.163 Angle : 0.541 7.642 20210 Z= 0.283 Chirality : 0.040 0.243 2167 Planarity : 0.004 0.050 2453 Dihedral : 14.318 59.558 2290 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.33 % Allowed : 12.32 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.21), residues: 1650 helix: 1.69 (0.21), residues: 684 sheet: -0.92 (0.33), residues: 224 loop : -0.06 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 325 TYR 0.020 0.001 TYR B 315 PHE 0.020 0.002 PHE A 939 TRP 0.013 0.001 TRP C 241 HIS 0.007 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (14784) covalent geometry : angle 0.54088 / 0.28 (20210) hydrogen bonds : bond 0.03381 / 2.29 ( 652) hydrogen bonds : angle 4.19929 / 2.96 ( 1797) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3300 Ramachandran restraints generated. 1650 Oldfield, 0 Emsley, 1650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7455 (tttp) cc_final: 0.6982 (ptpt) REVERT: A 112 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7696 (ptt-90) REVERT: A 168 GLU cc_start: 0.7499 (tt0) cc_final: 0.6977 (tp30) REVERT: A 221 GLN cc_start: 0.8429 (mt0) cc_final: 0.8158 (mm-40) REVERT: A 357 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6476 (mm-30) REVERT: A 371 PHE cc_start: 0.8331 (t80) cc_final: 0.7976 (t80) REVERT: A 466 TRP cc_start: 0.8327 (m-90) cc_final: 0.7962 (m-90) REVERT: A 539 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 638 ARG cc_start: 0.7628 (mtm110) cc_final: 0.7365 (mtm110) REVERT: A 726 TRP cc_start: 0.7285 (m-90) cc_final: 0.6933 (m-90) REVERT: A 1032 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: A 1169 LYS cc_start: 0.8922 (tttt) cc_final: 0.8582 (ttmt) REVERT: A 1184 MET cc_start: 0.8506 (mmm) cc_final: 0.8168 (mmm) REVERT: A 1210 GLU cc_start: 0.8672 (tt0) cc_final: 0.8280 (pm20) REVERT: B 180 LYS cc_start: 0.7900 (ptmt) cc_final: 0.7553 (mmtm) REVERT: B 191 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7604 (tm-30) REVERT: B 203 ARG cc_start: 0.8329 (ttm110) cc_final: 0.8023 (mtm110) REVERT: B 280 ASP cc_start: 0.7891 (t0) cc_final: 0.7502 (t0) REVERT: B 285 LYS cc_start: 0.8479 (mttp) cc_final: 0.8014 (mttm) REVERT: B 308 ASP cc_start: 0.6907 (p0) cc_final: 0.6551 (p0) REVERT: B 321 LYS cc_start: 0.7920 (mttt) cc_final: 0.7687 (mtmt) REVERT: B 394 GLU cc_start: 0.7359 (tp30) cc_final: 0.7031 (tp30) REVERT: C 301 GLU cc_start: 0.8120 (tt0) cc_final: 0.7591 (tp30) REVERT: C 396 ARG cc_start: 0.7071 (tpp-160) cc_final: 0.6733 (mpt180) REVERT: C 421 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7591 (ppp) REVERT: C 457 SER cc_start: 0.7010 (m) cc_final: 0.6570 (p) REVERT: C 462 MET cc_start: 0.7938 (mmt) cc_final: 0.7604 (mmm) REVERT: C 465 MET cc_start: 0.7615 (mtt) cc_final: 0.7144 (mtt) REVERT: C 477 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7932 (ttmm) outliers start: 34 outliers final: 29 residues processed: 229 average time/residue: 0.1408 time to fit residues: 45.8666 Evaluate side-chains 239 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP Chi-restraints excluded: chain A residue 1032 GLU Chi-restraints excluded: chain A residue 1112 HIS Chi-restraints excluded: chain A residue 1142 PHE Chi-restraints excluded: chain A residue 1182 THR Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 96 HIS Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 421 MET Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 446 THR Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 460 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 30.0000 chunk 27 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 527 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103049 restraints weight = 24028.619| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.85 r_work: 0.3474 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14784 Z= 0.116 Angle : 0.520 7.717 20210 Z= 0.274 Chirality : 0.039 0.222 2167 Planarity : 0.004 0.048 2453 Dihedral : 14.277 59.586 2290 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.19 % Allowed : 12.25 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1650 helix: 1.75 (0.21), residues: 682 sheet: -0.91 (0.33), residues: 216 loop : -0.05 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 325 TYR 0.018 0.001 TYR B 315 PHE 0.035 0.001 PHE A 591 TRP 0.016 0.001 TRP B 241 HIS 0.004 0.001 HIS B 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (14784) covalent geometry : angle 0.51955 / 0.27 (20210) hydrogen bonds : bond 0.03175 / 2.17 ( 652) hydrogen bonds : angle 4.14738 / 2.91 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.17 seconds wall clock time: 60 minutes 50.13 seconds (3650.13 seconds total)