Starting phenix.real_space_refine on Fri Oct 23 21:21:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.map" model { file = "/net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lcc_23271/10_2026/7lcc_23271.cif" } resolution = 3.66 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= 1.000 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 Zn 1 6.06 5 P 17 5.49 5 S 74 5.16 5 C 7100 2.51 5 N 1977 2.21 5 O 2112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11281 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1369, 10931 Classifications: {'peptide': 1369} Link IDs: {'PTRANS': 63, 'TRANS': 1305} Chain breaks: 1 Chain: "B" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 116 SG CYS A 125 41.692 14.661 64.944 1.00 42.22 S ATOM 142 SG CYS A 128 41.329 16.565 68.156 1.00 47.79 S ATOM 284 SG CYS A 146 43.235 17.512 64.552 1.00 33.37 S ATOM 290 SG CYS A 147 44.974 16.501 67.153 1.00 38.33 S Time building chain proxies: 2.18, per 1000 atoms: 0.19 Number of scatterers: 11281 At special positions: 0 Unit cell: (113.4, 104.76, 110.16, 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) Zn 1 29.99 S 74 16.00 P 17 15.00 O 2112 8.00 N 1977 7.00 C 7100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 333.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 147 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 146 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 128 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 125 " Number of angles added : 6 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2586 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 13 sheets defined 43.4% alpha, 12.1% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.028A pdb=" N CYS A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.667A pdb=" N TYR A 206 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 260 through 274 Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.221A pdb=" N SER A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 298 Processing helix chain 'A' and resid 369 through 375 Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 435 through 460 removed outlier: 3.714A pdb=" N GLN A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 500 through 519 removed outlier: 3.509A pdb=" N ILE A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.740A pdb=" N ASN A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 540 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 570 removed outlier: 4.529A pdb=" N VAL A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 626 through 637 Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.580A pdb=" N CYS A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 721 through 729 removed outlier: 3.544A pdb=" N VAL A 725 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 733 Processing helix chain 'A' and resid 765 through 773 Processing helix chain 'A' and resid 803 through 814 removed outlier: 3.861A pdb=" N VAL A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 828 Processing helix chain 'A' and resid 829 through 834 Processing helix chain 'A' and resid 835 through 837 No H-bonds generated for 'chain 'A' and resid 835 through 837' Processing helix chain 'A' and resid 838 through 842 removed outlier: 3.977A pdb=" N HIS A 842 " --> pdb=" O GLU A 838 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 838 through 842' Processing helix chain 'A' and resid 871 through 884 Processing helix chain 'A' and resid 889 through 895 Processing helix chain 'A' and resid 903 through 912 Processing helix chain 'A' and resid 917 through 931 Processing helix chain 'A' and resid 932 through 947 removed outlier: 3.566A pdb=" N LEU A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 959 removed outlier: 3.907A pdb=" N LEU A 955 " --> pdb=" O ALA A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 972 removed outlier: 3.526A pdb=" N PHE A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP A 966 " --> pdb=" O HIS A 962 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE A 967 " --> pdb=" O PHE A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.159A pdb=" N VAL A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS A 996 " --> pdb=" O VAL A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 Processing helix chain 'A' and resid 1018 through 1033 removed outlier: 3.535A pdb=" N SER A1032 " --> pdb=" O VAL A1028 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1050 Processing helix chain 'A' and resid 1065 through 1082 removed outlier: 4.278A pdb=" N THR A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A1071 " --> pdb=" O GLY A1067 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A1072 " --> pdb=" O GLN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1099 removed outlier: 3.759A pdb=" N LEU A1098 " --> pdb=" O ILE A1094 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A1099 " --> pdb=" O ALA A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1109 Processing helix chain 'A' and resid 1127 through 1136 Processing helix chain 'A' and resid 1148 through 1163 Processing helix chain 'A' and resid 1167 through 