Starting phenix.real_space_refine on Fri Sep 11 12:38:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.cif" model { file = "/net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yw7_6847/09_2026/5yw7_6847.cif" } resolution = 4.4 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 3 5.49 5 S 49 5.16 5 Cl 1 4.86 5 C 5785 2.51 5 N 1524 2.21 5 O 1582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8944 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 8880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8880 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1102} Chain breaks: 8 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'ARG:plan': 3, 'ASP:plan': 5, 'GLU:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.07, per 1000 atoms: 0.23 Number of scatterers: 8944 At special positions: 0 Unit cell: (107.61, 78.07, 132.93, 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) Cl 1 17.00 S 49 16.00 P 3 15.00 O 1582 8.00 N 1524 7.00 C 5785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 357.9 milliseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 69.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 232 through 243 removed outlier: 4.250A pdb=" N PHE B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.616A pdb=" N ASN B 262 " --> pdb=" O ARG B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 329 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 355 through 402 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 402 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 423 Processing helix chain 'B' and resid 423 through 457 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix Processing helix chain 'B' and resid 457 through 503 removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.595A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N MET B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 removed outlier: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 560 removed outlier: 3.655A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 615 removed outlier: 3.532A pdb=" N ALA B 576 " --> pdb=" O SER B 572 " (cutoff:3.500A) Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (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 796 through 806 Processing helix chain 'B' and resid 808 through 815 removed outlier: 3.579A pdb=" N LEU B 815 " --> pdb=" O ASP B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 846 removed outlier: 3.543A pdb=" N GLN B 846 " --> pdb=" O ARG B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 872 Processing helix chain 'B' and resid 893 through 897 removed outlier: 3.652A pdb=" N ALA B 897 " --> pdb=" O LEU B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 997 through 1007 removed outlier: 4.439A pdb=" N CYS B1001 " --> pdb=" O PRO B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1039 removed outlier: 3.532A pdb=" N LEU B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP B1039 " --> pdb=" O ALA B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1107 removed outlier: 3.541A 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 1127 removed outlier: 3.828A pdb=" N ILE B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1161 Proline residue: B1137 - end of helix removed outlier: 3.576A pdb=" N THR B1161 " --> pdb=" O ILE B1157 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1210 removed outlier: 3.588A pdb=" N LEU B1165 " --> pdb=" O THR B1161 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1218 Processing helix chain 'B' and resid 1219 through 1271 removed outlier: 3.724A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1289 removed outlier: 4.573A pdb=" N VAL B1281 " --> pdb=" O SER B1277 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1320 removed outlier: 3.639A pdb=" N TYR B1294 " --> pdb=" O MET B1290 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1384 through 1393 Processing helix chain 'B' and resid 1414 through 1420 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 Processing helix chain 'B' and resid 1483 through 1499 removed outlier: 3.855A pdb=" N LYS B1499 " --> pdb=" O ALA B1495 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1528 removed outlier: 4.097A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1539 through 1546 removed outlier: 3.674A pdb=" N ILE B1543 " --> pdb=" O ARG B1539 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B1546 " --> pdb=" O THR B1542 " (cutoff:3.500A) Processing helix chain 'B' and resid 1562 through 1570 removed outlier: 4.306A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS B1570 " --> pdb=" O LEU B1566 " (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: 6.709A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL B 851 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL B 887 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 853 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 900 " --> pdb=" O GLU B 911 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU B 911 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA B 902 " --> pdb=" O GLN B 909 