Starting phenix.real_space_refine on Fri Jul 3 13:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ibz_52819/07_2026/9ibz_52819.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ibz_52819/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ibz_52819/07_2026/9ibz_52819.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ibz_52819/07_2026/9ibz_52819.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ibz_52819/07_2026/9ibz_52819.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ibz_52819/07_2026/9ibz_52819.map" } 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-dev-6108/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, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'DCP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Time building chain proxies: 3.34, per 1000 atoms: 0.23 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: 1.10 Conformation dependent library (CDL) restraints added in 612.6 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: 1.81 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: 2.86 Time building geometry restraints manager: 1.50 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: 1.990 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.610 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- 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 : 0.495 12.188 20210 Z= 0.317 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 0.49518 / 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 : 0.545 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: 0.8002 (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: 0.1379 time to fit residues: 68.2502 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 : 0.553 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.129361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098025 restraints weight = 24196.609| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.01 r_work: 0.3373 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14784 Z= 0.153 Angle : 0.562 8.183 20210 Z= 0.299 Chirality : 0.040 0.156 2167 Planarity : 0.004 0.046 2453 Dihedral : 14.485 59.794 2298 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.76 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: -0.71 (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 A 638 TYR 0.024 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 0.00335 / 0.15 (14784) covalent geometry : angle 0.56229 / 0.30 (20210) hydrogen bonds : bond 0.04502 / 2.99 ( 652) hydrogen bonds : angle 4.96570 / 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 271 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.533 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: 0.7851 (mtm110) cc_final: 0.7398 (ttp-110) REVERT: A 168 GLU cc_start: 0.7428 (tt0) cc_final: 0.7012 (tp30) REVERT: A 221 GLN cc_start: 0.8399 (mt0) cc_final: 0.8165 (mm-40) REVERT: A 357 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6549 (mm-30) REVERT: A 466 TRP cc_start: 0.8447 (m-90) cc_final: 0.8007 (m-90) REVERT: A 562 ASP cc_start: 0.8845 (m-30) cc_final: 0.8469 (p0) REVERT: A 726 TRP cc_start: 0.7508 (m-90) cc_final: 0.6887 (m-90) REVERT: A 945 MET cc_start: 0.5690 (mtm) cc_final: 0.5414 (mtm) REVERT: A 1086 TYR cc_start: 0.8160 (t80) cc_final: 0.7911 (t80) REVERT: A 1090 MET cc_start: 0.8539 (mtt) cc_final: 0.8309 (mtp) REVERT: A 1169 LYS cc_start: 0.8972 (tttt) cc_final: 0.8612 (ttmt) REVERT: A 1184 MET cc_start: 0.8526 (mmm) cc_final: 0.8178 (mmm) REVERT: A 1210 GLU cc_start: 0.8671 (tt0) cc_final: 0.8299 (pm20) REVERT: B 180 LYS cc_start: 0.7965 (ptmt) cc_final: 0.7486 (mptt) REVERT: B 203 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8117 (mtm110) REVERT: B 280 ASP cc_start: 0.7900 (t0) cc_final: 0.7429 (t0) REVERT: B 285 LYS cc_start: 0.8562 (mttp) cc_final: 0.8146 (mttm) REVERT: B 308 ASP cc_start: 0.7034 (p0) cc_final: 0.6623 (p0) REVERT: B 321 LYS cc_start: 0.7965 (mttt) cc_final: 0.7709 (mtmt) REVERT: B 394 GLU cc_start: 0.7303 (tp30) cc_final: 0.7011 (tp30) REVERT: B 408 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8449 (mp0) REVERT: C 180 LYS cc_start: 0.8372 (tttt) cc_final: 0.8135 (tttp) REVERT: C 248 SER cc_start: 0.8314 (p) cc_final: 0.8080 (t) REVERT: C 301 GLU cc_start: 0.7995 (tt0) cc_final: 0.7589 (tp30) REVERT: C 396 ARG cc_start: 0.6888 (tpp-160) cc_final: 0.6600 (mpt180) REVERT: C 419 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7522 (mt-10) REVERT: C 457 SER cc_start: 0.7028 (m) cc_final: 0.6575 (p) REVERT: C 462 MET cc_start: 0.7931 (mmt) cc_final: 0.7598 (mmm) REVERT: C 465 MET cc_start: 0.7785 (mtt) cc_final: 0.7258 (mtp) REVERT: C 477 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8024 (ttmm) outliers start: 33 outliers final: 24 residues processed: 261 average time/residue: 0.1363 time to fit residues: 50.7377 Evaluate side-chains 237 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 3.9990 chunk 156 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3974 r_free = 0.3974 target = 0.128481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098447 restraints weight = 24542.436| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.89 r_work: 0.3340 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14784 Z= 0.177 Angle : 0.551 7.512 20210 Z= 0.291 Chirality : 0.041 0.200 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.585 59.864 2295 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.81 % Allowed : 9.79 % Favored : 87.41 % 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: 0.60 (0.21), residues: 1650 helix: 1.52 (0.20), residues: 667 sheet: -0.97 (0.35), residues: 212 loop : -0.09 (0.23), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 638 TYR 0.038 0.002 TYR C 432 PHE 0.022 0.002 PHE C 254 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 0.00403 / 0.18 (14784) covalent geometry : angle 0.55056 / 0.29 (20210) hydrogen bonds : bond 0.04009 / 2.69 ( 652) hydrogen bonds : angle 4.67444 / 3.32 ( 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 269 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 228 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7565 (ptt-90) REVERT: A 168 GLU cc_start: 0.7378 (tt0) cc_final: 0.6896 (tp30) REVERT: A 176 ARG cc_start: 0.8538 (mtp-110) cc_final: 0.8330 (mtp85) REVERT: A 221 GLN cc_start: 0.8459 (mt0) cc_final: 0.8197 (mm-40) REVERT: A 357 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6458 (mm-30) REVERT: A 726 TRP cc_start: 0.7402 (m-90) cc_final: 0.6689 (m-90) REVERT: A 1086 TYR cc_start: 0.8138 (t80) cc_final: 0.7856 (t80) REVERT: A 1090 MET cc_start: 0.8487 (mtt) cc_final: 0.8285 (mtp) REVERT: A 1169 LYS cc_start: 0.8973 (tttt) cc_final: 0.8604 (ttmt) REVERT: A 1184 MET cc_start: 0.8499 (mmm) cc_final: 0.8191 (mmm) REVERT: A 1210 GLU cc_start: 0.8708 (tt0) cc_final: 0.8288 (pm20) REVERT: B 180 LYS cc_start: 0.7864 (ptmt) cc_final: 0.7474 (mmtm) REVERT: B 203 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8017 (mtm110) REVERT: B 280 ASP cc_start: 0.7965 (t0) cc_final: 0.7486 (t0) REVERT: B 285 LYS cc_start: 0.8553 (mttp) cc_final: 0.8127 (mttm) REVERT: B 308 ASP cc_start: 0.6949 (p0) cc_final: 0.6564 (p0) REVERT: B 321 LYS cc_start: 0.7951 (mttt) cc_final: 0.7694 (mtmt) REVERT: B 394 GLU cc_start: 0.7173 (tp30) cc_final: 0.6908 (tp30) REVERT: C 180 LYS cc_start: 0.8329 (tttt) cc_final: 0.8101 (tttp) REVERT: C 199 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8066 (mt) REVERT: C 301 GLU cc_start: 0.8036 (tt0) cc_final: 0.7568 (tp30) REVERT: C 396 ARG cc_start: 0.6909 (tpp-160) cc_final: 0.6595 (mpt180) REVERT: C 421 MET cc_start: 0.8023 (ppp) cc_final: 0.7521 (ppp) REVERT: C 437 ILE cc_start: 0.4871 (OUTLIER) cc_final: 0.4053 (tp) REVERT: C 457 SER cc_start: 0.6988 (m) cc_final: 0.6535 (p) REVERT: C 462 MET cc_start: 0.7971 (mmt) cc_final: 0.7638 (mmm) REVERT: C 465 MET cc_start: 0.7787 (mtt) cc_final: 0.7243 (mtp) REVERT: C 477 LYS cc_start: 0.8433 (ttpt) cc_final: 0.7993 (ttmm) outliers start: 41 outliers final: 30 residues processed: 255 average time/residue: 0.1338 time to fit residues: 48.8713 Evaluate side-chains 248 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 51 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 0.0870 chunk 93 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.129324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098377 restraints weight = 24375.331| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.97 r_work: 0.3386 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14784 Z= 0.123 Angle : 0.517 11.176 20210 Z= 0.272 Chirality : 0.039 0.197 2167 Planarity : 0.004 0.048 2453 Dihedral : 14.557 59.917 2295 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.81 % Allowed : 10.27 % Favored : 86.93 % 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: 0.75 (0.21), residues: 1650 helix: 1.66 (0.21), residues: 669 sheet: -0.85 (0.36), residues: 199 loop : -0.06 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 638 TYR 0.026 0.001 TYR C 432 PHE 0.021 0.001 PHE A 939 TRP 0.015 0.001 TRP B 241 HIS 0.005 0.001 HIS C 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14784) covalent geometry : angle 0.51741 / 0.27 (20210) hydrogen bonds : bond 0.03541 / 2.40 ( 652) hydrogen bonds : angle 4.49860 / 3.19 ( 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 266 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7440 (tttp) cc_final: 0.6983 (ptpt) REVERT: A 112 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7616 (ptt-90) REVERT: A 168 GLU cc_start: 0.7354 (tt0) cc_final: 0.6880 (tp30) REVERT: A 221 GLN cc_start: 0.8437 (mt0) cc_final: 0.8185 (mm-40) REVERT: A 357 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6421 (mm-30) REVERT: A 466 TRP cc_start: 0.8312 (m-90) cc_final: 0.8028 (m-90) REVERT: A 726 TRP cc_start: 0.7389 (m-90) cc_final: 0.6484 (m-90) REVERT: A 1086 TYR cc_start: 0.8126 (t80) cc_final: 0.7818 (t80) REVERT: A 1090 MET cc_start: 0.8463 (mtt) cc_final: 0.8260 (mtp) REVERT: A 1169 LYS cc_start: 0.8981 (tttt) cc_final: 0.8625 (ttmt) REVERT: A 1184 MET cc_start: 0.8481 (mmm) cc_final: 0.8172 (mmm) REVERT: A 1210 GLU cc_start: 0.8670 (tt0) cc_final: 0.8280 (pm20) REVERT: B 180 LYS cc_start: 0.7930 (ptmt) cc_final: 0.7484 (mmtt) REVERT: B 203 ARG cc_start: 0.8395 (ttm110) cc_final: 0.7988 (mtm110) REVERT: B 280 ASP cc_start: 0.7947 (t0) cc_final: 0.7278 (t0) REVERT: B 285 LYS cc_start: 0.8518 (mttp) cc_final: 0.8086 (mttm) REVERT: B 308 ASP cc_start: 0.6878 (p0) cc_final: 0.6493 (p0) REVERT: B 321 LYS cc_start: 0.7952 (mttt) cc_final: 0.7695 (mtmt) REVERT: B 448 LEU cc_start: 0.8565 (mt) cc_final: 0.8350 (mp) REVERT: C 180 LYS cc_start: 0.8372 (tttt) cc_final: 0.8137 (tttp) REVERT: C 191 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 301 GLU cc_start: 0.8045 (tt0) cc_final: 0.7586 (tp30) REVERT: C 396 ARG cc_start: 0.6998 (tpp-160) cc_final: 0.6649 (mpt180) REVERT: C 421 MET cc_start: 0.7962 (ppp) cc_final: 0.7410 (ppp) REVERT: C 457 SER cc_start: 0.7010 (m) cc_final: 0.6589 (p) REVERT: C 462 MET cc_start: 0.7969 (mmt) cc_final: 0.7636 (mmm) REVERT: C 465 MET cc_start: 0.7754 (mtt) cc_final: 0.7228 (mtp) REVERT: C 477 LYS cc_start: 0.8421 (ttpt) cc_final: 0.7964 (ttmm) outliers start: 41 outliers final: 30 residues processed: 249 average time/residue: 0.1351 time to fit residues: 48.2704 Evaluate side-chains 243 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 213 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 931 ARG 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 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 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: 3.9990 chunk 78 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.129336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098712 restraints weight = 24380.566| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.93 r_work: 0.3376 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14784 Z= 0.128 Angle : 0.511 9.123 20210 Z= 0.270 Chirality : 0.039 0.197 2167 Planarity : 0.004 0.048 2453 Dihedral : 14.534 59.821 2294 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.08 % Allowed : 10.13 % Favored : 86.79 % 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: 0.77 (0.21), residues: 1650 helix: 1.66 (0.20), residues: 676 sheet: -0.84 (0.34), residues: 217 loop : -0.03 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 638 TYR 0.026 0.001 TYR C 432 PHE 0.031 0.001 PHE A 591 TRP 0.014 0.001 TRP B 241 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14784) covalent geometry : angle 0.51114 / 0.27 (20210) hydrogen bonds : bond 0.03433 / 2.33 ( 652) hydrogen bonds : angle 4.39721 / 3.11 ( 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 274 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7456 (tttp) cc_final: 0.6993 (ptpt) REVERT: A 112 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7602 (ptt-90) REVERT: A 168 GLU cc_start: 0.7360 (tt0) cc_final: 0.6904 (tp30) REVERT: A 221 GLN cc_start: 0.8439 (mt0) cc_final: 0.8185 (mm-40) REVERT: A 357 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6495 (mm-30) REVERT: A 466 TRP cc_start: 0.8269 (m-90) cc_final: 0.8011 (m-90) REVERT: A 638 ARG cc_start: 0.7103 (mtm-85) cc_final: 0.6796 (mtm-85) REVERT: A 726 TRP cc_start: 0.7380 (m-90) cc_final: 0.6925 (m-90) REVERT: A 1090 MET cc_start: 0.8518 (mtt) cc_final: 0.8312 (mtm) REVERT: A 1169 LYS cc_start: 0.8966 (tttt) cc_final: 0.8621 (ttmt) REVERT: A 1184 MET cc_start: 0.8496 (mmm) cc_final: 0.8189 (mmm) REVERT: A 1210 GLU cc_start: 0.8650 (tt0) cc_final: 0.8290 (pm20) REVERT: B 180 LYS cc_start: 0.7943 (ptmt) cc_final: 0.7572 (mmtm) REVERT: B 203 ARG cc_start: 0.8389 (ttm110) cc_final: 0.7981 (mtm110) REVERT: B 280 ASP cc_start: 0.7848 (t0) cc_final: 0.7477 (t0) REVERT: B 285 LYS cc_start: 0.8515 (mttp) cc_final: 0.8102 (mttm) REVERT: B 308 ASP cc_start: 0.6828 (p0) cc_final: 0.6468 (p0) REVERT: B 321 LYS cc_start: 0.7967 (mttt) cc_final: 0.7728 (mtmt) REVERT: C 180 LYS cc_start: 0.8358 (tttt) cc_final: 0.8155 (tttp) REVERT: C 191 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7561 (mt-10) REVERT: C 301 GLU cc_start: 0.8055 (tt0) cc_final: 0.7598 (tp30) REVERT: C 396 ARG cc_start: 0.7027 (tpp-160) cc_final: 0.6678 (mpt180) REVERT: C 421 MET cc_start: 0.7974 (ppp) cc_final: 0.7347 (ppp) REVERT: C 457 SER cc_start: 0.6982 (m) cc_final: 0.6561 (p) REVERT: C 462 MET cc_start: 0.7965 (mmt) cc_final: 0.7637 (mmm) REVERT: C 465 MET cc_start: 0.7777 (mtt) cc_final: 0.7263 (mtp) REVERT: C 477 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7959 (ttmm) outliers start: 45 outliers final: 32 residues processed: 255 average time/residue: 0.1390 time to fit residues: 50.5799 Evaluate side-chains 244 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 907 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 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 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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: 0.8980 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 ASN 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 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 = 0.3960 r_free = 0.3960 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098108 restraints weight = 24351.717| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.91 r_work: 0.3324 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14784 Z= 0.209 Angle : 0.557 8.451 20210 Z= 0.292 Chirality : 0.041 0.221 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.576 59.878 2294 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.94 % Allowed : 10.81 % Favored : 86.24 % 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: 0.62 (0.21), residues: 1650 helix: 1.56 (0.20), residues: 673 sheet: -0.83 (0.34), residues: 224 loop : -0.16 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 534 TYR 0.024 0.002 TYR C 432 PHE 0.024 0.002 PHE C 254 TRP 0.014 0.001 TRP B 241 HIS 0.007 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (14784) covalent geometry : angle 0.55672 / 0.29 (20210) hydrogen bonds : bond 0.03761 / 2.53 ( 652) hydrogen bonds : angle 4.45685 / 3.17 ( 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 263 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.549 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: 0.7966 (mtm110) cc_final: 0.7628 (ptt-90) REVERT: A 168 GLU cc_start: 0.7405 (tt0) cc_final: 0.6885 (tp30) REVERT: A 221 GLN cc_start: 0.8483 (mt0) cc_final: 0.8179 (mm-40) REVERT: A 357 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6509 (mm-30) REVERT: A 466 TRP cc_start: 0.8375 (m-90) cc_final: 0.8053 (m-90) REVERT: A 539 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8497 (tt) REVERT: A 726 TRP cc_start: 0.7351 (m-90) cc_final: 0.6972 (m-90) REVERT: A 1169 LYS cc_start: 0.8967 (tttt) cc_final: 0.8622 (ttmt) REVERT: A 1184 MET cc_start: 0.8513 (mmm) cc_final: 0.8207 (mmm) REVERT: A 1210 GLU cc_start: 0.8666 (tt0) cc_final: 0.8238 (pm20) REVERT: B 180 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7556 (mmtm) REVERT: B 203 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8005 (mtm110) REVERT: B 280 ASP cc_start: 0.7892 (t0) cc_final: 0.7484 (t0) REVERT: B 285 LYS cc_start: 0.8518 (mttp) cc_final: 0.8084 (mttm) REVERT: B 308 ASP cc_start: 0.6826 (p0) cc_final: 0.6455 (p0) REVERT: B 321 LYS cc_start: 0.7945 (mttt) cc_final: 0.7705 (mtmt) REVERT: C 180 LYS cc_start: 0.8306 (tttt) cc_final: 0.8057 (tttp) REVERT: C 253 ASP cc_start: 0.7808 (m-30) cc_final: 0.7571 (m-30) REVERT: C 301 GLU cc_start: 0.8128 (tt0) cc_final: 0.7615 (tp30) REVERT: C 396 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6661 (mpt180) REVERT: C 421 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7366 (ppp) REVERT: C 457 SER cc_start: 0.7017 (m) cc_final: 0.6593 (p) REVERT: C 462 MET cc_start: 0.7970 (mmt) cc_final: 0.7640 (mmm) REVERT: C 465 MET cc_start: 0.7763 (mtt) cc_final: 0.7258 (mtp) REVERT: C 477 LYS cc_start: 0.8390 (ttpt) cc_final: 0.7945 (ttmm) outliers start: 43 outliers final: 31 residues processed: 247 average time/residue: 0.1370 time to fit residues: 48.4091 Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 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 931 ARG Chi-restraints excluded: chain A residue 966 VAL 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 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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 387 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 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: 1.9990 chunk 74 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 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 305 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.132213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.102582 restraints weight = 24307.712| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.77 r_work: 0.3461 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14784 Z= 0.126 Angle : 0.521 8.356 20210 Z= 0.274 Chirality : 0.039 0.207 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.481 59.454 2294 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.81 % Allowed : 10.81 % 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: 0.76 (0.21), residues: 1650 helix: 1.61 (0.20), residues: 682 sheet: -0.73 (0.35), residues: 211 loop : -0.06 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 638 TYR 0.024 0.001 TYR C 432 PHE 0.020 0.001 PHE A 939 TRP 0.014 0.001 TRP B 241 HIS 0.004 0.001 HIS A 783 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (14784) covalent geometry : angle 0.52121 / 0.27 (20210) hydrogen bonds : bond 0.03407 / 2.32 ( 652) hydrogen bonds : angle 4.33457 / 3.07 ( 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 262 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7463 (tttp) cc_final: 0.6992 (ptpt) REVERT: A 112 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7617 (ptt-90) REVERT: A 168 GLU cc_start: 0.7376 (tt0) cc_final: 0.6885 (tp30) REVERT: A 221 GLN cc_start: 0.8410 (mt0) cc_final: 0.8148 (mm-40) REVERT: A 357 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6475 (mm-30) REVERT: A 466 TRP cc_start: 0.8312 (m-90) cc_final: 0.7992 (m-90) REVERT: A 539 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (tt) REVERT: A 638 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6676 (mtm-85) REVERT: A 726 TRP cc_start: 0.7342 (m-90) cc_final: 0.6970 (m-90) REVERT: A 1032 GLU cc_start: 0.7745 (pm20) cc_final: 0.7433 (pm20) REVERT: A 1169 LYS cc_start: 0.8929 (tttt) cc_final: 0.8591 (ttmt) REVERT: A 1184 MET cc_start: 0.8532 (mmm) cc_final: 0.8201 (mmm) REVERT: A 1210 GLU cc_start: 0.8637 (tt0) cc_final: 0.8258 (pm20) REVERT: B 180 LYS cc_start: 0.7927 (ptmt) cc_final: 0.7549 (mmtm) REVERT: B 203 ARG cc_start: 0.8378 (ttm110) cc_final: 0.7973 (mtm110) REVERT: B 280 ASP cc_start: 0.7879 (t0) cc_final: 0.7515 (t0) REVERT: B 285 LYS cc_start: 0.8491 (mttp) cc_final: 0.8051 (mttm) REVERT: B 308 ASP cc_start: 0.6844 (p0) cc_final: 0.6512 (p0) REVERT: B 321 LYS cc_start: 0.7940 (mttt) cc_final: 0.7714 (mtmt) REVERT: C 180 LYS cc_start: 0.8362 (tttt) cc_final: 0.8140 (tttp) REVERT: C 253 ASP cc_start: 0.7709 (m-30) cc_final: 0.7474 (m-30) REVERT: C 301 GLU cc_start: 0.8070 (tt0) cc_final: 0.7585 (tp30) REVERT: C 396 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.6712 (mpt180) REVERT: C 421 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7407 (ppp) REVERT: C 457 SER cc_start: 0.7008 (m) cc_final: 0.6567 (p) REVERT: C 462 MET cc_start: 0.7963 (mmt) cc_final: 0.7637 (mmm) REVERT: C 465 MET cc_start: 0.7695 (mtt) cc_final: 0.7212 (mtp) REVERT: C 477 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7915 (ttmm) outliers start: 41 outliers final: 33 residues processed: 249 average time/residue: 0.1155 time to fit residues: 41.1292 Evaluate side-chains 250 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 215 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 931 ARG Chi-restraints excluded: chain A residue 966 VAL 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 