1172 Processing helix chain 'A' and resid 1191 through 1199 removed outlier: 3.948A pdb=" N GLN A1197 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR A1198 " --> pdb=" O ALA A1194 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER A1199 " --> pdb=" O ILE A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1209 removed outlier: 5.950A pdb=" N ASN A1204 " --> pdb=" O LYS A1201 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A1205 " --> pdb=" O TYR A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 removed outlier: 3.541A pdb=" N SER A1226 " --> pdb=" O ASP A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1266 removed outlier: 3.552A pdb=" N ALA A1263 " --> pdb=" O SER A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1301 Processing helix chain 'A' and resid 1320 through 1325 removed outlier: 3.653A pdb=" N ASN A1324 " --> pdb=" O ALA A1320 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A1325 " --> pdb=" O GLU A1321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1320 through 1325' Processing helix chain 'A' and resid 1326 through 1333 removed outlier: 3.586A pdb=" N SER A1332 " --> pdb=" O GLU A1328 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A1333 " --> pdb=" O PHE A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1429 No H-bonds generated for 'chain 'A' and resid 1427 through 1429' Processing helix chain 'A' and resid 1449 through 1457 removed outlier: 3.619A pdb=" N ARG A1457 " --> pdb=" O VAL A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1462 No H-bonds generated for 'chain 'A' and resid 1460 through 1462' Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.741A pdb=" N CYS A 153 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213 removed outlier: 7.321A pdb=" N VAL A 217 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET A 196 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 344 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 3.751A pdb=" N ASP A 737 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 740 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 491 removed outlier: 4.666A pdb=" N LEU A 464 " --> pdb=" O ILE A 491 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 718 removed outlier: 3.540A pdb=" N ALA A 579 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 686 through 689 Processing sheet with id=AA7, first strand: chain 'A' and resid 843 through 846 Processing sheet with id=AA8, first strand: chain 'A' and resid 1086 through 1089 removed outlier: 4.064A pdb=" N ILE A1140 " --> pdb=" O LEU A1087 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A1139 " --> pdb=" O LEU A1175 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N CYS A1057 " --> pdb=" O ARG A1210 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A1212 " --> pdb=" O CYS A1057 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE A1059 " --> pdb=" O LEU A1212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1247 through 1249 Processing sheet with id=AB1, first strand: chain 'A' and resid 1423 through 1425 removed outlier: 6.202A pdb=" N ILE A1282 " --> pdb=" O MET A1424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1306 through 1308 Processing sheet with id=AB3, first strand: chain 'A' and resid 1311 through 1314 removed outlier: 3.919A pdb=" N ASP A1311 " --> pdb=" O ARG A1414 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A1415 " --> pdb=" O ILE A1398 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A1398 " --> pdb=" O GLN A1415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1392 through 1395 removed outlier: 3.705A pdb=" N ILE A1379 " --> pdb=" O ILE A1395 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE A1378 " --> pdb=" O LEU A1374 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU A1374 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A1380 " --> pdb=" O LYS A1372 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.93 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1855 1.32 - 1.44: 3103 1.44 - 1.57: 6462 1.57 - 1.69: 33 1.69 - 1.81: 112 Bond restraints: 11565 Sorted by residual: bond pdb=" N ARG A1375 " pdb=" CA ARG A1375 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" N GLU A1443 " pdb=" CA GLU A1443 " ideal model delta sigma weight residual 1.453 1.487 -0.034 9.20e-03 1.18e+04 1.36e+01 bond pdb=" N ILE A 390 " pdb=" CA ILE A 390 " ideal model delta sigma weight residual 1.459 1.492 -0.033 9.10e-03 1.21e+04 1.31e+01 bond pdb=" N ILE A1282 " pdb=" CA ILE A1282 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" CA SER A 781 " pdb=" CB SER A 781 " ideal model delta sigma weight residual 1.528 1.474 0.055 1.56e-02 4.11e+03 1.24e+01 ... (remaining 11560 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 10781 1.51 - 3.02: 4077 3.02 - 4.53: 780 4.53 - 6.04: 63 6.04 - 7.55: 7 Bond angle restraints: 15708 Sorted by residual: angle pdb=" CA PHE A 865 " pdb=" C PHE A 865 " pdb=" O PHE A 865 " ideal model delta sigma weight residual 121.99 117.44 4.55 1.14e+00 7.69e-01 1.59e+01 angle pdb=" CA TYR A 835 " pdb=" C TYR A 835 " pdb=" O TYR A 835 " ideal model delta sigma