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1365 through 1369 removed outlier: 7.090A pdb=" N ALA B1367 " --> pdb=" O GLN B1348 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLN B1348 " --> pdb=" O ALA B1367 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE B1369 " --> pdb=" O GLN B1346 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN B1346 " --> pdb=" O ILE B1369 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B1347 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE B1404 " --> pdb=" O ILE B1347 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ASN B1349 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG B1402 " --> pdb=" O ASN B1349 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1423 through 1425 removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1695 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: 1.53 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3342 1.38 - 1.56: 5688 1.56 - 1.73: 8 1.73 - 1.90: 75 1.90 - 2.08: 1 Bond restraints: 9114 Sorted by residual: bond pdb=" C4 AGS B2002 " pdb=" C5 AGS B2002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.11e+01 bond pdb=" C18 GBM B2001 " pdb=" S2 GBM B2001 " ideal model delta sigma weight residual 1.765 1.604 0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" C5 AGS B2002 " pdb=" C6 AGS B2002 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" PG AGS B2002 " pdb=" S1G AGS B2002 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" C8 AGS B2002 " pdb=" N7 AGS B2002 " ideal model delta sigma weight residual 1.311 1.357 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 12179 2.40 - 4.79: 151 4.79 - 7.19: 29 7.19 - 9.58: 7 9.58 - 11.98: 3 Bond angle restraints: 12369 Sorted by residual: angle pdb=" C5 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N3 AGS B2002 " ideal model delta sigma weight residual 126.80 118.59 8.21 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C4 AGS B2002 " pdb=" C5 AGS B2002 " pdb=" N7 AGS B2002 " ideal model delta sigma weight residual 110.73 106.71 4.02 4.52e-01 4.89e+00 7.91e+01 angle pdb=" C5 AGS B2002 " pdb=" N7 AGS B2002 " pdb=" C8 AGS B2002 " ideal model delta sigma weight residual 103.67 107.37 -3.70 4.26e-01 5.51e+00 7.52e+01 angle pdb=" N3 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N9 AGS B2002 " ideal model delta sigma weight residual 127.16 135.21 -8.05 1.06e+00 8.92e-01 5.78e+01 angle pdb=" C SER B 532 " pdb=" N LEU B 533 " pdb=" CA LEU B 533 " ideal model delta sigma weight residual 120.28 130.85 -10.57 1.44e+00 4.82e-01 5.39e+01 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.76: 5209 24.76 - 49.52: 206 49.52 - 74.28: 31 74.28 - 99.05: 0 99.05 - 123.81: 2 Dihedral angle restraints: 5448 sinusoidal: 2128 harmonic: 3320 Sorted by residual: dihedral pdb=" CA PHE B 295 " pdb=" C PHE B 295 " pdb=" N GLY B 296 " pdb=" CA GLY B 296 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" N SER B1501 " pdb=" C SER B1501 " pdb=" CA SER B1501 " pdb=" CB SER B1501 " ideal model delta harmonic sigma weight residual 122.80 133.62 -10.82 0 2.50e+00 1.60e-01 1.87e+01 dihedral pdb=" CA GLY B 296 " pdb=" C GLY B 296 " pdb=" N ARG B 297 " pdb=" CA ARG B 297 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 5445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1378 0.075 - 0.149: 98 0.149 - 0.224: 10 0.224 - 0.299: 4 0.299 - 0.373: 2 Chirality restraints: 1492 Sorted by residual: chirality pdb=" CA LYS B1444 " pdb=" N LYS B1444 " pdb=" C LYS B1444 " pdb=" CB LYS B1444 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA SER B1501 " pdb=" N SER B1501 " pdb=" C SER B1501 " pdb=" CB SER B1501 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA ASP B1133 " pdb=" N ASP B1133 " pdb=" C ASP B1133 " pdb=" CB ASP B1133 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1489 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM B2001 " -0.321 2.00e-02 2.50e+03 2.73e-01 9.29e+02 pdb=" C26 GBM B2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM B2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM B2001 " 0.478 2.00e-02 2.50e+03 pdb=" O6 GBM B2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 GBM B2001 " 0.081 2.00e-02 2.50e+03 7.61e-02 8.68e+01 pdb=" C17 GBM B2001 " -0.037 2.00e-02 2.50e+03 pdb=" N8 GBM B2001 " -0.039 2.00e-02 2.50e+03 pdb=" N9 GBM B2001 " -0.130 2.00e-02 2.50e+03 pdb=" O3 GBM B2001 " 0.047 2.00e-02 2.50e+03 pdb=" S2 GBM B2001 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B1128 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C ASP B1128 " -0.067 2.00e-02 2.50e+03 pdb=" O ASP B1128 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS B1129 " 0.023 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1778 2.78 - 3.31: 9102 3.31 - 3.84: 14871 3.84 - 4.37: 16363 4.37 - 4.90: 28009 Nonbonded interactions: 70123 Sorted by model distance: nonbonded pdb=" OD2 ASP B1031 " pdb=" OH TYR B1287 " model vdw 2.246 3.040 nonbonded pdb=" CB TYR B 512 " pdb=" NH2 ARG B1498 " model vdw 2.269 3.520 nonbonded pdb=" O SER B1126 " pdb=" ND2 ASN B1130 " model vdw 2.275 