Starting phenix.real_space_refine on Thu Mar 13 22:53:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ywd_6853/03_2025/5ywd_6853.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ywd_6853/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5ywd_6853/03_2025/5ywd_6853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ywd_6853/03_2025/5ywd_6853.map" model { file = "/net/cci-nas-00/data/ceres_data/5ywd_6853/03_2025/5ywd_6853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ywd_6853/03_2025/5ywd_6853.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'TYR:plan': 3, 'GLU:plan': 5, 'ARG:plan': 5, 'ASP:plan': 4} 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: 6.25, per 1000 atoms: 0.69 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: 2.50 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.04 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: 3.01 Time building geometry restraints manager: 2.92 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: 1.740 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.410 ------------------------------------------------------------------------------- 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= 0.225 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP B1339 HIS 0.009 0.001 HIS B1024 PHE 0.027 0.002 PHE B 432 TYR 0.014 0.002 TYR B 512 ARG 0.009 0.001 ARG B 370 *********************** 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 : 1.071 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: 0.8609 (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: 0.3953 (m-80) REVERT: B 370 ARG cc_start: 0.9219 (mmt-90) cc_final: 0.8622 (mmp80) REVERT: B 376 SER cc_start: 0.9497 (t) cc_final: 0.9173 (p) REVERT: B 429 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: B 497 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7329 (mtmt) REVERT: B 512 TYR cc_start: 0.8729 (p90) cc_final: 0.8376 (p90) REVERT: B 514 TRP cc_start: 0.8379 (m-10) cc_final: 0.7373 (m-10) REVERT: B 523 GLU cc_start: 0.9064 (tp30) cc_final: 0.8790 (tm-30) REVERT: B 529 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8512 (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: 0.8011 (m110) REVERT: B 574 SER cc_start: 0.7792 (OUTLIER) cc_final: 0.6675 (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: 0.9411 (p) REVERT: B 685 PHE cc_start: 0.6642 (t80) cc_final: 0.5729 (t80) REVERT: B 696 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.5257 (tp) REVERT: B 778 TRP cc_start: 0.8903 (p-90) cc_final: 0.8542 (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: 0.8325 (t0) REVERT: B 861 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.7798 (p0) REVERT: B 868 LEU cc_start: 0.9775 (tp) cc_final: 0.9468 (mm) REVERT: B 891 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8137 (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: 0.9106 (tppt) REVERT: B 1011 LEU cc_start: 0.8630 (tp) cc_final: 0.8407 (pt) REVERT: B 1012 LEU cc_start: 0.9076 (mt) cc_final: 0.8771 (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: 0.8670 (mm-30) REVERT: B 1092 LYS cc_start: 0.9187 (mttm) cc_final: 0.8643 (tptt) REVERT: B 1096 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8190 (tmt170) REVERT: B 1114 GLU cc_start: 0.8751 (tt0) cc_final: 0.8402 (tm-30) REVERT: B 1194 ASP cc_start: 0.9293 (t0) cc_final: 0.9086 (m-30) REVERT: B 1202 SER cc_start: 0.9244 (m) cc_final: 0.8162 (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: 0.8453 (mmm160) REVERT: B 1246 ARG cc_start: 0.8823 (mmt-90) cc_final: 0.8094 (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: 0.8494 (mmm) REVERT: B 1425 ILE cc_start: 0.9213 (mt) cc_final: 0.8652 (mt) REVERT: B 1505 MET cc_start: 0.8052 (ttm) cc_final: 