Starting phenix.real_space_refine on Mon Nov 17 23:51:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ywd_6853/11_2025/5ywd_6853.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ywd_6853/11_2025/5ywd_6853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5ywd_6853/11_2025/5ywd_6853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ywd_6853/11_2025/5ywd_6853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ywd_6853/11_2025/5ywd_6853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ywd_6853/11_2025/5ywd_6853.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 5806 2.51 5 N 1533 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8997 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1154, 8941 Classifications: {'peptide': 1154} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 36, 'TRANS': 1117} Chain breaks: 7 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 4, 'GLU:plan': 5, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.21, per 1000 atoms: 0.25 Number of scatterers: 8997 At special positions: 0 Unit cell: (93.895, 78.07, 138.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 4 15.00 Mg 2 11.99 O 1605 8.00 N 1533 7.00 C 5806 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: 0.90 Conformation dependent library (CDL) restraints added in 288.8 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 69.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 223 through 230 removed outlier: 3.501A pdb=" N LYS B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.326A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 258 through 276 Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.600A pdb=" N TRP B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 329 Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.763A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.759A pdb=" N MET B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 439 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 440 through 457 removed outlier: 4.388A pdb=" N TYR B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 504 removed outlier: 4.497A pdb=" N GLY B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.800A pdb=" N ALA B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 3.901A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 564 removed outlier: 3.663A pdb=" N PHE B 518 " --> pdb=" O TRP B 514 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.505A pdb=" N SER B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.500A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 3.820A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS B 602 " --> pdb=" O ARG B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 783 through 790 Processing helix chain 'B' and resid 795 through 806 removed outlier: 3.686A pdb=" N LYS B 800 " --> pdb=" O LYS B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 815 Processing helix chain 'B' and resid 824 through 828 removed outlier: 3.767A pdb=" N ILE B 828 " --> pdb=" O GLU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 846 removed outlier: 3.660A pdb=" N ARG B 835 " --> pdb=" O SER B 831 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 914 through 920 Processing helix chain 'B' and resid 1000 through 1009 removed outlier: 3.505A pdb=" N TYR B1004 " --> pdb=" O ALA B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1039 removed outlier: 3.615A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.576A pdb=" N SER B1073 " --> pdb=" O THR B1069 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE B1076 " --> pdb=" O CYS B1072 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B1107 " --> pdb=" O ASN B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1116 Processing helix chain 'B' and resid 1117 through 1135 Processing helix chain 'B' and resid 1135 through 1161 Processing helix chain 'B' and resid 1163 through 1166 Processing helix chain 'B' and resid 1167 through 1210 removed outlier: 4.156A pdb=" N LEU B1171 " --> pdb=" O ALA B1167 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B1184 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Proline residue: B1199 - end of helix Processing helix chain 'B' and resid 1210 through 1218 removed outlier: 3.514A pdb=" N ILE B1214 " --> pdb=" O GLY B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1219 through 1274 removed outlier: 4.209A pdb=" N LEU B1272 " --> pdb=" O ILE B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1278 through 1320 removed outlier: 4.422A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN B1293 " --> pdb=" O LEU B1289 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B1296 " --> pdb=" O SER B1292 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B1320 " --> pdb=" O HIS B1316 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1393 Processing helix chain 'B' and resid 1414 through 1420 removed outlier: 3.629A pdb=" N LEU B1418 " --> pdb=" O PRO B1414 " (cutoff:3.500A) Processing helix chain 'B' and resid 1435 through 1441 Processing helix chain 'B' and resid 1447 through 1458 Processing helix chain 'B' and resid 1460 through 1466 removed outlier: 3.507A pdb=" N ALA B1466 " --> pdb=" O LEU B1462 " (cutoff:3.500A) Processing helix chain 'B' and resid 1483 through 1499 removed