weight residual 121.94 117.35 4.59 1.15e+00 7.56e-01 1.59e+01 angle pdb=" CA VAL A 327 " pdb=" C VAL A 327 " pdb=" O VAL A 327 " ideal model delta sigma weight residual 121.19 117.10 4.09 1.03e+00 9.43e-01 1.58e+01 angle pdb=" CA GLY A1177 " pdb=" C GLY A1177 " pdb=" O GLY A1177 " ideal model delta sigma weight residual 121.41 117.92 3.49 8.80e-01 1.29e+00 1.58e+01 angle pdb=" CA ALA A 783 " pdb=" C ALA A 783 " pdb=" O ALA A 783 " ideal model delta sigma weight residual 121.94 117.37 4.57 1.15e+00 7.56e-01 1.58e+01 ... (remaining 15703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6303 17.75 - 35.49: 504 35.49 - 53.24: 135 53.24 - 70.98: 42 70.98 - 88.73: 5 Dihedral angle restraints: 6989 sinusoidal: 2989 harmonic: 4000 Sorted by residual: dihedral pdb=" C THR A 669 " pdb=" N THR A 669 " pdb=" CA THR A 669 " pdb=" CB THR A 669 " ideal model delta harmonic sigma weight residual -122.00 -135.89 13.89 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" C TYR A 731 " pdb=" N TYR A 731 " pdb=" CA TYR A 731 " pdb=" CB TYR A 731 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.64e+01 dihedral pdb=" N THR A 669 " pdb=" C THR A 669 " pdb=" CA THR A 669 " pdb=" CB THR A 669 " ideal model delta harmonic sigma weight residual 123.40 133.81 -10.41 0 2.50e+00 1.60e-01 1.73e+01 ... (remaining 6986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 919 0.087 - 0.175: 601 0.175 - 0.262: 192 0.262 - 0.350: 12 0.350 - 0.437: 3 Chirality restraints: 1727 Sorted by residual: chirality pdb=" CA THR A 669 " pdb=" N THR A 669 " pdb=" C THR A 669 " pdb=" CB THR A 669 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA TYR A 731 " pdb=" N TYR A 731 " pdb=" C TYR A 731 " pdb=" CB TYR A 731 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA ILE A 492 " pdb=" N ILE A 492 " pdb=" C ILE A 492 " pdb=" CB ILE A 492 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 1724 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 668 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ALA A 668 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 668 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 669 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 257 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C GLY A 257 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 257 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 258 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1447 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00 pdb=" C ALA A1447 " -0.035 2.00e-02 2.50e+03 pdb=" O ALA A1447 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS A1448 " 0.012 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 27 2.60 - 3.18: 8949 3.18 - 3.75: 15851 3.75 - 4.33: 22652 4.33 - 4.90: 35676 Nonbonded interactions: 83155 Sorted by model distance: nonbonded pdb=" OH TYR A 727 " pdb=" P DT B 1 " model vdw 2.026 3.400 nonbonded pdb=" CB ARG A1375 " pdb=" NE ARG A1375 " model vdw 2.467 2.816 nonbonded pdb=" O5' DA B 17 " pdb=" O4' DA B 17 " model vdw 2.476 2.432 nonbonded pdb=" N GLN A 795 " pdb=" O GLN A 795 " model vdw 2.536 2.496 nonbonded pdb=" N MET A1191 " pdb=" O MET A1191 " model vdw 2.541 2.496 ... (remaining 83150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.012 0.055 11569 Z= 0.928 Angle : 1.568 28.814 15714 Z= 1.192 Chirality : 0.111 0.437 1727 Planarity : 0.004 0.027 1974 Dihedral : 14.395 88.729 4403 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 6.10 % Allowed : 7.17 % Favored : 86.73 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1365 helix: 3.15 (0.22), residues: 454 sheet: 1.68 (0.42), residues: 159 loop : 0.07 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 681 TYR 0.026 0.002 TYR A 762 PHE 0.020 0.002 PHE A1369 TRP 0.020 0.002 TRP A 850 HIS 0.009 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.01218 / 0.93 (11565) covalent geometry : angle 1.52817 / 1.19 (15708) hydrogen bonds : bond 0.28020 / 18.85 ( 424) hydrogen bonds : angle 6.95016 / 5.02 ( 1182) metal coordination : bond 0.01141 / 0.57 ( 4) metal coordination : angle 18.14638 / 9.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.8657 (t0) cc_final: 0.8333 (t0) REVERT: A 233 LYS cc_start: 0.8042 (tptt) cc_final: 0.7750 (tptp) REVERT: A 343 ASP cc_start: 0.7911 (t0) cc_final: 0.7617 (p0) REVERT: A 361 LYS cc_start: 0.7951 (mttt) cc_final: 0.7692 (tttm) REVERT: A 390 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7949 (tp) REVERT: A 487 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8628 (tp) REVERT: A 669 THR cc_start: 0.8201 (t) cc_final: 0.6824 (t) REVERT: A 967 PHE cc_start: 0.8796 (m-80) cc_final: 0.8487 (m-80) REVERT: A 1021 TYR cc_start: 0.8145 (t80) cc_final: 0.7935 (t80) REVERT: A 1196 VAL cc_start: 0.9222 (m) cc_final: 0.8672 (t) REVERT: A 1352 MET cc_start: 0.8369 (ttm) cc_final: 0.8070 (ttp) REVERT: A 1426 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8931 (mt) outliers start: 74 outliers final: 21 residues processed: 337 average time/residue: 0.1016 time to fit residues: 49.5978 Evaluate side-chains 160 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 974 ARG Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1426 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 HIS A 347 HIS A 433 ASN A 509 GLN ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 HIS A 672 ASN A 742 GLN A 782 HIS A 790 HIS ** A 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN A 996 HIS A1166 ASN A1289 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110149 restraints weight = 16846.