0.7675 (mmt) REVERT: B 1507 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8310 (mp0) REVERT: B 1517 GLU cc_start: 0.9090 (tp30) cc_final: 0.8852 (tp30) REVERT: B 1536 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8269 (mp) REVERT: B 1552 LEU cc_start: 0.9618 (mt) cc_final: 0.9220 (tp) outliers start: 60 outliers final: 20 residues processed: 389 average time/residue: 0.2153 time to fit residues: 114.2911 Evaluate side-chains 250 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 223 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 B1301 ASN B1308 GLN B1348 GLN B1481 ASN B1484 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.092326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073894 restraints weight = 28983.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.076218 restraints weight = 19057.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.077861 restraints weight = 13772.213| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 9166 Z= 0.350 Angle : 0.769 9.418 12447 Z= 0.383 Chirality : 0.045 0.227 1502 Planarity : 0.005 0.044 1531 Dihedral : 7.576 140.755 1251 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.31 % Allowed : 4.86 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1138 helix: 0.96 (0.18), residues: 739 sheet: -0.42 (0.55), residues: 86 loop : -2.48 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1339 HIS 0.008 0.001 HIS B 562 PHE 0.040 0.003 PHE B1240 TYR 0.016 0.002 TYR B 230 ARG 0.010 0.001 ARG B 370 *********************** 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 258 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 255 time to evaluate : 1.221 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 243 LYS cc_start: 0.8891 (tttt) cc_final: 0.8678 (mptt) REVERT: B 305 PHE cc_start: 0.9097 (m-10) cc_final: 0.8754 (m-80) REVERT: B 314 PHE cc_start: 0.8149 (m-10) cc_final: 0.7929 (m-80) REVERT: B 419 ASN cc_start: 0.8832 (m-40) cc_final: 0.8483 (m110) REVERT: B 502 MET cc_start: 0.9541 (ttt) cc_final: 0.9271 (ttt) REVERT: B 512 TYR cc_start: 0.8431 (p90) cc_final: 0.7553 (p90) REVERT: B 581 SER cc_start: 0.9670 (m) cc_final: 0.9469 (p) REVERT: B 719 LYS cc_start: 0.9361 (mtmt) cc_final: 0.8993 (mttm) REVERT: B 791 GLU cc_start: 0.8245 (mp0) cc_final: 0.7630 (mp0) REVERT: B 802 VAL cc_start: 0.9669 (t) cc_final: 0.9200 (t) REVERT: B 855 ASP cc_start: 0.8682 (t0) cc_final: 0.8059 (t0) REVERT: B 868 LEU cc_start: 0.9667 (tp) cc_final: 0.9445 (mm) REVERT: B 869 MET cc_start: 0.8446 (tpp) cc_final: 0.8010 (tpp) REVERT: B 876 LEU cc_start: 0.9395 (tp) cc_final: 0.8869 (tp) REVERT: B 903 MET cc_start: 0.8914 (mmp) cc_final: 0.8689 (mmm) REVERT: B 1012 LEU cc_start: 0.9248 (mt) cc_final: 0.8905 (mp) REVERT: B 1079 CYS cc_start: 0.9119 (t) cc_final: 0.8859 (p) REVERT: B 1092 LYS cc_start: 0.9391 (mttm) cc_final: 0.8895 (tptt) REVERT: B 1202 SER cc_start: 0.9243 (m) cc_final: 0.8300 (p) REVERT: B 1427 GLN cc_start: 0.9114 (pp30) cc_final: 0.8667 (pp30) REVERT: B 1517 GLU cc_start: 0.8854 (tp30) cc_final: 0.8433 (tp30) REVERT: B 1552 LEU cc_start: 0.9336 (mt) cc_final: 0.9130 (tp) outliers start: 3 outliers final: 0 residues processed: 256 average time/residue: 0.2329 time to fit residues: 84.8441 Evaluate side-chains 189 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 90 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 474 GLN ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076220 restraints weight = 28744.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.078751 restraints weight = 18365.