3.120 nonbonded pdb=" O GLN B 846 " pdb=" NH2 ARG B 882 " model vdw 2.308 3.120 nonbonded pdb=" O THR B 783 " pdb=" ND2 ASN B 787 " model vdw 2.309 3.120 ... (remaining 70118 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.010 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 : 0.004 0.161 9114 Z= 0.277 Angle : 0.710 11.976 12369 Z= 0.444 Chirality : 0.046 0.373 1492 Planarity : 0.008 0.273 1516 Dihedral : 13.007 123.808 3286 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.49 % Allowed : 8.97 % Favored : 84.54 % Cbeta Deviations : 0.09 % 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: -2.58 (0.22), residues: 1122 helix: -1.14 (0.17), residues: 750 sheet: -1.78 (0.54), residues: 79 loop : -2.81 (0.31), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1494 TYR 0.014 0.001 TYR B 378 PHE 0.016 0.001 PHE B 305 TRP 0.010 0.001 TRP B1037 HIS 0.004 0.001 HIS B 584 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.28 ( 9114) covalent geometry : angle 0.71015 / 0.44 (12369) hydrogen bonds : bond 0.16066 / 10.29 ( 574) hydrogen bonds : angle 6.59212 / 4.75 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 0.437 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 227 LYS cc_start: 0.8996 (mtpp) cc_final: 0.7907 (tttt) REVERT: B 233 MET cc_start: 0.9511 (mmm) cc_final: 0.9075 (mmm) REVERT: B 263 TYR cc_start: 0.9117 (t80) cc_final: 0.8846 (t80) REVERT: B 270 PHE cc_start: 0.8821 (t80) cc_final: 0.8545 (t80) REVERT: B 299 LEU cc_start: 0.9230 (tp) cc_final: 0.8882 (tt) REVERT: B 306 ARG cc_start: 0.8570 (tpt90) cc_final: 0.8203 (tpp80) REVERT: B 320 ILE cc_start: 0.9508 (mt) cc_final: 0.9235 (mt) REVERT: B 367 LEU cc_start: 0.9377 (pp) cc_final: 0.9161 (pp) REVERT: B 374 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9136 (mm-40) REVERT: B 510 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9054 (mtmt) REVERT: B 581 SER cc_start: 0.9663 (m) cc_final: 0.9341 (p) REVERT: B 590 LEU cc_start: 0.9261 (mt) cc_final: 0.8896 (tp) REVERT: B 708 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8280 (tt) REVERT: B 730 MET cc_start: 0.7236 (mtm) cc_final: 0.6738 (mtp) REVERT: B 820 GLN cc_start: 0.9011 (mt0) cc_final: 0.8753 (mp10) REVERT: B 869 MET cc_start: 0.9030 (tmm) cc_final: 0.8492 (tmm) REVERT: B 886 LEU cc_start: 0.9249 (tt) cc_final: 0.8385 (tt) REVERT: B 1064 TYR cc_start: 0.7769 (m-80) cc_final: 0.7375 (m-80) REVERT: B 1078 LEU cc_start: 0.9037 (tp) cc_final: 0.8640 (tp) REVERT: B 1104 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.7933 (tpp80) REVERT: B 1146 SER cc_start: 0.9252 (m) cc_final: 0.8715 (p) REVERT: B 1190 GLN cc_start: 0.9228 (tp40) cc_final: 0.8865 (tt0) REVERT: B 1206 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 1214 ILE cc_start: 0.9600 (mt) cc_final: 0.9296 (tp) REVERT: B 1232 ASP cc_start: 0.8570 (t70) cc_final: 0.8351 (t70) REVERT: B 1246 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.9247 (mmp80) REVERT: B 1301 ASN cc_start: 0.8902 (m110) cc_final: 0.8693 (m110) REVERT: B 1305 MET cc_start: 0.8941 (tpt) cc_final: 0.8537 (tpt) REVERT: B 1490 PHE cc_start: 0.9192 (m-80) cc_final: 0.8672 (m-80) REVERT: B 1505 MET cc_start: 0.7959 (ttm) cc_final: 0.7382 (mmt) REVERT: B 1550 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8294 (ttt) REVERT: B 1551 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8399 (p) REVERT: B 1561 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7942 (p0) outliers start: 63 outliers final: 20 residues processed: 374 average time/residue: 0.0932 time to fit residues: 48.7347 Evaluate side-chains 225 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0070 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B 416 GLN B 846 GLN B1134 GLN B1135 HIS ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1541 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.080589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061140 restraints weight = 32937.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063117 restraints weight = 19465.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064470 restraints weight = 13297.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065412 restraints weight = 10005.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066061 restraints weight = 8137.246| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9114 Z= 0.195 Angle : 0.716 10.168 12369 Z= 0.364 Chirality : 0.044 0.170 1492 Planarity : 0.005 0.059 1516 Dihedral : 6.761 115.032 1236 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.31 % Allowed : 4.12 % Favored : 95.57 % 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: -0.95 (0.24), residues: 1122 helix: 0.18 (0.18), residues: 751 sheet: -1.48 (0.54), residues: 79 loop : -2.35 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG B1251 TYR 0.020 0.002 TYR B 512 PHE 0.021 0.002 PHE B1240 TRP 0.028 0.002 TRP B1247 HIS 0.004 0.001 HIS B1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.19 ( 9114) covalent geometry : angle 0.71616 / 0.36 (12369) hydrogen bonds : bond 0.06829 / 4.30 ( 574) hydrogen bonds : angle 5.03208 / 3.62 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 248 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 222 VAL cc_start: 0.8750 (m) cc_final: 0.8269 (p) REVERT: B 227 LYS cc_start: 0.9098 (mtpp) cc_final: 0.8050 (tttt) REVERT: B 233 MET cc_start: 0.9033 (mmm) cc_final: 0.8671 (mmm) REVERT: B 306 ARG cc_start: 0.8923 (tpt90) cc_final: 0.8690 (tpp80) REVERT: B 433 PHE cc_start: 0.8629 (m-10) cc_final: 0.8302 (m-10) REVERT: B 581 SER cc_start: 0.9665 (m) cc_final: 0.9405 (p) REVERT: B 602 LYS cc_start: 0.9242 (tptt) cc_final: 0.8887 (tptp) REVERT: B 808 LEU cc_start: 0.9153 (tp) cc_final: 0.8881 (tp) REVERT: B 869 MET cc_start: 0.8404 (tmm) cc_final: 0.7928 (tmm) REVERT: B 1078 LEU cc_start: 0.9194 (tp) cc_final: 0.8989 (tp) REVERT: B 1104 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8094 (tpp80) REVERT: B 1128 ASP cc_start: 0.8408 (m-30) cc_final: 0.7690 (m-30) REVERT: B 1148 LEU cc_start: 0.9196 (mm) cc_final: 0.8952 (mt) REVERT: B 1290 MET cc_start: 0.8972 (ttm) cc_final: 0.8610 (ttp) REVERT: B 1305 MET cc_start: 0.8510 (tpt) cc_final: 0.8272 (tpt) REVERT: B 1431 LEU cc_start: 0.8973 (mt) cc_final: 0.8709 (pt) REVERT: B 1490 PHE cc_start: 0.9129 (m-80) cc_final: 0.8789 (m-80) outliers start: 3 outliers final: 0 residues processed: 250 average time/residue: 0.0758 time to fit residues: 27.8637 Evaluate side-chains 170 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 0.0020 chunk 47 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 106 optimal weight: 0.0020 chunk 96 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B 781 ASN B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.082373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.062940 restraints weight = 32360.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.064890 restraints weight = 19462.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066248 restraints weight = 13329.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.067175 restraints weight = 10071.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.067793 restraints weight = 8216.508| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9114 Z= 0.149 Angle : 0.648 9.261 12369 Z= 0.322 Chirality : 0.041 0.152 1492 Planarity : 0.004 0.044 1516 Dihedral : 6.689 119.829 1236 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % 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: -0.07 (0.25), residues: 1122 helix: 0.89 (0.19), residues: 759 sheet: -1.32 (0.53), residues: 79 loop : -2.13 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 388 TYR 0.027 0.001 TYR B 512 PHE 0.030 0.002 PHE B 295 TRP 0.028 0.002 TRP B 514 HIS 0.003 0.001 HIS B1203 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 ( 9114) covalent geometry : angle 0.64822 / 0.32 (12369) hydrogen bonds : bond 0.06085 / 3.83 ( 574) hydrogen bonds : angle 4.55723 / 3.31 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8132 (tttt) REVERT: B 233 MET cc_start: 0.9004 (mmm) cc_final: 0.8648 (mmm) REVERT: B 319 CYS cc_start: 0.9076 (m) cc_final: 0.8593 (t) REVERT: B 361 LEU cc_start: 0.9616 (mm) cc_final: 0.9100 (tp) REVERT: B 420 LEU cc_start: 0.9088 (mt) cc_final: 0.8883 (mt) REVERT: B 581 SER cc_start: 0.9674 (m) cc_final: 0.9385 (p) REVERT: B 583 PHE cc_start: 0.9143 (m-10) cc_final: 0.8887 (m-10) REVERT: B 602 LYS cc_start: 0.9187 (tptt) cc_final: 0.8851 (tptp) REVERT: B 808 LEU cc_start: 0.9024 (tp) cc_final: 0.8584 (tp) REVERT: B 838 ILE cc_start: 0.9812 (mt) cc_final: 0.9598 (tp) REVERT: B 869 MET cc_start: 0.7983 (tmm) cc_final: 0.7757 (tmm) REVERT: B 1078 LEU cc_start: 0.9239 (tp) cc_final: 0.8984 (tp) REVERT: B 1104 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8084 (tpp80) REVERT: B 1128 ASP cc_start: 0.8292 (m-30) cc_final: 0.7660 (m-30) REVERT: B 1148 LEU cc_start: 0.9198 (mm) cc_final: 0.8967 (mt) REVERT: B 1246 ARG cc_start: 0.9499 (mmp80) cc_final: 0.9133 (mmp80) REVERT: B 1290 MET cc_start: 0.8780 (ttm) cc_final: 0.8360 (ttp) REVERT: B 1305 MET cc_start: 0.8530 (tpt) cc_final: 0.8303 (tpt) REVERT: B 1431 LEU cc_start: 0.9048 (mt) cc_final: 0.8650 (pt) REVERT: B 1490 PHE cc_start: 0.9102 (m-80) cc_final: 0.8705 (m-80) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.0763 time to fit residues: 26.7227 Evaluate side-chains 169 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 38 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B1134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.063290 restraints weight = 32784.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.065344 restraints weight = 19595.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.066669 restraints weight = 13329.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.067599 restraints weight = 10122.