outlier: 3.984A pdb=" N LYS B1499 " --> pdb=" O ALA B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1528 removed outlier: 4.040A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1539 through 1546 removed outlier: 3.641A pdb=" N ILE B1543 " --> pdb=" O ARG B1539 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B1546 " --> pdb=" O THR B1542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AA2, first strand: chain 'B' and resid 685 through 686 Processing sheet with id=AA3, first strand: chain 'B' and resid 771 through 773 removed outlier: 6.337A pdb=" N VAL B 851 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL B 887 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU B 853 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR B 709 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1362 through 1369 removed outlier: 6.484A pdb=" N LYS B1363 " --> pdb=" O SER B1351 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER B1351 " --> pdb=" O LYS B1363 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL B1365 " --> pdb=" O ASN B1349 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU B1350 " --> pdb=" O GLU B1400 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU B1400 " --> pdb=" O LEU B1350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1422 through 1425 removed outlier: 6.491A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B1374 " --> pdb=" O LEU B1548 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N MET B1550 " --> pdb=" O LYS B1374 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B1376 " --> pdb=" O MET B1550 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU B1552 " --> pdb=" O GLY B1376 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N CYS B1378 " --> pdb=" O LEU B1552 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2847 1.34 - 1.46: 2105 1.46 - 1.59: 4133 1.59 - 1.71: 6 1.71 - 1.83: 75 Bond restraints: 9166 Sorted by residual: bond pdb=" C ILE B1136 " pdb=" N PRO B1137 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.36e+00 bond pdb=" C ARG B 297 " pdb=" O ARG B 297 " ideal model delta sigma weight residual 1.237 1.219 0.018 1.17e-02 7.31e+03 2.25e+00 bond pdb=" CB GLN B 369 " pdb=" CG GLN B 369 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CB PHE B 432 " pdb=" CG PHE B 432 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.30e-02 1.89e+03 2.15e+00 bond pdb=" CB ASN B1293 " pdb=" CG ASN B1293 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.12e+00 ... (remaining 9161 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 12276 2.42 - 4.85: 131 4.85 - 7.27: 26 7.27 - 9.70: 10 9.70 - 12.12: 4 Bond angle restraints: 12447 Sorted by residual: angle pdb=" N GLY B 296 " pdb=" CA GLY B 296 " pdb=" C GLY B 296 " ideal model delta sigma weight residual 110.77 122.89 -12.12 1.93e+00 2.68e-01 3.94e+01 angle pdb=" N ALA B 294 " pdb=" CA ALA B 294 " pdb=" C ALA B 294 " ideal model delta sigma weight residual 111.07 116.41 -5.34 1.07e+00 8.73e-01 2.49e+01 angle pdb=" O1B ADP B2501 " pdb=" PB ADP B2501 " pdb=" O3B ADP B2501 " ideal model delta sigma weight residual 119.90 109.75 10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N SER B 302 " pdb=" CA SER B 302 " pdb=" C SER B 302 " ideal model delta sigma weight residual 111.28 107.64 3.64 1.09e+00 8.42e-01 1.11e+01 angle pdb=" O2B ADP B2502 " pdb=" PB ADP B2502 " pdb=" O3B ADP B2502 " ideal model delta sigma weight residual 119.90 109.96 9.94 3.00e+00 1.11e-01 1.10e+01 ... (remaining 12442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 5278 28.72 - 57.43: 179 57.43 - 86.15: 15 86.15 - 114.86: 2 114.86 - 143.58: 2 Dihedral angle restraints: 5476 sinusoidal: 2121 harmonic: 3355 Sorted by residual: dihedral pdb=" C5' ADP B2502 " pdb=" O5' ADP B2502 " pdb=" PA ADP B2502 " pdb=" O2A ADP B2502 " ideal model delta sinusoidal sigma weight residual -60.00 83.58 -143.58 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" O1B ADP B2502 " pdb=" O3A ADP B2502 " pdb=" PB ADP B2502 " pdb=" PA ADP B2502 " ideal model delta sinusoidal sigma weight residual -60.00 -177.39 117.39 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" CA PHE B 566 " pdb=" C PHE B 566 " pdb=" N LYS B 567 " pdb=" CA LYS B 567 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 5473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1041 0.036 - 0.073: 332 0.073 - 0.109: 100 0.109 - 0.146: 27 0.146 - 0.182: 2 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA ALA B 294 " pdb=" N ALA B 294 " pdb=" C ALA B 294 " pdb=" CB ALA B 294 " both_signs ideal model delta sigma weight residual False 2.48 2.30 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA TYR B1294 " pdb=" N TYR B1294 " pdb=" C TYR B1294 " pdb=" CB TYR B1294 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CA ILE B1504 " pdb=" N ILE B1504 " pdb=" C ILE B1504 " pdb=" CB ILE B1504 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 1499 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 550 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 551 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 551 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 551 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 432 " 0.016 2.00e-02 2.50e+03 1.23e-02 2.64e+00 pdb=" CG PHE B 432 