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080540 restraints weight = 13018.126| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9166 Z= 0.198 Angle : 0.688 10.645 12447 Z= 0.331 Chirality : 0.042 0.186 1502 Planarity : 0.004 0.080 1531 Dihedral : 7.060 143.057 1251 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.41 % Allowed : 3.93 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1138 helix: 1.58 (0.19), residues: 731 sheet: -0.04 (0.57), residues: 86 loop : -1.96 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 514 HIS 0.006 0.001 HIS B1024 PHE 0.024 0.002 PHE B1240 TYR 0.014 0.001 TYR B 454 ARG 0.005 0.000 ARG B1124 *********************** 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 267 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.898 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 219 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 305 PHE cc_start: 0.9019 (m-10) cc_final: 0.8591 (m-80) REVERT: B 314 PHE cc_start: 0.8190 (m-10) cc_final: 0.7944 (m-80) REVERT: B 419 ASN cc_start: 0.8916 (m-40) cc_final: 0.8546 (m110) REVERT: B 502 MET cc_start: 0.9493 (ttt) cc_final: 0.9256 (ttt) REVERT: B 512 TYR cc_start: 0.8409 (p90) cc_final: 0.7350 (p90) REVERT: B 514 TRP cc_start: 0.8260 (m-10) cc_final: 0.6835 (m-10) REVERT: B 530 MET cc_start: 0.9386 (tpp) cc_final: 0.9107 (tpp) REVERT: B 547 ASN cc_start: 0.8208 (m-40) cc_final: 0.7998 (m110) REVERT: B 562 HIS cc_start: 0.8388 (t70) cc_final: 0.8153 (t70) REVERT: B 615 SER cc_start: 0.9187 (t) cc_final: 0.8967 (p) REVERT: B 719 LYS cc_start: 0.9376 (mtmt) cc_final: 0.8949 (mttm) REVERT: B 801 MET cc_start: 0.8643 (tmm) cc_final: 0.8406 (tmm) REVERT: B 802 VAL cc_start: 0.9718 (t) cc_final: 0.9444 (t) REVERT: B 855 ASP cc_start: 0.8603 (t0) cc_final: 0.7967 (t0) REVERT: B 869 MET cc_start: 0.8461 (tpp) cc_final: 0.8016 (tpp) REVERT: B 903 MET cc_start: 0.9000 (mmp) cc_final: 0.8738 (mmm) REVERT: B 1005 LEU cc_start: 0.8453 (mt) cc_final: 0.8226 (pp) REVERT: B 1012 LEU cc_start: 0.9130 (mt) cc_final: 0.8890 (mp) REVERT: B 1079 CYS cc_start: 0.9120 (t) cc_final: 0.8857 (p) REVERT: B 1092 LYS cc_start: 0.9302 (mttm) cc_final: 0.8869 (tptt) REVERT: B 1202 SER cc_start: 0.9212 (m) cc_final: 0.7939 (p) REVERT: B 1428 ASP cc_start: 0.8828 (t0) cc_final: 0.8139 (p0) REVERT: B 1506 ASP cc_start: 0.8528 (t0) cc_final: 0.8274 (t0) REVERT: B 1507 GLU cc_start: 0.9080 (pt0) cc_final: 0.8682 (pt0) REVERT: B 1517 GLU cc_start: 0.8833 (tp30) cc_final: 0.8456 (tp30) outliers start: 4 outliers final: 1 residues processed: 264 average time/residue: 0.1713 time to fit residues: 65.9277 Evaluate side-chains 199 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 88 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 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 = 0.3571 r_free = 0.3571 target = 0.094788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.076145 restraints weight = 28828.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.078621 restraints weight = 18635.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.080373 restraints weight = 13256.390| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9166 Z= 0.194 Angle : 0.677 10.998 12447 Z= 0.326 Chirality : 0.042 0.166 1502 Planarity : 0.004 0.055 1531 Dihedral : 6.791 139.427 1251 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.21 % Allowed : 3.31 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.25), residues: 1138 helix: 1.71 (0.19), residues: 737 sheet: 0.15 (0.57), residues: 86 loop : -1.94 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1033 HIS 0.006 0.001 HIS B1024 PHE 0.015 0.001 PHE B1240 TYR 0.014 0.001 TYR B 454 ARG 0.008 0.000 ARG B 526 *********************** 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 238 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 0.938 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 