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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 285 LYS 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 407 LEU Chi-restraints excluded: chain C residue 421 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 0.1980 chunk 133 optimal weight: 0.3980 chunk 142 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 136 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.132433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103228 restraints weight = 23945.714| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.79 r_work: 0.3481 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2336 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= 0.118 Angle : 0.518 7.884 20210 Z= 0.271 Chirality : 0.039 0.212 2167 Planarity : 0.004 0.050 2453 Dihedral : 14.412 59.965 2294 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.60 % Allowed : 11.29 % Favored : 86.11 % 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: 1.69 (0.20), residues: 682 sheet: -0.73 (0.34), residues: 211 loop : -0.05 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 529 TYR 0.019 0.001 TYR C 432 PHE 0.020 0.001 PHE A 939 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 0.00259 / 0.12 (14784) covalent geometry : angle 0.51849 / 0.27 (20210) hydrogen bonds : bond 0.03302 / 2.25 ( 652) hydrogen bonds : angle 4.23455 / 3.00 ( 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 258 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7473 (tttp) cc_final: 0.7001 (ptpt) REVERT: A 112 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7638 (ptt-90) REVERT: A 168 GLU cc_start: 0.7430 (tt0) cc_final: 0.6902 (tp30) REVERT: A 221 GLN cc_start: 0.8395 (mt0) cc_final: 0.8151 (mm-40) REVERT: A 357 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6471 (mm-30) REVERT: A 466 TRP cc_start: 0.8298 (m-90) cc_final: 0.7945 (m-90) REVERT: A 539 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8464 (tt) REVERT: A 638 ARG cc_start: 0.7085 (mtm-85) cc_final: 0.6712 (mtm-85) REVERT: A 726 TRP cc_start: 0.7364 (m-90) cc_final: 0.6974 (m-90) REVERT: A 1032 GLU cc_start: 0.7730 (pm20) cc_final: 0.7408 (pm20) REVERT: A 1169 LYS cc_start: 0.8941 (tttt) cc_final: 0.8608 (ttmt) REVERT: A 1184 MET cc_start: 0.8531 (mmm) cc_final: 0.8188 (mmm) REVERT: A 1210 GLU cc_start: 0.8615 (tt0) cc_final: 0.8253 (pm20) REVERT: B 113 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8089 (mm-30) REVERT: B 180 LYS cc_start: 0.7936 (ptmt) cc_final: 0.7576 (mmtm) REVERT: B 203 ARG cc_start: 0.8374 (ttm110) cc_final: 0.7956 (mtm110) REVERT: B 280 ASP cc_start: 0.7896 (t0) cc_final: 0.7521 (t0) REVERT: B 285 LYS cc_start: 0.8503 (mttp) cc_final: 0.8068 (mttm) REVERT: B 308 ASP cc_start: 0.6812 (p0) cc_final: 0.6488 (p0) REVERT: B 321 LYS cc_start: 0.7939 (mttt) cc_final: 0.7714 (mtmt) REVERT: C 180 LYS cc_start: 0.8374 (tttt) cc_final: 0.8164 (tttp) REVERT: C 301 GLU cc_start: 0.8061 (tt0) cc_final: 0.7599 (tp30) REVERT: C 396 ARG cc_start: 0.7079 (tpp-160) cc_final: 0.6735 (mpt180) REVERT: C 421 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7451 (ppp) REVERT: C 457 SER cc_start: 0.7008 (m) cc_final: 0.6585 (p) REVERT: C 462 MET cc_start: 0.7953 (mmt) cc_final: 0.7634 (mmm) REVERT: C 465 MET cc_start: 0.7644 (mtt) cc_final: 0.7183 (mtp) REVERT: C 477 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7963 (ttmm) outliers start: 38 outliers final: 33 residues processed: 246 average time/residue: 0.1208 time to fit residues: 42.5586 Evaluate side-chains 251 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 827 THR Chi-restraints excluded: chain A residue 870 ASP 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 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 305 ASN Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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 287 ASN 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 407 LEU Chi-restraints excluded: chain C residue 421 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 124 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS A 781 ASN ** B 210 GLN ** 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 = 0.4068 r_free = 0.4068 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.102948 restraints weight = 24380.456| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.90 r_work: 0.3460 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14784 