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 432 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 432 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 316 " 0.023 5.00e-02 4.00e+02 3.50e-02 1.97e+00 pdb=" N PRO B 317 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.020 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 66 2.60 - 3.18: 7928 3.18 - 3.75: 14223 3.75 - 4.33: 18156 4.33 - 4.90: 29979 Nonbonded interactions: 70352 Sorted by model distance: nonbonded pdb=" OE1 GLN B 775 " pdb="MG MG B2503 " model vdw 2.031 2.170 nonbonded pdb=" O3B ADP B2501 " pdb="MG MG B2503 " model vdw 2.091 2.170 nonbonded pdb=" NE2 GLN B 775 " pdb="MG MG B2503 " model vdw 2.132 2.250 nonbonded pdb=" O PRO B 769 " pdb=" OG1 THR B 848 " model vdw 2.259 3.040 nonbonded pdb=" NE2 HIS B 562 " pdb=" O SER B 569 " model vdw 2.260 3.120 ... (remaining 70347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 0.044 9166 Z= 0.184 Angle : 0.728 12.121 12447 Z= 0.374 Chirality : 0.040 0.182 1502 Planarity : 0.004 0.048 1531 Dihedral : 14.120 143.579 3292 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.20 % Allowed : 8.57 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.22), residues: 1138 helix: -0.15 (0.17), residues: 737 sheet: -0.89 (0.57), residues: 86 loop : -3.02 (0.28), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 370 TYR 0.014 0.002 TYR B 512 PHE 0.027 0.002 PHE B 432 TRP 0.009 0.001 TRP B1339 HIS 0.009 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9166) covalent geometry : angle 0.72766 (12447) hydrogen bonds : bond 0.12441 ( 607) hydrogen bonds : angle 5.32094 ( 1782) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 0.353 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: B 226 SER cc_start: 0.9578 (t) cc_final: 0.9352 (p) REVERT: B 243 LYS cc_start: 0.8947 (tttt) cc_final: 0.8610 (mptt) REVERT: B 257 MET cc_start: 0.9155 (mmm) cc_final: 0.8705 (mmm) REVERT: B 314 PHE cc_start: 0.5124 (m-10) cc_final: 0.3951 (m-80) REVERT: B 370 ARG cc_start: 0.9219 (mmt-90) cc_final: 0.8623 (mmp80) REVERT: B 376 SER cc_start: 0.9497 (t) cc_final: 0.9177 (p) REVERT: B 429 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8295 (mtm) REVERT: B 497 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7330 (mtmt) REVERT: B 512 TYR cc_start: 0.8729 (p90) cc_final: 0.8375 (p90) REVERT: B 514 TRP cc_start: 0.8379 (m-10) cc_final: 0.7370 (m-10) REVERT: B 523 GLU cc_start: 0.9064 (tp30) cc_final: 0.8793 (tm-30) REVERT: B 529 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8514 (tm-30) REVERT: B 530 MET cc_start: 0.9529 (tpp) cc_final: 0.9146 (tpp) REVERT: B 547 ASN cc_start: 0.8279 (m-40) cc_final: 0.8004 (m110) REVERT: B 574 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.6661 (p) REVERT: B 580 LEU cc_start: 0.8488 (tp) cc_final: 0.8165 (mt) REVERT: B 581 SER cc_start: 0.9631 (m) cc_final: 0.9410 (p) REVERT: B 685 PHE cc_start: 0.6642 (t80) cc_final: 0.5869 (t80) REVERT: B 696 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6043 (tp) REVERT: B 778 TRP cc_start: 0.8903 (p-90) cc_final: 0.8543 (p-90) REVERT: B 781 ASN cc_start: 0.8222 (t0) cc_final: 0.7890 (m-40) REVERT: B 855 ASP cc_start: 0.8781 (t0) cc_final: 0.8328 (t0) REVERT: B 861 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.7795 (p0) REVERT: B 868 LEU cc_start: 0.9775 (tp) cc_final: 0.9469 (mm) REVERT: B 891 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8138 (mt) REVERT: B 892 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: B 915 LYS cc_start: 0.9438 (mttt) cc_final: 0.9107 (tppt) REVERT: B 1011 LEU cc_start: 0.8630 (tp) cc_final: 0.8404 (pt) REVERT: B 1012 LEU cc_start: 0.9076 (mt) cc_final: 0.8758 (mp) REVERT: B 1079 CYS cc_start: 0.9220 (t) cc_final: 0.8804 (p) REVERT: B 1087 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8717 (mm-30) REVERT: B 1092 LYS cc_start: 0.9187 (mttm) cc_final: 0.8808 (mmtm) REVERT: B 1114 GLU cc_start: 0.8751 (tt0) cc_final: 0.8400 (tm-30) REVERT: B 1194 ASP cc_start: 0.9293 (t0) cc_final: 0.9085 (m-30) REVERT: B 1202 SER cc_start: 0.9244 (m) cc_final: 0.8165 (p) REVERT: B 1220 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9185 (mp0) REVERT: B 1222 ARG cc_start: 0.9217 (mmt-90) cc_final: 0.8454 (mmm160) REVERT: B 1246 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8095 (mmm-85) REVERT: B 1281 VAL cc_start: 0.9708 (t) cc_final: 0.9457 (p) REVERT: B 1395 MET cc_start: 0.8874 (mmt) cc_final: 0.8491 (mmm) REVERT: B 1425 ILE cc_start: 0.9213 (mt) cc_final: 0.8656 (mt) REVERT: B 1505 MET cc_start: 0.8052 (ttm) cc_final: 0.7680 (mmt) REVERT: B 1507 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8311 (mp0) REVERT: B 1517 GLU cc_start: 0.9090 (tp30) cc_final: 0.8850 (tp30) REVERT: B 1536 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8271 (mp) REVERT: B 1552 LEU cc_start: 0.9618 (mt) cc_final: 0.9192 (tp) outliers start: 60 outliers final: 20 residues processed: 389 average time/residue: 0.0962 time to fit residues: 51.4884 Evaluate side-chains 252 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN B 419 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS B1308 GLN B1348 GLN B1484 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.096218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.077325 restraints weight = 28682.