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068165 restraints weight = 8290.296| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9114 Z= 0.141 Angle : 0.632 8.065 12369 Z= 0.315 Chirality : 0.041 0.140 1492 Planarity : 0.004 0.047 1516 Dihedral : 6.557 116.682 1236 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.10 % Allowed : 2.27 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.25), residues: 1122 helix: 1.08 (0.19), residues: 753 sheet: -1.11 (0.53), residues: 79 loop : -1.87 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1419 TYR 0.013 0.001 TYR B 378 PHE 0.026 0.002 PHE B1223 TRP 0.016 0.001 TRP B1247 HIS 0.002 0.001 HIS B1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 9114) covalent geometry : angle 0.63235 / 0.32 (12369) hydrogen bonds : bond 0.05653 / 3.55 ( 574) hydrogen bonds : angle 4.41626 / 3.25 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9115 (mtpp) cc_final: 0.8123 (tttt) REVERT: B 233 MET cc_start: 0.9095 (mmm) cc_final: 0.8599 (mmm) REVERT: B 319 CYS cc_start: 0.9092 (m) cc_final: 0.8618 (t) REVERT: B 361 LEU cc_start: 0.9564 (mm) cc_final: 0.9073 (tp) REVERT: B 503 LEU cc_start: 0.9120 (mm) cc_final: 0.8683 (tp) REVERT: B 512 TYR cc_start: 0.7429 (p90) cc_final: 0.7097 (p90) REVERT: B 583 PHE cc_start: 0.9133 (m-10) cc_final: 0.8866 (m-10) REVERT: B 602 LYS cc_start: 0.9159 (tptt) cc_final: 0.8846 (tptp) REVERT: B 699 ILE cc_start: 0.8747 (mm) cc_final: 0.8534 (mm) REVERT: B 808 LEU cc_start: 0.9039 (tp) cc_final: 0.8800 (tp) REVERT: B 1078 LEU cc_start: 0.9260 (tp) cc_final: 0.9001 (tp) REVERT: B 1104 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.7962 (tpp80) REVERT: B 1124 ARG cc_start: 0.8522 (mmp80) cc_final: 0.8058 (mmp80) REVERT: B 1128 ASP cc_start: 0.8329 (m-30) cc_final: 0.7411 (m-30) REVERT: B 1246 ARG cc_start: 0.9468 (mmp80) cc_final: 0.9086 (mmp80) REVERT: B 1258 CYS cc_start: 0.8955 (t) cc_final: 0.8752 (t) REVERT: B 1305 MET cc_start: 0.8559 (tpt) cc_final: 0.8319 (tpt) REVERT: B 1398 MET cc_start: 0.4314 (ttm) cc_final: 0.2279 (mtm) REVERT: B 1490 PHE cc_start: 0.9108 (m-80) cc_final: 0.8642 (m-80) REVERT: B 1505 MET cc_start: 0.6421 (mmp) cc_final: 0.5622 (ttp) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.0741 time to fit residues: 24.9685 Evaluate side-chains 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 85 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 64.0279 > 50:) chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B1134 GLN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.062866 restraints weight = 32776.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064831 restraints weight = 19552.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066157 restraints weight = 13344.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.067066 restraints weight = 10112.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.067667 restraints weight = 8254.798| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9114 Z= 0.152 Angle : 0.626 7.896 12369 Z= 0.313 Chirality : 0.041 0.145 1492 Planarity : 0.004 0.048 1516 Dihedral : 6.519 116.034 1236 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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: 0.37 (0.25), residues: 1122 helix: 1.13 (0.18), residues: 764 sheet: -0.89 (0.55), residues: 79 loop : -1.80 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1419 TYR 0.048 0.002 TYR B 512 PHE 0.021 0.002 PHE B 433 TRP 0.022 0.002 TRP B 514 HIS 0.003 0.001 HIS B1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 9114) covalent geometry : angle 0.62558 / 0.31 (12369) hydrogen bonds : bond 0.05392 / 3.38 ( 574) hydrogen bonds : angle 4.40886 / 3.21 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8122 (tttt) REVERT: B 233 MET cc_start: 0.9097 (mmm) cc_final: 0.8796 (tpp) REVERT: B 319 CYS cc_start: 0.9057 (m) cc_final: 0.8599 (t) REVERT: B 361 LEU cc_start: 0.9561 (mm) cc_final: 0.9041 (tp) REVERT: B 530 MET cc_start: 0.9050 (mmt) cc_final: 0.8666 (mmt) REVERT: B 583 PHE cc_start: 0.9104 (m-10) cc_final: 0.8835 (m-10) REVERT: B 602 LYS cc_start: 0.9168 (tptt) cc_final: 0.8871 (tptp) REVERT: B 710 MET cc_start: 0.8718 (tpp) cc_final: 0.8433 (tpp) REVERT: B 808 LEU cc_start: 0.9016 (tp) cc_final: 0.8696 (tp) REVERT: B 1078 LEU cc_start: 0.9280 (tp) cc_final: 0.9023 (tp) REVERT: B 1091 LEU cc_start: 0.8938 (tt) cc_final: 0.8727 (tt) REVERT: B 1104 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.7961 (tpp80) REVERT: B 1124 ARG cc_start: 0.8575 (mmp80) cc_final: 0.8115 (mmp80) REVERT: B 1128 ASP cc_start: 0.8367 (m-30) cc_final: 0.7524 (m-30) REVERT: B 1246 ARG cc_start: 0.9367 (mmp80) cc_final: 0.9061 (mmp80) REVERT: B 1490 PHE cc_start: 0.9077 (m-80) cc_final: 0.8635 (m-80) REVERT: B 1505 MET cc_start: 0.6502 (mmp) cc_final: 0.5786 (ttp) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0752 time to fit residues: 22.9972 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.081655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062685 restraints weight = 32889.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064651 restraints weight = 19718.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.065980 restraints weight = 13434.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.066885 restraints weight = 10092.