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115886 restraints weight = 9808.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.117972 restraints weight = 5927.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118495 restraints weight = 4986.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.119081 restraints weight = 4861.732| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11569 Z= 0.170 Angle : 0.678 13.879 15714 Z= 0.369 Chirality : 0.045 0.247 1727 Planarity : 0.005 0.048 1974 Dihedral : 12.640 86.803 1735 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.37 % Allowed : 12.70 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.21), residues: 1365 helix: 2.15 (0.23), residues: 474 sheet: 2.27 (0.40), residues: 146 loop : -0.23 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 502 TYR 0.021 0.002 TYR A 762 PHE 0.020 0.002 PHE A1369 TRP 0.013 0.001 TRP A 543 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (11565) covalent geometry : angle 0.65937 / 0.37 (15708) hydrogen bonds : bond 0.07429 / 4.87 ( 424) hydrogen bonds : angle 5.39579 / 3.92 ( 1182) metal coordination : bond 0.01459 / 0.75 ( 4) metal coordination : angle 8.21270 / 4.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8705 (mt) cc_final: 0.8350 (tp) REVERT: A 233 LYS cc_start: 0.7727 (tptt) cc_final: 0.7513 (tptp) REVERT: A 306 MET cc_start: 0.8026 (mtt) cc_final: 0.7808 (mtp) REVERT: A 343 ASP cc_start: 0.7848 (t0) cc_final: 0.6966 (p0) REVERT: A 390 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8227 (tp) REVERT: A 487 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8346 (tp) REVERT: A 512 MET cc_start: 0.8260 (tpp) cc_final: 0.7894 (mmt) REVERT: A 547 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6864 (mt-10) REVERT: A 665 PHE cc_start: 0.8241 (t80) cc_final: 0.7862 (t80) REVERT: A 676 TYR cc_start: 0.7869 (m-10) cc_final: 0.7366 (m-10) REVERT: A 679 TYR cc_start: 0.7941 (m-80) cc_final: 0.7553 (m-80) REVERT: A 913 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7937 (pp) REVERT: A 989 ILE cc_start: 0.8768 (mt) cc_final: 0.8412 (mm) REVERT: A 1481 SER cc_start: 0.8507 (t) cc_final: 0.8199 (p) outliers start: 53 outliers final: 33 residues processed: 195 average time/residue: 0.0934 time to fit residues: 27.1034 Evaluate side-chains 161 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1166 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1219 ARG Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1371 ILE Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [113, 46, 89, 21, 63, 93, 92, 51, 9, 83, 131] chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 0.0270 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN ** A 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.144467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104976 restraints weight = 17231.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109682 restraints weight = 9776.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113175 restraints weight = 6265.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113081 restraints weight = 5200.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113665 restraints weight = 5010.777| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11569 Z= 0.179 Angle : 0.604 10.587 15714 Z= 0.331 Chirality : 0.044 0.162 1727 Planarity : 0.004 0.046 1974 Dihedral : 12.261 87.533 1719 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.37 % Allowed : 14.67 % Favored : 80.96 % 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: 0.90 (0.21), residues: 1365 helix: 1.67 (0.23), residues: 480 sheet: 1.64 (0.39), residues: 169 loop : -0.41 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 974 TYR 0.020 0.002 TYR A 661 PHE 0.017 0.002 PHE A1105 TRP 0.010 0.001 TRP A 770 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (11565) covalent geometry : angle 0.59265 / 0.33 (15708) hydrogen bonds : bond 0.06018 / 4.02 ( 424) hydrogen bonds : angle 5.11139 / 3.72 ( 1182) metal coordination : bond 0.01352 / 0.68 ( 4) metal coordination : angle 6.10009 / 3.