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.079818 restraints weight = 18704.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081610 restraints weight = 13405.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082911 restraints weight = 10300.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083824 restraints weight = 8369.887| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9166 Z= 0.170 Angle : 0.710 10.527 12447 Z= 0.346 Chirality : 0.044 0.238 1502 Planarity : 0.004 0.045 1531 Dihedral : 7.360 136.722 1251 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.31 % Allowed : 3.82 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.25), residues: 1138 helix: 1.16 (0.18), residues: 738 sheet: -0.38 (0.55), residues: 86 loop : -2.41 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1394 TYR 0.018 0.002 TYR B 230 PHE 0.046 0.002 PHE B1240 TRP 0.010 0.001 TRP B1033 HIS 0.005 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9166) covalent geometry : angle 0.70971 (12447) hydrogen bonds : bond 0.05710 ( 607) hydrogen bonds : angle 4.36594 ( 1782) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.489 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: B 295 PHE cc_start: 0.7092 (m-80) cc_final: 0.6800 (m-10) REVERT: B 314 PHE cc_start: 0.8113 (m-10) cc_final: 0.7864 (m-80) REVERT: B 419 ASN cc_start: 0.8793 (m-40) cc_final: 0.8418 (m110) REVERT: B 421 VAL cc_start: 0.8392 (t) cc_final: 0.8129 (t) REVERT: B 502 MET cc_start: 0.9556 (ttt) cc_final: 0.9175 (ttt) REVERT: B 512 TYR cc_start: 0.8197 (p90) cc_final: 0.7227 (p90) REVERT: B 514 TRP cc_start: 0.8197 (m-10) cc_final: 0.6913 (m-10) REVERT: B 581 SER cc_start: 0.9679 (m) cc_final: 0.9450 (p) REVERT: B 719 LYS cc_start: 0.9257 (mtmt) cc_final: 0.9042 (mtpt) REVERT: B 778 TRP cc_start: 0.8983 (p-90) cc_final: 0.8640 (p-90) REVERT: B 781 ASN cc_start: 0.7625 (t0) cc_final: 0.7155 (m-40) REVERT: B 855 ASP cc_start: 0.8513 (t0) cc_final: 0.7923 (t0) REVERT: B 869 MET cc_start: 0.8336 (tpp) cc_final: 0.7897 (tpp) REVERT: B 1005 LEU cc_start: 0.8467 (mt) cc_final: 0.8229 (pp) REVERT: B 1012 LEU cc_start: 0.9206 (mt) cc_final: 0.8896 (mp) REVERT: B 1079 CYS cc_start: 0.9070 (t) cc_final: 0.8826 (p) REVERT: B 1092 LYS cc_start: 0.9301 (mttm) cc_final: 0.9001 (mmtm) REVERT: B 1202 SER cc_start: 0.9171 (m) cc_final: 0.7942 (p) REVERT: B 1222 ARG cc_start: 0.8709 (mmt-90) cc_final: 0.8398 (mmm-85) REVERT: B 1428 ASP cc_start: 0.8769 (t70) cc_final: 0.8467 (t70) REVERT: B 1505 MET cc_start: 0.8239 (ttm) cc_final: 0.8029 (mmt) REVERT: B 1507 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8470 (mp0) REVERT: B 1517 GLU cc_start: 0.8811 (tp30) cc_final: 0.8383 (tp30) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.0838 time to fit residues: 32.1414 Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 98 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B1301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.097264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078592 restraints weight = 28723.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080973 restraints weight = 18881.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.082707 restraints weight = 13654.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084005 restraints weight = 10597.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084948 restraints weight = 8641.126| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9166 Z= 0.140 Angle : 0.679 11.563 12447 Z= 0.322 Chirality : 0.042 0.213 1502 Planarity : 0.004 0.085 1531 Dihedral : 6.903 141.696 1251 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1138 helix: 1.75 (0.19), residues: 730 sheet: -0.23 (0.56), residues: 86 loop : -1.86 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1218 TYR 0.015 0.001 TYR B 454 PHE 0.024 0.002 PHE B 433 TRP 0.015 0.001 TRP B 899 HIS 0.006 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9166) covalent geometry : angle 0.67888 (12447) hydrogen bonds : bond 0.05085 ( 607) hydrogen bonds : angle 4.06269 ( 1782) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 257 time to evaluate : 0.427 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: symmetry clash REVERT: B 314 PHE cc_start: 0.8131 (m-10) cc_final: 0.7877 (m-80) REVERT: B 387 LEU cc_start: 0.9673 (tp) cc_final: 0.9417 (tp) REVERT: B 419 ASN cc_start: 0.8849 (m-40) cc_final: 0.8486 (m110) REVERT: B 421 VAL cc_start: 0.8170 (t) cc_final: 0.7912 (t) REVERT: B 512 TYR cc_start: 0.8073 (p90) cc_final: 0.7204 (p90) REVERT: B 514 TRP cc_start: 0.8095 (m-10) cc_final: 0.6787 (m-10) REVERT: B 562 HIS cc_start: 0.8387 (t70) cc_final: 0.8124 (t-90) REVERT: B 719 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8852 (mttm) REVERT: B 778 TRP cc_start: 0.9004 (p-90) cc_final: 0.8685 (p-90) REVERT: B 802 VAL cc_start: 0.9609 (t) cc_final: 0.9181 (t) REVERT: B 855 ASP cc_start: 0.8375 (t0) cc_final: 0.7833 (t0) REVERT: B 1005 LEU cc_start: 0.8424 (mt) cc_final: 0.8222 (pp) REVERT: B 1012 LEU cc_start: 0.9149 (mt) cc_final: 0.8919 (mp) REVERT: B 1064 TYR cc_start: 0.8447 (m-80) cc_final: 0.7909 (m-80) REVERT: B 1079 CYS cc_start: 0.9079 (t) cc_final: 0.8834 (p) REVERT: B 1092 LYS cc_start: 0.9208 (mttm) cc_final: 