219 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 305 PHE cc_start: 0.8968 (m-10) cc_final: 0.8752 (m-80) REVERT: B 314 PHE cc_start: 0.8266 (m-10) cc_final: 0.7778 (m-80) REVERT: B 387 LEU cc_start: 0.9615 (tp) cc_final: 0.9307 (tp) REVERT: B 502 MET cc_start: 0.9468 (ttt) cc_final: 0.9199 (ttt) REVERT: B 512 TYR cc_start: 0.8354 (p90) cc_final: 0.7198 (p90) REVERT: B 514 TRP cc_start: 0.8341 (m-10) cc_final: 0.6990 (m-10) REVERT: B 547 ASN cc_start: 0.8226 (m-40) cc_final: 0.7999 (m110) REVERT: B 719 LYS cc_start: 0.9324 (mtmt) cc_final: 0.8962 (mttp) REVERT: B 802 VAL cc_start: 0.9726 (t) cc_final: 0.9414 (t) REVERT: B 855 ASP cc_start: 0.8564 (t0) cc_final: 0.7966 (t0) REVERT: B 869 MET cc_start: 0.8555 (tpp) cc_final: 0.6736 (tpp) REVERT: B 903 MET cc_start: 0.8797 (mmp) cc_final: 0.8588 (mmm) REVERT: B 1005 LEU cc_start: 0.8481 (mt) cc_final: 0.8267 (pp) REVERT: B 1012 LEU cc_start: 0.9187 (mt) cc_final: 0.8938 (mp) REVERT: B 1079 CYS cc_start: 0.9143 (t) cc_final: 0.8856 (p) REVERT: B 1092 LYS cc_start: 0.9297 (mttm) cc_final: 0.8861 (tptt) REVERT: B 1202 SER cc_start: 0.9013 (m) cc_final: 0.8122 (p) REVERT: B 1206 GLU cc_start: 0.8391 (pm20) cc_final: 0.7999 (mp0) REVERT: B 1507 GLU cc_start: 0.9101 (pt0) cc_final: 0.8838 (pt0) REVERT: B 1517 GLU cc_start: 0.8760 (tp30) cc_final: 0.8442 (tp30) REVERT: B 1552 LEU cc_start: 0.9471 (mt) cc_final: 0.9057 (tp) outliers start: 2 outliers final: 0 residues processed: 237 average time/residue: 0.1663 time to fit residues: 57.9855 Evaluate side-chains 183 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 HIS B1234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.095177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.076481 restraints weight = 28576.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.078994 restraints weight = 18275.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.080806 restraints weight = 12962.693| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5280 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= 0.199 Angle : 0.679 11.027 12447 Z= 0.327 Chirality : 0.042 0.156 1502 Planarity : 0.004 0.050 1531 Dihedral : 6.500 131.974 1251 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.21 % Allowed : 2.48 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1138 helix: 1.81 (0.19), residues: 735 sheet: 0.33 (0.56), residues: 86 loop : -1.80 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 778 HIS 0.006 0.001 HIS B1024 PHE 0.018 0.001 PHE B 432 TYR 0.035 0.002 TYR B 893 ARG 0.007 0.000 ARG B1246 *********************** 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 231 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.988 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 219 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 233 MET cc_start: 0.8621 (mmp) cc_final: 0.8383 (tpp) REVERT: B 305 PHE cc_start: 0.9097 (m-10) cc_final: 0.8743 (m-80) REVERT: B 314 PHE cc_start: 0.8132 (m-10) cc_final: 0.7841 (m-80) REVERT: B 451 LEU cc_start: 0.9432 (tp) cc_final: 0.9210 (pp) REVERT: B 502 MET cc_start: 0.9478 (ttt) cc_final: 0.8396 (tmm) REVERT: B 512 TYR cc_start: 0.8283 (p90) cc_final: 0.7154 (p90) REVERT: B 719 LYS cc_start: 0.9387 (mtmt) cc_final: 0.9017 (mttm) REVERT: B 778 TRP cc_start: 0.9062 (p-90) cc_final: 0.8740 (p-90) REVERT: B 802 VAL cc_start: 0.9765 (t) cc_final: 0.9542 (p) REVERT: B 855 ASP cc_start: 0.8605 (t0) cc_final: 0.8012 (t0) REVERT: B 903 MET cc_start: 0.8811 (mmp) cc_final: 0.8603 (mmm) REVERT: B 1012 LEU cc_start: 0.9234 (mt) cc_final: 0.9000 (mp) REVERT: B 1079 CYS cc_start: 0.9180 (t) cc_final: 0.8868 (p) REVERT: B 1092 LYS cc_start: 0.9232 (mttm) cc_final: 0.8823 (tptt) REVERT: B 1110 MET