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 0.289 Fit side-chains REVERT: A 169 LEU cc_start: 0.8689 (mt) cc_final: 0.8348 (tp) REVERT: A 188 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7888 (t0) REVERT: A 233 LYS cc_start: 0.7777 (tptt) cc_final: 0.7564 (tptp) REVERT: A 306 MET cc_start: 0.8441 (mtt) cc_final: 0.8036 (mtp) REVERT: A 343 ASP cc_start: 0.7778 (t0) cc_final: 0.6974 (p0) REVERT: A 390 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (tp) REVERT: A 487 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 490 MET cc_start: 0.8089 (ttp) cc_final: 0.7741 (ptm) REVERT: A 547 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: A 589 ARG cc_start: 0.6544 (mtp85) cc_final: 0.6317 (mtp85) REVERT: A 665 PHE cc_start: 0.8303 (t80) cc_final: 0.7877 (t80) REVERT: A 679 TYR cc_start: 0.7980 (m-80) cc_final: 0.7713 (m-80) REVERT: A 913 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8155 (pp) REVERT: A 989 ILE cc_start: 0.8778 (mt) cc_final: 0.8460 (mm) REVERT: A 1232 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8330 (tp) REVERT: A 1296 GLU cc_start: 0.7895 (tp30) cc_final: 0.7617 (tp30) REVERT: A 1481 SER cc_start: 0.8522 (t) cc_final: 0.8209 (p) outliers start: 53 outliers final: 36 residues processed: 170 average time/residue: 0.0861 time to fit residues: 22.3641 Evaluate side-chains 159 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 760 SER Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1203 CYS Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1232 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1395 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [81, 45, 84, 122, 116, 71, 130, 21, 22, 41, 30] chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN A 636 ASN A1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105384 restraints weight = 17196.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.110273 restraints weight = 9792.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113924 restraints weight = 6180.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113844 restraints weight = 5091.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114172 restraints weight = 4888.138| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11569 Z= 0.130 Angle : 0.543 8.613 15714 Z= 0.296 Chirality : 0.041 0.151 1727 Planarity : 0.004 0.046 1974 Dihedral : 11.929 88.310 1713 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.12 % Allowed : 15.58 % Favored : 80.30 % 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: 0.91 (0.22), residues: 1365 helix: 1.74 (0.23), residues: 473 sheet: 1.53 (0.41), residues: 165 loop : -0.38 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.019 0.001 TYR A 762 PHE 0.013 0.001 PHE A1369 TRP 0.015 0.001 TRP A 956 HIS 0.009 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (11565) covalent geometry : angle 0.53402 / 0.30 (15708) hydrogen bonds : bond 0.04896 / 3.28 ( 424) hydrogen bonds : angle 4.87807 / 3.54 ( 1182) metal coordination : bond 0.00880 / 0.44 ( 4) metal coordination : angle 5.13907 / 2.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.326 Fit side-chains REVERT: A 169 LEU cc_start: 0.8726 (mt) cc_final: 0.8442 (tp) REVERT: A 233 LYS cc_start: 0.7754 (tptt) cc_final: 0.7544 (tptp) REVERT: A 306 MET cc_start: 0.8388 (mtt) cc_final: 0.8020 (mtp) REVERT: A 343 ASP cc_start: 0.7810 (t0) cc_final: 0.7104 (p0) REVERT: A 359 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7580 (tttp) REVERT: A 360 MET cc_start: 0.8720 (mmt) cc_final: 0.8354 (mmp) REVERT: A 390 ILE cc_start: 0.8598 (tp) cc_final: 0.8313 (tp) REVERT: A 487 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 490 MET cc_start: 0.8035 (ttp) cc_final: 0.7813 (ptm) REVERT: A 547 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: A 587 GLN cc_start: 0.6991 (tp40) cc_final: 0.6708 (tp40) REVERT: A 665 PHE cc_start: 0.8313 (t80) cc_final: 0.7841 (t80) REVERT: A 913 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8223 (pp) REVERT: A 989 ILE cc_start: 0.8786 (mt) cc_final: 0.8470 (mm) REVERT: A 1296 GLU cc_start: 0.7805 (tp30) cc_final: 0.7482 (tp30) REVERT: A 1318 ASP cc_start: 0.8420 (t0) cc_final: 0.8171 (m-30) REVERT: A 1481 SER cc_start: 0.8564 (t) cc_final: 0.8280 (p) REVERT: A 1493 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6927 (pt0) outliers start: 50 outliers final: 32 residues processed: 161 average time/residue: 0.0854 time to fit residues: 20.6393 Evaluate side-chains 154 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [120, 49, 90, 40, 35, 8, 50, 3, 126, 66, 114] chunk 120 optimal weight: 0.0070 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 overall best weight: 2.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.103035 restraints weight = 17220.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107670 restraints weight = 10540.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109764 restraints weight = 6732.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110270 restraints weight = 5880.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111062 restraints weight = 5736.728| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11569 Z= 0.227 Angle : 0.612 9.779 15714 Z= 0.330 Chirality : 0.044 0.146 1727 Planarity : 0.004 0.044 1974 Dihedral : 11.885 89.953 1710 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.36 % Allowed : 15.66 % Favored : 78.98 % 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: 0.64 (0.22), residues: 1365 helix: 1.50 (0.23), residues: 473 sheet: 1.39 (0.41), residues: 169 loop : -0.53 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 332 TYR 0.022 0.002 TYR A 661 PHE 0.016 0.002 PHE A1105 TRP 0.011 0.001 TRP A 850 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.23 (11565) covalent geometry : angle 0.60156 / 0.33 (15708) hydrogen bonds : bond 0.05464 / 3.69 ( 424) hydrogen bonds : angle 5.00573 / 3.63 ( 1182) metal coordination : bond 0.01438 / 0.72 ( 4) metal coordination : angle 5.80760 / 3.