Z= 0.136 Angle : 0.530 9.194 20210 Z= 0.277 Chirality : 0.039 0.227 2167 Planarity : 0.004 0.050 2453 Dihedral : 14.385 59.918 2294 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.74 % Allowed : 11.64 % Favored : 85.63 % 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: 0.78 (0.21), residues: 1650 helix: 1.66 (0.20), residues: 683 sheet: -0.81 (0.33), residues: 218 loop : -0.04 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 325 TYR 0.020 0.001 TYR C 432 PHE 0.021 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 0.00311 / 0.14 (14784) covalent geometry : angle 0.52976 / 0.28 (20210) hydrogen bonds : bond 0.03334 / 2.27 ( 652) hydrogen bonds : angle 4.24902 / 3.01 ( 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 253 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7452 (tttp) cc_final: 0.6978 (ptpt) REVERT: A 112 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7640 (ptt-90) REVERT: A 168 GLU cc_start: 0.7454 (tt0) cc_final: 0.6922 (tp30) REVERT: A 221 GLN cc_start: 0.8421 (mt0) cc_final: 0.8156 (mm-40) REVERT: A 357 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6466 (mm-30) REVERT: A 466 TRP cc_start: 0.8292 (m-90) cc_final: 0.7960 (m-90) REVERT: A 539 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8490 (tt) REVERT: A 726 TRP cc_start: 0.7340 (m-90) cc_final: 0.6979 (m-90) REVERT: A 1032 GLU cc_start: 0.7740 (pm20) cc_final: 0.7400 (pm20) REVERT: A 1169 LYS cc_start: 0.8933 (tttt) cc_final: 0.8605 (ttmt) REVERT: A 1184 MET cc_start: 0.8513 (mmm) cc_final: 0.8161 (mmm) REVERT: A 1210 GLU cc_start: 0.8644 (tt0) cc_final: 0.8257 (pm20) REVERT: B 113 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 180 LYS cc_start: 0.7916 (ptmt) cc_final: 0.7561 (mmtm) REVERT: B 191 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 203 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8044 (mtm110) REVERT: B 280 ASP cc_start: 0.7874 (t0) cc_final: 0.7506 (t0) REVERT: B 285 LYS cc_start: 0.8500 (mttp) cc_final: 0.8059 (mttm) REVERT: B 308 ASP cc_start: 0.6769 (p0) cc_final: 0.6443 (p0) REVERT: B 321 LYS cc_start: 0.7936 (mttt) cc_final: 0.7714 (mtmt) REVERT: C 180 LYS cc_start: 0.8368 (tttt) cc_final: 0.8148 (tttp) REVERT: C 251 TRP cc_start: 0.6506 (m100) cc_final: 0.5658 (m100) REVERT: C 301 GLU cc_start: 0.8072 (tt0) cc_final: 0.7564 (tp30) REVERT: C 396 ARG cc_start: 0.7056 (tpp-160) cc_final: 0.6730 (mpt180) REVERT: C 421 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7438 (ppp) REVERT: C 457 SER cc_start: 0.7023 (m) cc_final: 0.6587 (p) REVERT: C 462 MET cc_start: 0.7932 (mmt) cc_final: 0.7607 (mmm) REVERT: C 465 MET cc_start: 0.7641 (mtt) cc_final: 0.7184 (mtp) REVERT: C 477 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7948 (ttmm) outliers start: 40 outliers final: 33 residues processed: 240 average time/residue: 0.1086 time to fit residues: 37.3803 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 : 0.309 ------------------------------------------------------------------------------- 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 827 THR Chi-restraints excluded: chain A residue 870 ASP 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 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 305 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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 387 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 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: 0.9990 chunk 75 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 90 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 HIS ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 ASN C 287 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.132564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.103174 restraints weight = 24014.227| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.88 r_work: 0.3472 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2458 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= 0.117 Angle : 0.516 8.137 20210 Z= 0.271 Chirality : 0.039 0.224 2167 Planarity : 0.004 0.049 2453 Dihedral : 14.339 59.961 2294 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.74 % Allowed : 11.43 % Favored : 85.83 % 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: 0.84 (0.21), residues: 1650 helix: 1.72 (0.20), residues: 683 sheet: -0.79 (0.33), residues: 218 loop : -0.01 (0.24), residues: 