cc_start: 0.8238 (mmm) cc_final: 0.7945 (mmm) REVERT: B 1206 GLU cc_start: 0.8420 (pm20) cc_final: 0.8156 (pm20) REVERT: B 1222 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7919 (ttp80) REVERT: B 1246 ARG cc_start: 0.8353 (tpp-160) cc_final: 0.7577 (mmm-85) REVERT: B 1395 MET cc_start: 0.8691 (tpt) cc_final: 0.8469 (tpt) REVERT: B 1428 ASP cc_start: 0.8876 (t0) cc_final: 0.8110 (p0) REVERT: B 1503 PHE cc_start: 0.8364 (m-10) cc_final: 0.8106 (m-10) REVERT: B 1505 MET cc_start: 0.8385 (mmt) cc_final: 0.8167 (mmp) REVERT: B 1506 ASP cc_start: 0.8553 (t0) cc_final: 0.8338 (t0) REVERT: B 1507 GLU cc_start: 0.9057 (pt0) cc_final: 0.8821 (pt0) REVERT: B 1517 GLU cc_start: 0.8717 (tp30) cc_final: 0.8365 (tp30) REVERT: B 1552 LEU cc_start: 0.9556 (mt) cc_final: 0.9065 (tp) outliers start: 2 outliers final: 0 residues processed: 230 average time/residue: 0.1791 time to fit residues: 60.9150 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 : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 GLN B1481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.090741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.072650 restraints weight = 29686.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.075008 restraints weight = 19100.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.076709 restraints weight = 13633.851| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9166 Z= 0.306 Angle : 0.742 10.986 12447 Z= 0.367 Chirality : 0.044 0.191 1502 Planarity : 0.004 0.052 1531 Dihedral : 6.561 122.428 1251 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 3.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1138 helix: 1.54 (0.18), residues: 747 sheet: 0.29 (0.58), residues: 86 loop : -1.82 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 232 HIS 0.005 0.001 HIS B1024 PHE 0.024 0.002 PHE B 270 TYR 0.025 0.002 TYR B 230 ARG 0.004 0.001 ARG B1246 *********************** 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 215 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.005 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 219 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 305 PHE cc_start: 0.9229 (m-10) cc_final: 0.8808 (m-80) REVERT: B 314 PHE cc_start: 0.8230 (m-10) cc_final: 0.7940 (m-80) REVERT: B 378 TYR cc_start: 0.9063 (t80) cc_final: 0.8811 (t80) REVERT: B 502 MET cc_start: 0.9467 (ttt) cc_final: 0.8587 (tmm) REVERT: B 512 TYR cc_start: 0.8697 (p90) cc_final: 0.7352 (p90) REVERT: B 710 MET cc_start: 0.8562 (mmp) cc_final: 0.8202 (mmp) REVERT: B 719 LYS cc_start: 0.9489 (mtmt) cc_final: 0.9116 (mttp) REVERT: B 778 TRP cc_start: 0.9041 (p-90) cc_final: 0.8797 (p-90) REVERT: B 855 ASP cc_start: 0.8711 (t0) cc_final: 0.8185 (t0) REVERT: B 903 MET cc_start: 0.8824 (mmp) cc_final: 0.8501 (mmm) REVERT: B 1005 LEU cc_start: 0.8509 (mt) cc_final: 0.8253 (pp) REVERT: B 1012 LEU cc_start: 0.9283 (mt) cc_final: 0.9055 (mp) REVERT: B 1079 CYS cc_start: 0.9176 (t) cc_final: 0.8892 (p) REVERT: B 1092 LYS cc_start: 0.9295 (mttm) cc_final: 0.8961 (tptt) REVERT: B 1206 GLU cc_start: 0.8493 (pm20) cc_final: 0.8167 (pm20) REVERT: B 1507 GLU cc_start: 0.9044 (pt0) cc_final: 0.8815 (pt0) REVERT: B 1517 GLU cc_start: 0.8784 (tp30) cc_final: 0.8420 (tp30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1693 time to fit residues: 54.6837 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 : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075059 restraints weight = 28807.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.077527 restraints weight = 18450.