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 123 time to evaluate : 0.263 Fit side-chains REVERT: A 169 LEU cc_start: 0.8771 (mt) cc_final: 0.8442 (tp) REVERT: A 188 ASN cc_start: 0.8314 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 233 LYS cc_start: 0.7814 (tptt) cc_final: 0.7604 (tptp) REVERT: A 306 MET cc_start: 0.8525 (mtt) cc_final: 0.8049 (mtp) REVERT: A 343 ASP cc_start: 0.7677 (t0) cc_final: 0.7094 (p0) REVERT: A 390 ILE cc_start: 0.8607 (tp) cc_final: 0.8326 (tp) REVERT: A 547 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: A 589 ARG cc_start: 0.6850 (mtp85) cc_final: 0.6556 (mtp85) REVERT: A 665 PHE cc_start: 0.8362 (t80) cc_final: 0.7873 (t80) REVERT: A 913 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 989 ILE cc_start: 0.8721 (mt) cc_final: 0.8389 (mm) REVERT: A 1252 HIS cc_start: 0.7356 (p-80) cc_final: 0.6483 (t70) REVERT: A 1296 GLU cc_start: 0.7983 (tp30) cc_final: 0.7713 (tp30) REVERT: A 1481 SER cc_start: 0.8520 (t) cc_final: 0.8253 (p) REVERT: A 1493 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6996 (pt0) outliers start: 65 outliers final: 45 residues processed: 173 average time/residue: 0.0912 time to fit residues: 23.5568 Evaluate side-chains 165 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 333 ASN Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 533 TRP Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1229 LEU Chi-restraints excluded: chain A residue 1264 THR Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1477 LEU Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [25, 122, 44, 55, 117, 70, 75, 68, 60, 45, 98] chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN A 421 HIS A1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.142772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.102653 restraints weight = 17660.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107325 restraints weight = 10771.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109840 restraints weight = 6917.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109943 restraints weight = 6007.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110471 restraints weight = 5884.716| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11569 Z= 0.123 Angle : 0.533 8.102 15714 Z= 0.288 Chirality : 0.041 0.140 1727 Planarity : 0.004 0.042 1974 Dihedral : 11.634 89.765 1708 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.96 % Allowed : 16.98 % Favored : 79.06 % 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 (0.22), residues: 1365 helix: 1.47 (0.23), residues: 492 sheet: 1.35 (0.42), residues: 165 loop : -0.50 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1460 TYR 0.019 0.001 TYR A 702 PHE 0.012 0.001 PHE A 630 TRP 0.012 0.001 TRP A 956 HIS 0.008 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11565) covalent geometry : angle 0.52438 / 0.29 (15708) hydrogen bonds : bond 0.04482 / 3.04 ( 424) hydrogen bonds : angle 4.79915 / 3.48 ( 1182) metal coordination : bond 0.00772 / 0.39 ( 4) metal coordination : angle 4.81186 / 2.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8718 (mt) cc_final: 0.8432 (tp) REVERT: A 188 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7857 (t0) REVERT: A 233 LYS cc_start: 0.7803 (tptt) cc_final: 0.7485 (tptp) REVERT: A 343 ASP cc_start: 0.7718 (t0) cc_final: 0.7104 (p0) REVERT: A 390 ILE cc_start: 0.8579 (tp) cc_final: 0.8297 (tp) REVERT: A 547 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: A 587 GLN cc_start: 0.7039 (tp40) cc_final: 0.6764 (tp40) REVERT: A 637 MET cc_start: 0.8017 (mtm) cc_final: 0.7802 (mtt) REVERT: A 665 PHE cc_start: 0.8289 (t80) cc_final: 0.7815 (t80) REVERT: A 913 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8396 (pp) REVERT: A 989 ILE cc_start: 0.8759 (mt) cc_final: 0.8455 (mm) REVERT: A 1252 HIS cc_start: 0.7361 (p-80) cc_final: 0.6514 (t70) REVERT: A 1296 GLU cc_start: 0.8018 (tp30) cc_final: 0.7785 (tp30) REVERT: A 1318 ASP cc_start: 0.8501 (t0) cc_final: 0.8164 (m-30) REVERT: A 1481 SER cc_start: 0.8627 (t) cc_final: 0.8367 (p) REVERT: A 1493 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7062 (pt0) outliers start: 48 outliers final: 36 residues processed: 161 average time/residue: 0.0852 time to fit residues: 21.1409 Evaluate side-chains 160 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 533 TRP Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1193 SER Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [98, 30, 25, 21, 11, 68, 29, 60, 103, 5, 70] chunk 98 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 0.0070 chunk 70 optimal weight: 2.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.144781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.106318 restraints weight = 16929.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110406 restraints weight = 10064.