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.067468 restraints weight = 8214.303| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9114 Z= 0.160 Angle : 0.638 7.806 12369 Z= 0.321 Chirality : 0.041 0.146 1492 Planarity : 0.004 0.043 1516 Dihedral : 6.509 115.799 1236 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: 0.38 (0.25), residues: 1122 helix: 1.11 (0.18), residues: 761 sheet: -0.35 (0.59), residues: 72 loop : -1.84 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1419 TYR 0.021 0.001 TYR B 512 PHE 0.031 0.002 PHE B1393 TRP 0.023 0.001 TRP B 514 HIS 0.003 0.001 HIS B1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 9114) covalent geometry : angle 0.63796 / 0.32 (12369) hydrogen bonds : bond 0.05280 / 3.31 ( 574) hydrogen bonds : angle 4.35632 / 3.18 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8096 (tttt) REVERT: B 233 MET cc_start: 0.9229 (mmm) cc_final: 0.8933 (tpp) REVERT: B 319 CYS cc_start: 0.9087 (m) cc_final: 0.8600 (t) REVERT: B 361 LEU cc_start: 0.9609 (mm) cc_final: 0.9140 (tp) REVERT: B 506 MET cc_start: 0.8198 (pmm) cc_final: 0.7990 (pmm) REVERT: B 508 LEU cc_start: 0.9466 (tp) cc_final: 0.9073 (tp) REVERT: B 530 MET cc_start: 0.9061 (mmt) cc_final: 0.8782 (mmt) REVERT: B 583 PHE cc_start: 0.9109 (m-10) cc_final: 0.8854 (m-10) REVERT: B 602 LYS cc_start: 0.9188 (tptt) cc_final: 0.8883 (tptp) REVERT: B 710 MET cc_start: 0.8759 (tpp) cc_final: 0.8501 (tpp) REVERT: B 808 LEU cc_start: 0.9059 (tp) cc_final: 0.8750 (tp) REVERT: B 1078 LEU cc_start: 0.9274 (tp) cc_final: 0.9029 (tt) REVERT: B 1091 LEU cc_start: 0.8940 (tt) cc_final: 0.8720 (tt) REVERT: B 1104 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.7995 (tpp80) REVERT: B 1124 ARG cc_start: 0.8642 (mmp80) cc_final: 0.8153 (mmp80) REVERT: B 1128 ASP cc_start: 0.8394 (m-30) cc_final: 0.7449 (m-30) REVERT: B 1246 ARG cc_start: 0.9513 (mmp80) cc_final: 0.9077 (mmp80) REVERT: B 1258 CYS cc_start: 0.8960 (t) cc_final: 0.8744 (t) REVERT: B 1424 ILE cc_start: 0.9248 (tp) cc_final: 0.8937 (tp) REVERT: B 1490 PHE cc_start: 0.9098 (m-80) cc_final: 0.8893 (m-80) REVERT: B 1504 ILE cc_start: 0.8698 (pt) cc_final: 0.8337 (pt) REVERT: B 1505 MET cc_start: 0.6598 (mmp) cc_final: 0.6043 (ttp) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.0749 time to fit residues: 23.3763 Evaluate side-chains 148 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 102 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063719 restraints weight = 33126.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065597 restraints weight = 19843.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.066943 restraints weight = 13604.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067848 restraints weight = 10296.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.068438 restraints weight = 8436.860| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9114 Z= 0.136 Angle : 0.614 7.952 12369 Z= 0.308 Chirality : 0.041 0.184 1492 Planarity : 0.004 0.044 1516 Dihedral : 6.356 113.966 1236 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 0.58 (0.25), residues: 1122 helix: 1.25 (0.18), residues: 762 sheet: -0.39 (0.60), residues: 72 loop : -1.73 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1419 TYR 0.038 0.001 TYR B 512 PHE 0.021 0.002 PHE B 433 TRP 0.024 0.001 TRP B 514 HIS 0.003 0.000 HIS B1024 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 9114) covalent geometry : angle 0.61391 / 0.31 (12369) hydrogen bonds : bond 0.05146 / 3.25 ( 574) hydrogen bonds : angle 4.29832 / 3.15 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8048 (tttt) REVERT: B 233 MET cc_start: 0.9125 (mmm) cc_final: 0.8644 (mmm) REVERT: B 319 CYS cc_start: 0.9029 (m) cc_final: 0.8453 (t) REVERT: B 323 ILE cc_start: 0.9345 (mm) cc_final: 0.9088 (mm) REVERT: B 361 LEU cc_start: 0.9561 (mm) cc_final: 0.9102 (tp) REVERT: B 394 LYS cc_start: 0.9175 (tppp) cc_final: 0.8829 (tppt) REVERT: B 530 MET cc_start: 0.9037 (mmt) cc_final: 0.8763 (mmt) REVERT: B 602 LYS cc_start: 0.9133 (tptt) cc_final: 0.8912 (tptm) REVERT: B 710 MET cc_start: 0.8712 (tpp) cc_final: 0.8431 (tpp) REVERT: B 730 MET cc_start: 0.6264 (mtt) cc_final: 0.5912 (mmm) REVERT: B 808 LEU cc_start: 0.9147 (tp) cc_final: 0.8799 (tp) REVERT: B 1078 LEU cc_start: 0.9311 (tp) cc_final: 0.9045 (tt) REVERT: B 1091 LEU cc_start: 0.8944 (tt) cc_final: 0.8721 (tt) REVERT: B 1104 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7940 (tpp80) REVERT: B 1124 ARG cc_start: 0.8514 (mmp80) cc_final: 0.8100 (mmp80) REVERT: B 1128 ASP cc_start: 0.8229 (m-30) cc_final: 0.7328 (m-30) REVERT: B 1229 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8395 (tm-30) REVERT: B 1246 ARG cc_start: 0.9311 (mmp80) cc_final: 0.9077 (mmp80) REVERT: B 1258 CYS cc_start: 0.8855 (t) cc_final: 0.8627 (t) REVERT: B 1377 ILE cc_start: 0.9505 (mm) cc_final: 0.9269 (mp) REVERT: B 1504 ILE cc_start: 0.8819 (pt) cc_final: 0.8411 (pt) REVERT: B 1505 MET cc_start: 0.6626 (mmp) cc_final: 0.6151 (ttp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0740 time to fit residues: 23.9100 Evaluate side-chains 157 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 0.0270 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.082785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.063853 restraints weight = 32903.