0.8909 (mmtm) REVERT: B 1202 SER cc_start: 0.9131 (m) cc_final: 0.8285 (p) REVERT: B 1222 ARG cc_start: 0.8605 (mmt-90) cc_final: 0.8170 (mmm160) REVERT: B 1427 GLN cc_start: 0.9064 (pp30) cc_final: 0.8846 (pp30) REVERT: B 1505 MET cc_start: 0.8181 (ttm) cc_final: 0.7940 (mmt) REVERT: B 1507 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8449 (mp0) REVERT: B 1517 GLU cc_start: 0.8668 (tp30) cc_final: 0.8297 (tp30) REVERT: B 1536 ILE cc_start: 0.8822 (pt) cc_final: 0.7984 (pt) outliers start: 2 outliers final: 0 residues processed: 257 average time/residue: 0.0785 time to fit residues: 29.6802 Evaluate side-chains 201 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 32 optimal weight: 0.0270 chunk 54 optimal weight: 0.8980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN B 374 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 ASN ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.098161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079759 restraints weight = 29047.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082170 restraints weight = 19129.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083958 restraints weight = 13830.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.085176 restraints weight = 10653.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086148 restraints weight = 8721.540| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9166 Z= 0.131 Angle : 0.655 10.978 12447 Z= 0.311 Chirality : 0.041 0.154 1502 Planarity : 0.004 0.069 1531 Dihedral : 6.543 136.457 1251 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1138 helix: 1.89 (0.19), residues: 733 sheet: 0.37 (0.56), residues: 81 loop : -1.76 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 526 TYR 0.022 0.001 TYR B 230 PHE 0.020 0.001 PHE B1204 TRP 0.010 0.001 TRP B 231 HIS 0.006 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9166) covalent geometry : angle 0.65504 (12447) hydrogen bonds : bond 0.04807 ( 607) hydrogen bonds : angle 3.97243 ( 1782) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 249 time to evaluate : 0.349 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 PHE cc_start: 0.8267 (m-10) cc_final: 0.7785 (m-80) REVERT: B 387 LEU cc_start: 0.9594 (tp) cc_final: 0.9344 (tp) REVERT: B 421 VAL cc_start: 0.8186 (t) cc_final: 0.7782 (t) REVERT: B 429 MET cc_start: 0.8113 (mtt) cc_final: 0.7883 (mtt) REVERT: B 433 PHE cc_start: 0.8722 (m-10) cc_final: 0.8360 (m-80) REVERT: B 512 TYR cc_start: 0.8013 (p90) cc_final: 0.7186 (p90) REVERT: B 514 TRP cc_start: 0.8106 (m-10) cc_final: 0.6968 (m-10) REVERT: B 719 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8886 (mttm) REVERT: B 730 MET cc_start: 0.5407 (ttt) cc_final: 0.4711 (tpp) REVERT: B 778 TRP cc_start: 0.9004 (p-90) cc_final: 0.8259 (p-90) REVERT: B 802 VAL cc_start: 0.9685 (t) cc_final: 0.9361 (t) REVERT: B 855 ASP cc_start: 0.8382 (t0) cc_final: 0.7820 (t0) REVERT: B 1012 LEU cc_start: 0.9132 (mt) cc_final: 0.8905 (mp) REVERT: B 1079 CYS cc_start: 0.9075 (t) cc_final: 0.8852 (p) REVERT: B 1092 LYS cc_start: 0.9149 (mttm) cc_final: 0.8903 (mmtm) REVERT: B 1110 MET cc_start: 0.8019 (mmm) cc_final: 0.7766 (mmm) REVERT: B 1202 SER cc_start: 0.9092 (m) cc_final: 0.8811 (p) REVERT: B 1219 TYR cc_start: 0.8460 (m-10) cc_final: 0.8228 (m-80) REVERT: B 1222 ARG cc_start: 0.8611 (mmt-90) cc_final: 0.8153 (mmm160) REVERT: B 1246 ARG cc_start: 0.8381 (tpp-160) cc_final: 0.7665 (mmm-85) REVERT: B 1249 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7517 (mt-10) REVERT: B 1262 ILE cc_start: 0.8996 (mm) cc_final: 0.8766 (mm) REVERT: B 1517 GLU cc_start: 0.8646 (tp30) cc_final: 0.8277 (tp30) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.0766 time to fit residues: 28.4589 Evaluate side-chains 199 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 34 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 94 optimal weight: 0.0270 chunk 113 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080304 restraints weight = 29060.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.082682 restraints weight = 19065.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084474 restraints weight = 13798.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085734 restraints weight = 10645.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086690 restraints weight = 8703.369| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9166 Z= 0.132 Angle : 0.660 11.188 12447 Z= 0.309 Chirality : 0.041 0.200 1502 Planarity : 0.003 0.051 1531 Dihedral : 6.295 130.323 1251 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1138 helix: 1.96 (0.19), residues: 732 sheet: 0.39 (0.57), residues: 86 loop : -1.78 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1246 TYR 0.015 0.001 TYR B 454 PHE 0.026 0.001 PHE B 372 TRP 0.008 0.001 TRP B 688 HIS 0.005 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9166) covalent geometry : angle 0.66028 (12447) hydrogen bonds : bond 0.04541 ( 607) hydrogen bonds : angle 3.91959 ( 1782) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.349 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: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.8356 (mmp) cc_final: 0.8118 (tpp) REVERT: B 314 PHE cc_start: 0.8036 (m-10) cc_final: 0.7755 (m-80) REVERT: B 421 VAL cc_start: 0.7876 (t) cc_final: 0.7583 (t) REVERT: B 429 MET cc_start: 0.8295 (mtt) cc_final: 0.7928 (mtt) REVERT: B 433 PHE cc_start: 0.8796 (m-10) cc_final: 0.8375 (m-80) REVERT: B 512 TYR cc_start: 0.8019 (p90) cc_final: 0.7219 (p90) REVERT: B 778 TRP cc_start: 0.9084 (p-90) cc_final: 0.8173 (p-90) REVERT: B 802 VAL cc_start: 0.9682 (t) cc_final: 0.9371 (t) REVERT: B 855 ASP cc_start: 0.8369 (t0) cc_final: 0.7821 (t0) REVERT: B 1012 LEU cc_start: 0.9200 (mt) cc_final: 0.8964 (mp) REVERT: B 1079 CYS cc_start: 0.9065 (t) cc_final: 0.8841 (p) REVERT: B 1092 LYS cc_start: 0.9178 (mttm) cc_final: 0.8905 (mmtm) REVERT: B 1202 SER cc_start: 0.9130 (m) cc_final: 0.8900 (p) REVERT: B 1206 GLU cc_start: 0.8584 (pt0) cc_final: 0.8198 (pt0) REVERT: B 1222 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.8065 (mmm160) REVERT: B 1229 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8587 (tm-30) REVERT: B 1234 ASN cc_start: 0.9335 (t0) cc_final: 0.9088 (t0) REVERT: B 1517 GLU cc_start: 0.8614 (tp30) cc_final: 0.8256 (tp30) REVERT: B 1552 LEU cc_start: 0.9142 (tp) cc_final: 0.8620 (tp) REVERT: B 1569 GLN cc_start: 0.7271 (mm-40) cc_final: 0.7003 (mm-40) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0753 time to fit residues: 26.8042 Evaluate side-chains 190 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 4 optimal weight: 0.0020 chunk 75 optimal weight: 1.9990 chunk 91 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 overall best weight: 0.6568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.096807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.078250 restraints weight = 28677.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080691 restraints weight = 18614.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082483 restraints weight = 13341.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083804 restraints weight = 10247.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084785 restraints weight = 8300.764| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9166 Z= 0.135 Angle : 0.663 11.258 12447 Z= 0.314 Chirality : 0.041 0.164 1502 Planarity : 0.003 0.050 1531 Dihedral : 5.971 118.827 1251 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1138 helix: 1.98 (0.19), residues: 727 sheet: 0.51 (0.56), residues: 86 loop : -1.56 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1394 TYR 0.030 0.001 TYR B1254 PHE 0.026 0.001 PHE B 372 TRP 0.009 0.001 TRP B 778 HIS 0.004 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9166) covalent geometry : angle 0.66314 (12447) hydrogen bonds : bond 0.04595 ( 607) hydrogen bonds : angle 3.90163 ( 1782) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.463 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: symmetry clash REVERT: B 314 PHE cc_start: 0.8117 (m-10) cc_final: 0.7825 (m-80) REVERT: B 421 VAL cc_start: 0.7907 (t) cc_final: 0.7571 (t) REVERT: B 429 MET cc_start: 0.8464 (mtt) cc_final: 0.8223 (mtt) REVERT: B 433 PHE cc_start: 0.8783 (m-10) cc_final: 0.8371 (m-80) REVERT: B 512 TYR cc_start: 0.8275 (p90) cc_final: 0.7321 (p90) REVERT: B 778 TRP cc_start: 0.9137 (p-90) cc_final: 0.8485 (p-90) REVERT: B 802 VAL cc_start: 0.9739 (t) cc_final: 0.9499 (t) REVERT: B 855 ASP cc_start: 0.8460 (t0) cc_final: 0.7909 (t0) REVERT: B 903 MET cc_start: 0.8584 (mmm) cc_final: 0.8355 (mmm) REVERT: B 1005 LEU cc_start: 0.8493 (mt) cc_final: 0.8284 (pp) REVERT: B 1012 LEU cc_start: 0.9203 (mt) cc_final: 0.8960 (mp) REVERT: B 1079 CYS cc_start: 0.9062 (t) cc_final: 0.8820 (p) REVERT: B 1092 LYS cc_start: 0.9177 (mttm) cc_final: 0.8895 (mmtm) REVERT: B 1206 GLU cc_start: 0.8564 (pt0) cc_final: 0.8346 (pt0) REVERT: B 1222 ARG cc_start: 0.8587 (mmt-90) cc_final: 0.8091 (mmm160) REVERT: B 1234 ASN cc_start: 0.9421 (t0) cc_final: 0.9187 (t0) REVERT: B 1517 GLU cc_start: 0.8708 (tp30) cc_final: 0.8351 (tp30) REVERT: B 1552 LEU cc_start: 0.9210 (tp) cc_final: 0.8894 (tp) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.0728 time to fit residues: 26.4036 Evaluate side-chains 181 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 61 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.077851 restraints weight = 29070.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080331 restraints weight = 18689.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082143 restraints weight = 13338.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083476 restraints weight = 10209.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084461 restraints weight = 8232.549| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9166 Z= 0.139 Angle : 0.669 11.598 12447 Z= 0.314 Chirality : 0.042 0.175 1502 Planarity : 0.003 0.050 1531 Dihedral : 5.741 106.076 1251 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1138 helix: 1.95 (0.19), residues: 733 sheet: 0.57 (0.55), residues: 86 loop : -1.53 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1394 TYR 0.012 0.001 TYR B 512 PHE 0.016 0.002 PHE B 321 TRP 0.008 0.001 TRP B 514 HIS 0.005 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9166) covalent geometry : angle 0.66854 (12447) hydrogen bonds : bond 0.04564 ( 607) hydrogen bonds : angle 3.93583 ( 1782) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.356 