749 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 0.020 0.001 PHE A 939 TRP 0.016 0.001 TRP B 241 HIS 0.005 0.001 HIS A 527 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14784) covalent geometry : angle 0.51560 / 0.27 (20210) hydrogen bonds : bond 0.03221 / 2.20 ( 652) hydrogen bonds : angle 4.19259 / 2.97 ( 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 255 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7465 (tttp) cc_final: 0.6996 (ptpt) REVERT: A 112 ARG cc_start: 0.7992 (mtm110) cc_final: 0.7642 (ptt-90) REVERT: A 168 GLU cc_start: 0.7456 (tt0) cc_final: 0.6932 (tp30) REVERT: A 221 GLN cc_start: 0.8416 (mt0) cc_final: 0.8152 (mm-40) REVERT: A 357 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6452 (mm-30) REVERT: A 466 TRP cc_start: 0.8274 (m-90) cc_final: 0.7925 (m-90) REVERT: A 539 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 638 ARG cc_start: 0.6918 (mtm110) cc_final: 0.6561 (mtm-85) REVERT: A 726 TRP cc_start: 0.7342 (m-90) cc_final: 0.6985 (m-90) REVERT: A 945 MET cc_start: 0.6067 (mtm) cc_final: 0.5784 (mtm) REVERT: A 1032 GLU cc_start: 0.7718 (pm20) cc_final: 0.7398 (pm20) REVERT: A 1169 LYS cc_start: 0.8938 (tttt) cc_final: 0.8610 (ttmt) REVERT: A 1184 MET cc_start: 0.8505 (mmm) cc_final: 0.8150 (mmm) REVERT: A 1210 GLU cc_start: 0.8637 (tt0) cc_final: 0.8259 (pm20) REVERT: B 113 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 180 LYS cc_start: 0.7907 (ptmt) cc_final: 0.7552 (mmtm) REVERT: B 203 ARG cc_start: 0.8361 (ttm110) cc_final: 0.8039 (mtm110) REVERT: B 280 ASP cc_start: 0.7869 (t0) cc_final: 0.7484 (t0) REVERT: B 285 LYS cc_start: 0.8491 (mttp) cc_final: 0.8040 (mttm) REVERT: B 308 ASP cc_start: 0.6710 (p0) cc_final: 0.6381 (p0) REVERT: B 321 LYS cc_start: 0.7932 (mttt) cc_final: 0.7700 (mtmt) REVERT: C 180 LYS cc_start: 0.8367 (tttt) cc_final: 0.8148 (tttp) REVERT: C 301 GLU cc_start: 0.8079 (tt0) cc_final: 0.7577 (tp30) REVERT: C 396 ARG cc_start: 0.7104 (tpp-160) cc_final: 0.6739 (mpt180) REVERT: C 421 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7457 (ppp) REVERT: C 457 SER cc_start: 0.7035 (m) cc_final: 0.6596 (p) REVERT: C 462 MET cc_start: 0.7945 (mmt) cc_final: 0.7623 (mmm) REVERT: C 465 MET cc_start: 0.7630 (mtt) cc_final: 0.7156 (mtt) REVERT: C 477 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7931 (ttmm) outliers start: 40 outliers final: 35 residues processed: 241 average time/residue: 0.1227 time to fit residues: 42.2109 Evaluate side-chains 249 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 712 HIS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 870 ASP 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 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 305 ASN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain B residue 371 VAL 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 287 ASN 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 407 LEU Chi-restraints excluded: chain C residue 421 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 30.0000 chunk 27 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 38 optimal weight: 0.0870 chunk 109 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 143 optimal weight: 0.0270 chunk 108 optimal weight: 0.6980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.133162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.103205 restraints weight = 24277.192| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.93 r_work: 0.3476 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 14784 Z= 0.195 Angle : 0.794 59.184 20210 Z= 0.462 Chirality : 0.040 0.321 2167 Planarity : 0.004 0.057 2453 Dihedral : 14.340 59.967 2294 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.46 % Allowed : 11.91 % Favored : 85.63 % Cbeta Deviations : 0.06 % 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: 0.84 (0.21), residues: 1650 helix: 1.72 (0.20), residues: 683 sheet: -0.78 (0.33), residues: 218 loop : -0.01 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 325 TYR 0.017 0.001 TYR B 315 PHE 0.051 0.002 PHE A 591 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 0.00380 / 0.20 (14784) covalent geometry : angle 0.79378 / 0.46 (20210) hydrogen bonds : bond 0.03281 / 2.26 ( 652) hydrogen bonds : angle 4.21391 / 2.98 ( 1797) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.75 seconds wall clock time: 60 minutes 17.42 seconds (3617.42 seconds total)