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113749 restraints weight = 6608.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113777 restraints weight = 5409.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114353 restraints weight = 5223.908| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 11569 Z= 0.104 Angle : 0.505 8.047 15714 Z= 0.273 Chirality : 0.040 0.147 1727 Planarity : 0.003 0.042 1974 Dihedral : 11.464 89.968 1708 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.13 % Allowed : 17.97 % Favored : 78.90 % 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: 0.69 (0.22), residues: 1365 helix: 1.53 (0.23), residues: 486 sheet: 1.38 (0.42), residues: 165 loop : -0.51 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.018 0.001 TYR A 702 PHE 0.014 0.001 PHE A 191 TRP 0.010 0.001 TRP A 956 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11565) covalent geometry : angle 0.49832 / 0.27 (15708) hydrogen bonds : bond 0.03746 / 2.56 ( 424) hydrogen bonds : angle 4.63059 / 3.36 ( 1182) metal coordination : bond 0.00475 / 0.24 ( 4) metal coordination : angle 4.27273 / 2.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8739 (mt) cc_final: 0.8462 (tp) REVERT: A 233 LYS cc_start: 0.7797 (tptt) cc_final: 0.7482 (tptp) REVERT: A 306 MET cc_start: 0.8237 (mtt) cc_final: 0.8022 (mtp) REVERT: A 343 ASP cc_start: 0.7611 (t0) cc_final: 0.7102 (p0) REVERT: A 360 MET cc_start: 0.8313 (mmt) cc_final: 0.8014 (mmp) REVERT: A 390 ILE cc_start: 0.8577 (tp) cc_final: 0.8311 (tp) REVERT: A 547 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: A 587 GLN cc_start: 0.6955 (tp40) cc_final: 0.6737 (tp40) REVERT: A 665 PHE cc_start: 0.8347 (t80) cc_final: 0.7833 (t80) REVERT: A 913 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8438 (pp) REVERT: A 989 ILE cc_start: 0.8779 (mt) cc_final: 0.8496 (mm) REVERT: A 1252 HIS cc_start: 0.7234 (p-80) cc_final: 0.6449 (t70) REVERT: A 1318 ASP cc_start: 0.8436 (t0) cc_final: 0.8207 (m-30) REVERT: A 1367 THR cc_start: 0.9020 (m) cc_final: 0.8738 (m) REVERT: A 1481 SER cc_start: 0.8640 (t) cc_final: 0.8411 (p) REVERT: A 1493 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7095 (pt0) outliers start: 38 outliers final: 29 residues processed: 159 average time/residue: 0.0841 time to fit residues: 20.7594 Evaluate side-chains 150 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [21, 108, 98, 124, 77, 80, 126, 57, 74, 113, 18] chunk 21 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 126 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.103333 restraints weight = 17577.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107729 restraints weight = 10644.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110663 restraints weight = 7043.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110519 restraints weight = 6057.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110985 restraints weight = 5850.812| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11569 Z= 0.139 Angle : 0.529 8.873 15714 Z= 0.284 Chirality : 0.041 0.138 1727 Planarity : 0.004 0.039 1974 Dihedral : 11.425 89.651 1707 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.46 % Allowed : 18.05 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1365 helix: 1.56 (0.24), residues: 481 sheet: 1.32 (0.42), residues: 165 loop : -0.54 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.019 0.001 TYR A 702 PHE 0.013 0.001 PHE A 630 TRP 0.008 0.001 TRP A 850 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11565) covalent geometry : angle 0.52100 / 0.28 (15708) hydrogen bonds : bond 0.04107 / 2.81 ( 424) hydrogen bonds : angle 4.65003 / 3.38 ( 1182) metal coordination : bond 0.00802 / 0.40 ( 4) metal coordination : angle 4.71419 / 2.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8727 (mt) cc_final: 0.8442 (tp) REVERT: A 233 LYS cc_start: 0.7800 (tptt) cc_final: 0.7486 (tptp) REVERT: A 306 MET cc_start: 0.8354 (mtt) cc_final: 0.8017 (mtp) REVERT: A 343 ASP cc_start: 0.7584 (t0) cc_final: 0.7137 (p0) REVERT: A 390 ILE cc_start: 0.8578 (tp) cc_final: 0.8319 (tp) REVERT: A 547 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6921 (mt-10) REVERT: A 665 PHE cc_start: 0.8367 (t80) cc_final: 0.7919 (t80) REVERT: A 913 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8472 (pp) REVERT: A 989 ILE cc_start: 0.8744 (mt) cc_final: 0.8442 (mm) REVERT: A 1252 HIS cc_start: 0.7248 (p-80) cc_final: 0.6487 (t70) REVERT: A 1318 ASP cc_start: 0.8423 (t0) cc_final: 0.8171 (m-30) REVERT: A 1481 SER cc_start: 0.8570 (t) cc_final: 0.8296 (p) REVERT: A 1493 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7101 (pt0) outliers start: 42 outliers final: 36 residues processed: 154 average time/residue: 0.0815 time to fit residues: 19.6021 Evaluate side-chains 156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 533 TRP Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1387 SER Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [93, 47, 87, 24, 3, 85, 130, 100, 128, 31, 107] chunk 93 optimal weight: 0.0000 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 3 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106125 restraints weight = 16943.