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: B 233 MET cc_start: 0.8421 (mmp) cc_final: 0.8186 (tpp) REVERT: B 314 PHE cc_start: 0.8080 (m-10) cc_final: 0.7835 (m-80) REVERT: B 421 VAL cc_start: 0.7964 (t) cc_final: 0.7613 (t) REVERT: B 512 TYR cc_start: 0.8215 (p90) cc_final: 0.7260 (p90) REVERT: B 710 MET cc_start: 0.8453 (mmp) cc_final: 0.8228 (mmp) REVERT: B 730 MET cc_start: 0.6012 (tpt) cc_final: 0.5434 (tpp) REVERT: B 801 MET cc_start: 0.9014 (tmm) cc_final: 0.8596 (tmm) REVERT: B 802 VAL cc_start: 0.9753 (t) cc_final: 0.9459 (t) REVERT: B 855 ASP cc_start: 0.8508 (t0) cc_final: 0.7966 (t0) REVERT: B 876 LEU cc_start: 0.9115 (tt) cc_final: 0.8828 (mm) REVERT: B 893 TYR cc_start: 0.7606 (m-10) cc_final: 0.7107 (m-80) REVERT: B 903 MET cc_start: 0.8622 (mmm) cc_final: 0.8335 (mmm) REVERT: B 1005 LEU cc_start: 0.8444 (mt) cc_final: 0.8241 (pp) REVERT: B 1012 LEU cc_start: 0.9183 (mt) cc_final: 0.8910 (mp) REVERT: B 1079 CYS cc_start: 0.9071 (t) cc_final: 0.8817 (p) REVERT: B 1092 LYS cc_start: 0.9164 (mttm) cc_final: 0.8887 (mmtm) REVERT: B 1110 MET cc_start: 0.8177 (mmm) cc_final: 0.7920 (mmm) REVERT: B 1222 ARG cc_start: 0.8494 (mmt-90) cc_final: 0.8020 (mmm160) REVERT: B 1285 LEU cc_start: 0.9232 (mm) cc_final: 0.8564 (tt) REVERT: B 1305 MET cc_start: 0.8388 (tmm) cc_final: 0.8138 (tmm) REVERT: B 1503 PHE cc_start: 0.7833 (m-10) cc_final: 0.7523 (m-10) REVERT: B 1505 MET cc_start: 0.8096 (mmt) cc_final: 0.7625 (mtm) REVERT: B 1517 GLU cc_start: 0.8667 (tp30) cc_final: 0.8310 (tp30) REVERT: B 1552 LEU cc_start: 0.9207 (tp) cc_final: 0.8922 (tp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.0705 time to fit residues: 24.9013 Evaluate side-chains 186 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN B 419 ASN ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS B1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.073187 restraints weight = 29631.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075534 restraints weight = 19235.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.077254 restraints weight = 13744.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078514 restraints weight = 10521.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.079346 restraints weight = 8521.407| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9166 Z= 0.207 Angle : 0.754 11.557 12447 Z= 0.364 Chirality : 0.045 0.193 1502 Planarity : 0.004 0.057 1531 Dihedral : 5.898 95.195 1251 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.10 % Allowed : 1.24 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1138 helix: 1.61 (0.19), residues: 741 sheet: 0.42 (0.56), residues: 86 loop : -1.65 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 370 TYR 0.011 0.001 TYR B1294 PHE 0.030 0.002 PHE B 432 TRP 0.018 0.002 TRP B 232 HIS 0.005 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9166) covalent geometry : angle 0.75430 (12447) hydrogen bonds : bond 0.05066 ( 607) hydrogen bonds : angle 4.28703 ( 1782) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 512 TYR cc_start: 0.8405 (p90) cc_final: 0.7339 (p90) REVERT: B 710 MET cc_start: 0.8451 (mmp) cc_final: 0.8088 (mmp) REVERT: B 855 ASP cc_start: 0.8670 (t0) cc_final: 0.7963 (t0) REVERT: B 886 LEU cc_start: 0.9444 (tt) cc_final: 0.9181 (tt) REVERT: B 903 MET cc_start: 0.8399 (mmm) cc_final: 0.8107 (mmm) REVERT: B 1005 LEU cc_start: 0.8520 (mt) cc_final: 0.8286 (pp) REVERT: B 1012 LEU cc_start: 0.9309 (mt) cc_final: 0.9056 (mp) REVERT: B 1079 CYS cc_start: 0.9125 (t) cc_final: 0.8875 (p) REVERT: B 1092 LYS cc_start: 0.9201 (mttm) cc_final: 0.8874 (mmtm) REVERT: B 1100 SER cc_start: 0.9185 (m) cc_final: 0.8763 (p) REVERT: B 1222 ARG cc_start: 0.8731 (mmt-90) cc_final: 0.8075 (mmm160) REVERT: B 1305 MET cc_start: 0.8530 (tmm) cc_final: 0.8301 (tmm) REVERT: B 1503 PHE cc_start: 0.8001 (m-10) cc_final: 0.7615 (m-10) REVERT: B 1505 MET cc_start: 0.8128 (mmt) cc_final: 0.7734 (mtm) REVERT: B 1517 GLU cc_start: 0.8681 (tp30) cc_final: 0.8350 (tp30) REVERT: B 1536 ILE cc_start: 0.8474 (pt) cc_final: 0.8259 (pt) REVERT: B 1552 LEU cc_start: 0.9247 (tp) cc_final: 0.8744 (tp) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.0765 time to fit residues: 25.0477 Evaluate side-chains 165 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 0.0270 chunk 48 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 85 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077174 restraints weight = 28772.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.079640 restraints weight = 18597.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081433 restraints weight = 13293.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.082777 restraints weight = 10215.