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.079330 restraints weight = 13126.703| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9166 Z= 0.194 Angle : 0.707 11.624 12447 Z= 0.337 Chirality : 0.043 0.222 1502 Planarity : 0.004 0.052 1531 Dihedral : 6.197 111.073 1251 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1138 helix: 1.79 (0.19), residues: 742 sheet: 0.28 (0.57), residues: 86 loop : -1.54 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 688 HIS 0.004 0.001 HIS B1024 PHE 0.028 0.002 PHE B1204 TYR 0.017 0.001 TYR B 893 ARG 0.004 0.000 ARG B1353 *********************** 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 227 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 270 PHE cc_start: 0.8877 (m-80) cc_final: 0.8538 (m-80) REVERT: B 305 PHE cc_start: 0.9167 (m-10) cc_final: 0.8759 (m-80) REVERT: B 314 PHE cc_start: 0.8149 (m-10) cc_final: 0.7882 (m-80) REVERT: B 378 TYR cc_start: 0.9030 (t80) cc_final: 0.8784 (t80) REVERT: B 433 PHE cc_start: 0.8850 (m-10) cc_final: 0.8491 (m-80) REVERT: B 502 MET cc_start: 0.9405 (ttt) cc_final: 0.8123 (tmm) REVERT: B 506 MET cc_start: 0.8260 (tpp) cc_final: 0.8014 (tpt) REVERT: B 512 TYR cc_start: 0.8455 (p90) cc_final: 0.7350 (p90) REVERT: B 719 LYS cc_start: 0.9413 (mtmt) cc_final: 0.8987 (mttp) REVERT: B 730 MET cc_start: 0.5895 (tpp) cc_final: 0.5125 (tpt) REVERT: B 778 TRP cc_start: 0.8986 (p-90) cc_final: 0.8773 (p-90) REVERT: B 855 ASP cc_start: 0.8565 (t0) cc_final: 0.8022 (t0) REVERT: B 903 MET cc_start: 0.8802 (mmp) cc_final: 0.8459 (mmm) REVERT: B 1005 LEU cc_start: 0.8455 (mt) cc_final: 0.8215 (pp) REVERT: B 1012 LEU cc_start: 0.9295 (mt) cc_final: 0.9053 (mp) REVERT: B 1079 CYS cc_start: 0.9148 (t) cc_final: 0.8868 (p) REVERT: B 1092 LYS cc_start: 0.9288 (mttm) cc_final: 0.9014 (mmtm) REVERT: B 1110 MET cc_start: 0.8269 (mmm) cc_final: 0.8043 (mmm) REVERT: B 1206 GLU cc_start: 0.8478 (pm20) cc_final: 0.8256 (pm20) REVERT: B 1249 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 1503 PHE cc_start: 0.8070 (m-10) cc_final: 0.7746 (m-10) REVERT: B 1505 MET cc_start: 0.7870 (mmp) cc_final: 0.7236 (mtp) REVERT: B 1507 GLU cc_start: 0.9027 (pt0) cc_final: 0.8825 (pt0) REVERT: B 1517 GLU cc_start: 0.8653 (tp30) cc_final: 0.8334 (tp30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1630 time to fit residues: 55.3935 Evaluate side-chains 182 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 37 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 B 547 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.075739 restraints weight = 29085.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.078257 restraints weight = 18614.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080069 restraints weight = 13203.957| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9166 Z= 0.194 Angle : 0.708 11.806 12447 Z= 0.340 Chirality : 0.043 0.176 1502 Planarity : 0.004 0.051 1531 Dihedral : 5.981 98.764 1251 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1138 helix: 1.77 (0.19), residues: 742 sheet: 0.30 (0.57), residues: 86 loop : -1.51 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 688 HIS 0.004 0.001 HIS B1024 PHE 0.016 0.001 PHE B1164 TYR 0.018 0.001 TYR B 893 ARG 0.004 0.000 ARG B 370 *********************** 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 227 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7464 (tm-30) REVERT: B 305 PHE cc_start: 0.9196 (m-10) cc_final: 0.8805 (m-80) REVERT: B 314 PHE cc_start: 0.8122 (m-10) cc_final: 0.7873 (m-80) REVERT: B 378 TYR cc_start: 0.9051 (t80) cc_final: 0.8790 (t80) REVERT: B 429 MET cc_start: 0.8011 (mtt) cc_final: 0.7603 (mtt) REVERT: B 433 PHE cc_start: 0.8953 (m-10) cc_final: 0.8503 (m-80) REVERT: B 502 MET cc_start: 0.9382 (ttt) cc_final: 0.8202 (tmm) REVERT: B 506 MET cc_start: 0.8085 (tpp) cc_final: 0.7867 (tpt) REVERT: B 512 TYR cc_start: 0.8407 (p90) cc_final: 0.7410 (p90) REVERT: B 562 HIS cc_start: 0.7931 (t70) cc_final: 0.7729 (t70) REVERT: B 710 MET cc_start: 0.8529 (mmp) cc_final: 0.8155 (mmp) REVERT: B 717 CYS cc_start: 0.7673 (m) cc_final: 0.7458 (m) REVERT: B 719 LYS cc_start: 0.9443 (mtmt) cc_final: 0.9046 (mttp) REVERT: B 730 MET cc_start: 0.5703 (tpp) cc_final: 0.5032 (tpp) REVERT: B 855 ASP cc_start: 0.8600 (t0) cc_final: 0.8015 (t0) REVERT: B 886 LEU cc_start: 0.9393 (tt) cc_final: 0.9164 (tt) REVERT: B 900 ILE cc_start: 0.9253 (mp) cc_final: 0.9013 (mp) REVERT: B 903 MET cc_start: 0.8728 (mmp) cc_final: 0.8392 (mmm) REVERT: B 1005 LEU cc_start: 0.8460 (mt) cc_final: 0.8221 (pp) REVERT: B 1079 CYS cc_start: 0.9344 (t) cc_final: 0.8898 (p) REVERT: B 1092 LYS cc_start: 0.9284 (mttm) cc_final: 0.8946 (mmtm) REVERT: B 1110 MET cc_start: 0.8310 (mmm) cc_final: 0.8109 (mmm) REVERT: B 1206 GLU cc_start: 0.8481 (pm20) cc_final: 0.8210 (pm20) REVERT: B 1246 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8467 (mmm-85) REVERT: B 1507 GLU cc_start: 0.9009 (pt0) cc_final: 0.8604 (pp20) REVERT: B 1517 GLU cc_start: 0.8674 (tp30) cc_final: 0.8337 (tp30) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1635 time to fit residues: 55.1823 Evaluate side-chains 177 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 0.0980 chunk 110 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3558 r_free = 0.3558 target = 0.093925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075597 restraints weight = 28919.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078066 restraints weight = 18350.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079829 restraints weight = 12991.232| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9166 Z= 0.209 Angle : 0.736 11.972 12447 Z= 0.352 Chirality : 0.044 0.175 1502 Planarity : 0.004 0.059 1531 Dihedral : 5.873 88.680 1251 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1138 helix: 1.61 (0.19), residues: 748 sheet: 0.34 (0.56), residues: 86 loop : -1.57 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 778 HIS 0.005 0.001 HIS B1024 PHE 0.025 0.002 PHE B 217 TYR 0.011 0.001 TYR B 512 ARG 0.009 0.000 ARG B1246 *********************** 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 217 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 219 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 305 PHE cc_start: 0.9189 (m-10) cc_final: 0.8739 (m-80) REVERT: B 314 PHE cc_start: 0.8023 (m-10) cc_final: 0.7772 (m-80) REVERT: B 320 ILE cc_start: 0.9656 (mt) cc_final: 0.9440 (mt) REVERT: B 378 TYR cc_start: 0.9092 (t80) cc_final: 0.8690 (t80) REVERT: B 502 MET cc_start: 0.9371 (ttt) cc_final: 0.8219 (tmm) REVERT: B 506 MET cc_start: 0.8205 (tpp) cc_final: 0.7962 (tpt) REVERT: B 512 TYR cc_start: 0.8463 (p90) cc_final: 0.7440 (p90) REVERT: B 710 MET cc_start: 0.8505 (mmp) cc_final: 0.8181 (mmp) REVERT: B 719 LYS cc_start: 0.9420 (mtmt) cc_final: 0.9070 (mttp) REVERT: B 730 MET cc_start: 0.5478 (tpp) cc_final: 0.4832 (tpp) REVERT: B 855 ASP cc_start: 0.8570 (t0) cc_final: 0.7984 (t0) REVERT: B 869 MET cc_start: 0.8566 (tpp) cc_final: 0.6418 (tpp) REVERT: B 886 LEU cc_start: 0.9411 (tt) cc_final: 0.9181 (tt) REVERT: B 903 MET cc_start: 0.8808 (mmp) cc_final: 0.8445 (mmm) REVERT: B 1005 LEU cc_start: 0.8424 (mt) cc_final: 0.8187 (pp) REVERT: B 1079 CYS cc_start: 0.9372 (t) cc_final: 0.8990 (p) REVERT: B 1092 LYS cc_start: 0.9265 (mttm) cc_final: 0.8992 (mmtm) REVERT: B 1206 GLU cc_start: 0.8465 (pm20) cc_final: 0.8167 (pm20) REVERT: B 1285 LEU cc_start: 0.9298 (mm) cc_final: 0.8616 (tt) REVERT: B 1503 PHE cc_start: 0.8113 (m-10) cc_final: 0.7575 (m-10) REVERT: B 1505 MET cc_start: 0.8207 (mmt) cc_final: 0.7692 (mtp) REVERT: B 1507 GLU cc_start: 0.8987 (pt0) cc_final: 0.8638 (pp20) REVERT: B 1517 GLU cc_start: 0.8577 (tp30) cc_final: 0.8274 (tp30) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1630 time to fit residues: 52.7958 Evaluate side-chains 168 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 0.0010 chunk 65 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076417 restraints weight = 29121.