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065763 restraints weight = 19736.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.067083 restraints weight = 13551.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.067841 restraints weight = 10271.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.068489 restraints weight = 8507.828| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.137 Angle : 0.630 7.824 12369 Z= 0.315 Chirality : 0.041 0.165 1492 Planarity : 0.004 0.045 1516 Dihedral : 6.381 113.525 1236 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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 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: 0.54 (0.25), residues: 1122 helix: 1.21 (0.18), residues: 761 sheet: -0.40 (0.60), residues: 72 loop : -1.67 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1419 TYR 0.031 0.001 TYR B 512 PHE 0.018 0.002 PHE B1204 TRP 0.026 0.001 TRP B 514 HIS 0.004 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 9114) covalent geometry : angle 0.62974 / 0.31 (12369) hydrogen bonds : bond 0.05029 / 3.19 ( 574) hydrogen bonds : angle 4.32892 / 3.18 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9068 (mtpp) cc_final: 0.7993 (tttt) REVERT: B 233 MET cc_start: 0.9155 (mmm) cc_final: 0.8642 (mmm) REVERT: B 257 MET cc_start: 0.7647 (ptp) cc_final: 0.7006 (ptp) REVERT: B 319 CYS cc_start: 0.8994 (m) cc_final: 0.8457 (t) REVERT: B 323 ILE cc_start: 0.9300 (mm) cc_final: 0.9023 (mm) REVERT: B 361 LEU cc_start: 0.9570 (mm) cc_final: 0.9104 (tp) REVERT: B 394 LYS cc_start: 0.9176 (tppp) cc_final: 0.8914 (tppp) REVERT: B 509 LEU cc_start: 0.9301 (mt) cc_final: 0.9091 (mt) REVERT: B 530 MET cc_start: 0.9036 (mmt) cc_final: 0.8765 (mmt) REVERT: B 602 LYS cc_start: 0.9133 (tptt) cc_final: 0.8893 (tptm) REVERT: B 710 MET cc_start: 0.8760 (tpp) cc_final: 0.8485 (tpp) REVERT: B 808 LEU cc_start: 0.9113 (tp) cc_final: 0.8751 (tp) REVERT: B 893 TYR cc_start: 0.7709 (m-80) cc_final: 0.7509 (m-80) REVERT: B 1078 LEU cc_start: 0.9304 (tp) cc_final: 0.9020 (tp) REVERT: B 1091 LEU cc_start: 0.8943 (tt) cc_final: 0.8717 (tt) REVERT: B 1104 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7915 (tpp80) REVERT: B 1124 ARG cc_start: 0.8517 (mmp80) cc_final: 0.8093 (mmp80) REVERT: B 1128 ASP cc_start: 0.8249 (m-30) cc_final: 0.7278 (m-30) REVERT: B 1229 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 1246 ARG cc_start: 0.9462 (mmp80) cc_final: 0.9079 (mmp80) REVERT: B 1258 CYS cc_start: 0.8863 (t) cc_final: 0.8643 (t) REVERT: B 1290 MET cc_start: 0.8597 (ttt) cc_final: 0.8361 (ttm) REVERT: B 1295 LEU cc_start: 0.9501 (mt) cc_final: 0.9282 (mm) REVERT: B 1490 PHE cc_start: 0.8863 (m-80) cc_final: 0.8458 (m-80) REVERT: B 1505 MET cc_start: 0.6693 (mmp) cc_final: 0.6142 (ttp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0736 time to fit residues: 23.4448 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.082047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.063091 restraints weight = 33071.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.065028 restraints weight = 19884.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066324 restraints weight = 13613.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.067146 restraints weight = 10301.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.067780 restraints weight = 8496.020| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9114 Z= 0.147 Angle : 0.646 7.970 12369 Z= 0.321 Chirality : 0.042 0.173 1492 Planarity : 0.004 0.045 1516 Dihedral : 6.425 113.805 1236 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: 0.59 (0.25), residues: 1122 helix: 1.27 (0.19), residues: 753 sheet: -0.33 (0.61), residues: 72 loop : -1.67 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1419 TYR 0.030 0.001 TYR B 512 PHE 0.022 0.001 PHE B 433 TRP 0.022 0.001 TRP B 514 HIS 0.005 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 ( 9114) covalent geometry : angle 0.64552 / 0.32 (12369) hydrogen bonds : bond 0.04985 / 3.18 ( 574) hydrogen bonds : angle 4.32533 / 3.17 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8015 (tttt) REVERT: B 233 MET cc_start: 0.9254 (mmm) cc_final: 0.8986 (tpp) REVERT: B 319 CYS cc_start: 0.8997 (m) cc_final: 0.8550 (t) REVERT: B 323 ILE cc_start: 0.9331 (mm) cc_final: 0.9057 (mm) REVERT: B 394 LYS cc_start: 0.9102 (tppp) cc_final: 0.8858 (tppp) REVERT: B 530 MET cc_start: 0.9056 (mmt) cc_final: 0.8750 (mmt) REVERT: B 586 LEU cc_start: 0.9674 (tp) cc_final: 0.9393 (tp) REVERT: B 590 LEU cc_start: 0.9254 (mt) cc_final: 0.8887 (mt) REVERT: B 602 LYS cc_start: 0.9149 (tptt) cc_final: 0.8904 (tptm) REVERT: B 710 MET cc_start: 0.8782 (tpp) cc_final: 0.8532 (tpp) REVERT: B 808 LEU cc_start: 0.9095 (tp) cc_final: 0.8762 (tp) REVERT: B 1078 LEU cc_start: 0.9339 (tp) cc_final: 0.9034 (tt) REVERT: B 1091 LEU cc_start: 0.8954 (tt) cc_final: 0.8752 (tt) REVERT: B 1104 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7942 (tpp80) REVERT: B 1124 ARG cc_start: 0.8569 (mmp80) cc_final: 0.8142 (mmp80) REVERT: B 1128 ASP cc_start: 0.8339 (m-30) cc_final: 0.7527 (m-30) REVERT: B 1146 SER cc_start: 0.9293 (m) cc_final: 0.8839 (p) REVERT: B 1229 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 1246 ARG cc_start: 0.9470 (mmp80) cc_final: 0.9047 (mmp80) REVERT: B 1258 CYS cc_start: 0.8898 (t) cc_final: 0.8672 (t) REVERT: B 1295 LEU cc_start: 0.9530 (mt) cc_final: 0.9299 (mm) REVERT: B 1431 LEU cc_start: 0.9258 (mt) cc_final: 0.8870 (mm) REVERT: B 1490 PHE cc_start: 0.8890 (m-80) cc_final: 0.8530 (m-80) REVERT: B 1505 MET cc_start: 0.6656 (mmp) cc_final: 0.6176 (ttp) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0744 time to fit residues: 22.4036 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 0.9980 chunk 38 optimal weight: 0.0020 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 11 optimal weight: 0.3980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.082896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.064033 restraints weight = 32971.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066029 restraints weight = 19699.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067348 restraints weight = 13380.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068218 restraints weight = 10089.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068832 restraints weight = 8262.214| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9114 Z= 0.133 Angle : 0.653 9.281 12369 Z= 0.319 Chirality : 0.042 0.182 1492 Planarity : 0.004 0.044 1516 Dihedral : 6.463 112.640 1236 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.63 (0.25), residues: 1122 helix: 1.23 (0.19), residues: 758 sheet: -0.25 (0.60), residues: 72 loop : -1.50 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 388 TYR 0.032 0.001 TYR B 512 PHE 0.025 0.002 PHE B 295 TRP 0.025 0.001 TRP B 514 HIS 0.005 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9114) covalent geometry : angle 0.65265 / 0.32 (12369) hydrogen bonds : bond 0.04891 / 3.13 ( 574) hydrogen bonds : angle 4.29743 / 3.16 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LYS cc_start: 0.8998 (mtpp) cc_final: 0.8021 (tttt) REVERT: B 319 CYS cc_start: 0.8947 (m) cc_final: 0.8511 (t) REVERT: B 323 ILE cc_start: 0.9331 (mm) cc_final: 0.9051 (mm) REVERT: B 394 LYS cc_start: 0.9087 (tppp) cc_final: 0.8792 (tppp) REVERT: B 509 LEU cc_start: 0.9246 (mt) cc_final: 0.9041 (mt) REVERT: B 586 LEU cc_start: 0.9667 (tp) cc_final: 0.9343 (tp) REVERT: B 590 LEU cc_start: 0.9216 (mt) cc_final: 0.8886 (mt) REVERT: B 602 LYS cc_start: 0.9096 (tptt) cc_final: 0.8689 (tppt) REVERT: B 710 MET cc_start: 0.8837 (tpp) cc_final: 0.8580 (tpp) REVERT: B 808 LEU cc_start: 0.9026 (tp) cc_final: 0.8674 (tp) REVERT: B 1104 ARG cc_start: 0.8415 (mmm-85) cc_final: 0.7905 (tpp80) REVERT: B 1124 ARG cc_start: 0.8511 (mmp80) cc_final: 0.8105 (mmp80) REVERT: B 1128 ASP cc_start: 0.8265 (m-30) cc_final: 0.7309 (m-30) REVERT: B 1146 SER cc_start: 0.9301 (m) cc_final: 0.8853 (p) REVERT: B 1229 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 1246 ARG cc_start: 0.9410 (mmp80) cc_final: 0.9070 (mmp80) REVERT: B 1258 CYS cc_start: 0.8927 (t) cc_final: 0.8608 (t) REVERT: B 1295 LEU cc_start: 0.9508 (mt) cc_final: 0.9293 (mm) REVERT: B 1390 LEU cc_start: 0.9691 (mm) cc_final: 0.9352 (tp) REVERT: B 1431 LEU cc_start: 0.9201 (mt) cc_final: 0.8879 (mm) REVERT: B 1490 PHE cc_start: 0.8852 (m-80) cc_final: 0.8504 (m-80) REVERT: B 1505 MET cc_start: 0.6852 (mmp) cc_final: 0.6407 (ttp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.0757 time to fit residues: 23.7892 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 98 optimal weight: 0.0570 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.083277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064282 restraints weight = 32618.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066129 restraints weight = 19865.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.067452 restraints weight = 13775.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.068339 restraints weight = 10462.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068886 restraints weight = 8560.576| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9114 Z= 0.132 Angle : 0.656 11.850 12369 Z= 0.321 Chirality : 0.042 0.175 1492 Planarity : 0.004 0.046 1516 Dihedral : 6.445 111.387 1236 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.67 (0.25), residues: 1122 helix: 1.25 (0.18), residues: 761 sheet: -0.19 (0.61), residues: 72 loop : -1.52 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1419 TYR 0.022 0.001 TYR B 512 PHE 0.021 0.002 PHE B 295 TRP 0.017 0.001 TRP B 514 HIS 0.005 0.001 HIS B 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9114) covalent geometry : angle 0.65590 / 0.32 (12369) hydrogen bonds : bond 0.04811 / 3.08 ( 574) hydrogen bonds : angle 4.22847 / 3.11 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1554.70 seconds wall clock time: 27 minutes 37.34 seconds (1657.34 seconds total)