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.083764 restraints weight = 8233.856| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9166 Z= 0.133 Angle : 0.733 11.835 12447 Z= 0.342 Chirality : 0.044 0.183 1502 Planarity : 0.004 0.054 1531 Dihedral : 5.669 86.203 1251 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1138 helix: 1.78 (0.18), residues: 751 sheet: 0.54 (0.56), residues: 86 loop : -1.59 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1353 TYR 0.011 0.001 TYR B 893 PHE 0.023 0.002 PHE B 314 TRP 0.013 0.001 TRP B 899 HIS 0.004 0.001 HIS B1024 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9166) covalent geometry : angle 0.73344 (12447) hydrogen bonds : bond 0.04737 ( 607) hydrogen bonds : angle 4.09446 ( 1782) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 ILE cc_start: 0.9652 (mt) cc_final: 0.9405 (mp) REVERT: B 429 MET cc_start: 0.8028 (mtt) cc_final: 0.7508 (mtt) REVERT: B 433 PHE cc_start: 0.8837 (m-10) cc_final: 0.8331 (m-80) REVERT: B 512 TYR cc_start: 0.8287 (p90) cc_final: 0.7391 (p90) REVERT: B 802 VAL cc_start: 0.9749 (t) cc_final: 0.9532 (p) REVERT: B 855 ASP cc_start: 0.8379 (t0) cc_final: 0.7836 (t0) REVERT: B 903 MET cc_start: 0.8629 (mmm) cc_final: 0.8360 (mmm) REVERT: B 1012 LEU cc_start: 0.9214 (mt) cc_final: 0.8943 (mp) REVERT: B 1079 CYS cc_start: 0.9044 (t) cc_final: 0.8781 (p) REVERT: B 1092 LYS cc_start: 0.9135 (mttm) cc_final: 0.8845 (mmtm) REVERT: B 1100 SER cc_start: 0.9134 (m) cc_final: 0.8706 (p) REVERT: B 1202 SER cc_start: 0.9176 (p) cc_final: 0.8972 (t) REVERT: B 1222 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8025 (mmm160) REVERT: B 1285 LEU cc_start: 0.9231 (mm) cc_final: 0.8531 (tt) REVERT: B 1305 MET cc_start: 0.8514 (tmm) cc_final: 0.8246 (tmm) REVERT: B 1503 PHE cc_start: 0.7836 (m-10) cc_final: 0.7498 (m-10) REVERT: B 1505 MET cc_start: 0.8294 (mmt) cc_final: 0.7836 (mtm) REVERT: B 1517 GLU cc_start: 0.8671 (tp30) cc_final: 0.8335 (tp30) REVERT: B 1552 LEU cc_start: 0.9188 (tp) cc_final: 0.8890 (tp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.0786 time to fit residues: 27.8571 Evaluate side-chains 175 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1538 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076121 restraints weight = 29447.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078574 restraints weight = 18899.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080351 restraints weight = 13463.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.081634 restraints weight = 10297.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082580 restraints weight = 8338.597| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9166 Z= 0.155 Angle : 0.762 11.638 12447 Z= 0.362 Chirality : 0.045 0.218 1502 Planarity : 0.004 0.054 1531 Dihedral : 5.715 82.070 1251 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.25), residues: 1138 helix: 1.76 (0.18), residues: 753 sheet: 0.50 (0.58), residues: 86 loop : -1.70 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 370 TYR 0.025 0.001 TYR B 893 PHE 0.018 0.002 PHE B 432 TRP 0.013 0.001 TRP B 232 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9166) covalent geometry : angle 0.76248 (12447) hydrogen bonds : bond 0.04727 ( 607) hydrogen bonds : angle 4.13685 ( 1782) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 512 TYR cc_start: 0.8360 (p90) cc_final: 0.7607 (p90) REVERT: B 710 MET cc_start: 0.8388 (mmp) cc_final: 0.8154 (mmp) REVERT: B 730 MET cc_start: 0.6080 (tpt) cc_final: 0.5401 (tpp) REVERT: B 802 VAL cc_start: 0.9741 (t) cc_final: 0.9538 (p) REVERT: B 855 ASP cc_start: 0.8457 (t0) cc_final: 0.7915 (t0) REVERT: B 893 TYR cc_start: 0.7542 (m-80) cc_final: 0.7305 (m-80) REVERT: B 903 MET cc_start: 0.8591 (mmm) cc_final: 0.8266 (mmm) REVERT: B 1012 LEU cc_start: 0.9260 (mt) cc_final: 0.9003 (mp) REVERT: B 1079 CYS cc_start: 0.9084 (t) cc_final: 0.8794 (p) REVERT: B 1092 LYS cc_start: 0.9146 (mttm) cc_final: 0.8850 (mmtm) REVERT: B 1100 SER cc_start: 0.9145 (m) cc_final: 0.8721 (p) REVERT: B 1222 ARG cc_start: 0.8617 (mmt-90) cc_final: 0.8148 (mmm160) REVERT: B 1305 MET cc_start: 0.8507 (tmm) cc_final: 0.8243 (tmm) REVERT: B 1503 PHE cc_start: 0.7853 (m-10) cc_final: 0.7549 (m-10) REVERT: B 1505 MET cc_start: 0.8223 (mmt) cc_final: 0.7931 (mtp) REVERT: B 1507 GLU cc_start: 0.8924 (pm20) cc_final: 0.8673 (pm20) REVERT: B 1517 GLU cc_start: 0.8661 (tp30) cc_final: 0.8299 (tp30) REVERT: B 1552 LEU cc_start: 0.9220 (tp) cc_final: 0.8717 (tp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.0744 time to fit residues: 24.8913 Evaluate side-chains 169 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.075469 restraints weight = 29164.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077780 restraints weight = 18998.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079513 restraints weight = 13724.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.080705 restraints weight = 10609.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.081638 restraints weight = 8709.939| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9166 Z= 0.163 Angle : 0.759 11.681 12447 Z= 0.357 Chirality : 0.045 0.208 1502 Planarity : 0.004 0.052 1531 Dihedral : 5.779 82.504 1251 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1138 helix: 1.75 (0.19), residues: 742 sheet: 0.59 (0.59), residues: 78 loop : -1.67 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.024 0.001 TYR B 893 PHE 0.018 0.002 PHE B 321 TRP 0.013 0.002 TRP B 232 HIS 0.005 0.001 HIS B1316 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9166) covalent geometry : angle 0.75876 (12447) hydrogen bonds : bond 0.04668 ( 607) hydrogen bonds : angle 4.18324 ( 1782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.56 seconds wall clock time: 28 minutes 49.80 seconds (1729.80 seconds total)