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078958 restraints weight = 18589.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.080774 restraints weight = 13177.392| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9166 Z= 0.185 Angle : 0.722 11.928 12447 Z= 0.348 Chirality : 0.044 0.278 1502 Planarity : 0.004 0.052 1531 Dihedral : 5.727 83.013 1251 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1138 helix: 1.63 (0.19), residues: 748 sheet: 0.33 (0.56), residues: 86 loop : -1.56 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 778 HIS 0.004 0.001 HIS B1316 PHE 0.019 0.001 PHE B 217 TYR 0.052 0.002 TYR B 893 ARG 0.007 0.000 ARG B1246 ********************** 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 220 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.977 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 219 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 305 PHE cc_start: 0.9167 (m-10) cc_final: 0.8735 (m-80) REVERT: B 314 PHE cc_start: 0.8041 (m-10) cc_final: 0.7809 (m-80) REVERT: B 320 ILE cc_start: 0.9634 (mt) cc_final: 0.9404 (mt) REVERT: B 378 TYR cc_start: 0.9033 (t80) cc_final: 0.8685 (t80) REVERT: B 502 MET cc_start: 0.9325 (ttt) cc_final: 0.8184 (tmm) REVERT: B 506 MET cc_start: 0.8143 (tpp) cc_final: 0.7940 (tpt) REVERT: B 512 TYR cc_start: 0.8393 (p90) cc_final: 0.7421 (p90) REVERT: B 710 MET cc_start: 0.8535 (mmp) cc_final: 0.8176 (mmp) REVERT: B 719 LYS cc_start: 0.9400 (mtmt) cc_final: 0.9083 (mttp) REVERT: B 730 MET cc_start: 0.5430 (tpp) cc_final: 0.4801 (tpp) REVERT: B 855 ASP cc_start: 0.8463 (t0) cc_final: 0.7893 (t0) REVERT: B 903 MET cc_start: 0.8828 (mmp) cc_final: 0.8498 (mmm) REVERT: B 1079 CYS cc_start: 0.9370 (t) cc_final: 0.8946 (p) REVERT: B 1092 LYS cc_start: 0.9283 (mttm) cc_final: 0.8959 (mmtm) REVERT: B 1206 GLU cc_start: 0.8426 (pm20) cc_final: 0.8124 (pm20) REVERT: B 1285 LEU cc_start: 0.9252 (mm) cc_final: 0.8507 (tt) REVERT: B 1406 ASP cc_start: 0.7640 (t70) cc_final: 0.7269 (m-30) REVERT: B 1503 PHE cc_start: 0.8107 (m-10) cc_final: 0.7648 (m-10) REVERT: B 1505 MET cc_start: 0.8255 (mmt) cc_final: 0.7777 (mtp) REVERT: B 1507 GLU cc_start: 0.8978 (pt0) cc_final: 0.8686 (pp20) REVERT: B 1517 GLU cc_start: 0.8537 (tp30) cc_final: 0.8268 (tp30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1748 time to fit residues: 57.1647 Evaluate side-chains 173 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.0370 chunk 38 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.076745 restraints weight = 28646.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.079267 restraints weight = 18293.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081081 restraints weight = 12974.805| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9166 Z= 0.188 Angle : 0.719 12.064 12447 Z= 0.344 Chirality : 0.043 0.216 1502 Planarity : 0.004 0.054 1531 Dihedral : 5.657 79.648 1251 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1138 helix: 1.68 (0.18), residues: 750 sheet: 0.41 (0.56), residues: 86 loop : -1.55 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 288 HIS 0.004 0.001 HIS B1024 PHE 0.016 0.001 PHE B 217 TYR 0.038 0.001 TYR B 893 ARG 0.007 0.000 ARG B1246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2884.90 seconds wall clock time: 51 minutes 9.21 seconds (3069.21 seconds total)