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109975 restraints weight = 10154.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113155 restraints weight = 6739.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113442 restraints weight = 5476.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114071 restraints weight = 5315.624| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11569 Z= 0.105 Angle : 0.507 8.164 15714 Z= 0.274 Chirality : 0.040 0.153 1727 Planarity : 0.003 0.040 1974 Dihedral : 11.338 89.329 1707 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.22 % Allowed : 18.47 % Favored : 78.32 % 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: 0.72 (0.22), residues: 1365 helix: 1.62 (0.24), residues: 481 sheet: 1.37 (0.43), residues: 165 loop : -0.53 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1375 TYR 0.018 0.001 TYR A 702 PHE 0.015 0.001 PHE A 630 TRP 0.008 0.001 TRP A 956 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11565) covalent geometry : angle 0.50050 / 0.27 (15708) hydrogen bonds : bond 0.03640 / 2.48 ( 424) hydrogen bonds : angle 4.55403 / 3.31 ( 1182) metal coordination : bond 0.00503 / 0.25 ( 4) metal coordination : angle 4.23089 / 2.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8698 (mt) cc_final: 0.8432 (tp) REVERT: A 233 LYS cc_start: 0.7828 (tptt) cc_final: 0.7517 (tptp) REVERT: A 306 MET cc_start: 0.8319 (mtt) cc_final: 0.8058 (mtp) REVERT: A 343 ASP cc_start: 0.7566 (t0) cc_final: 0.7147 (p0) REVERT: A 360 MET cc_start: 0.8215 (mmt) cc_final: 0.7862 (mmp) REVERT: A 390 ILE cc_start: 0.8572 (tp) cc_final: 0.8311 (tp) REVERT: A 547 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6900 (mt-10) REVERT: A 637 MET cc_start: 0.8036 (mtm) cc_final: 0.7822 (mtt) REVERT: A 665 PHE cc_start: 0.8341 (t80) cc_final: 0.7886 (t80) REVERT: A 913 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8464 (pp) REVERT: A 989 ILE cc_start: 0.8758 (mt) cc_final: 0.8477 (mm) REVERT: A 1252 HIS cc_start: 0.7208 (p-80) cc_final: 0.6485 (t70) REVERT: A 1318 ASP cc_start: 0.8355 (t0) cc_final: 0.8116 (m-30) REVERT: A 1367 THR cc_start: 0.9084 (m) cc_final: 0.8766 (m) REVERT: A 1481 SER cc_start: 0.8640 (t) cc_final: 0.8409 (p) REVERT: A 1493 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7139 (pt0) outliers start: 39 outliers final: 34 residues processed: 155 average time/residue: 0.0903 time to fit residues: 20.8682 Evaluate side-chains 156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [94, 51, 8, 104, 21, 11, 22, 77, 72, 129, 90] chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS A 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.143986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.104851 restraints weight = 17027.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109672 restraints weight = 10116.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112705 restraints weight = 6439.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112637 restraints weight = 5296.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113154 restraints weight = 5236.799| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11569 Z= 0.116 Angle : 0.515 8.335 15714 Z= 0.277 Chirality : 0.041 0.188 1727 Planarity : 0.003 0.038 1974 Dihedral : 11.293 89.080 1705 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.13 % Allowed : 18.47 % Favored : 78.40 % 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: 0.70 (0.22), residues: 1365 helix: 1.58 (0.24), residues: 482 sheet: 1.35 (0.43), residues: 165 loop : -0.53 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 589 TYR 0.023 0.001 TYR A 702 PHE 0.016 0.001 PHE A 865 TRP 0.007 0.001 TRP A 850 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11565) covalent geometry : angle 0.50818 / 0.28 (15708) hydrogen bonds : bond 0.03745 / 2.55 ( 424) hydrogen bonds : angle 4.56865 / 3.31 ( 1182) metal coordination : bond 0.00630 / 0.32 ( 4) metal coordination : angle 4.29597 / 2.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8719 (mt) cc_final: 0.8443 (tp) REVERT: A 233 LYS cc_start: 0.7838 (tptt) cc_final: 0.7522 (tptp) REVERT: A 306 MET cc_start: 0.8376 (mtt) cc_final: 0.8081 (mtp) REVERT: A 343 ASP cc_start: 0.7574 (t0) cc_final: 0.7152 (p0) REVERT: A 360 MET cc_start: 0.8154 (mmt) cc_final: 0.7768 (mmp) REVERT: A 390 ILE cc_start: 0.8576 (tp) cc_final: 0.8316 (tp) REVERT: A 547 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: A 637 MET cc_start: 0.8057 (mtm) cc_final: 0.7844 (mtt) REVERT: A 665 PHE cc_start: 0.8377 (t80) cc_final: 0.7930 (t80) REVERT: A 913 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8481 (pp) REVERT: A 989 ILE cc_start: 0.8760 (mt) cc_final: 0.8475 (mm) REVERT: A 1252 HIS cc_start: 0.7182 (p-80) cc_final: 0.6431 (t70) REVERT: A 1318 ASP cc_start: 0.8353 (t0) cc_final: 0.8114 (m-30) REVERT: A 1367 THR cc_start: 0.9129 (m) cc_final: 0.8836 (m) REVERT: A 1481 SER cc_start: 0.8587 (t) cc_final: 0.8345 (p) REVERT: A 1493 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7147 (pt0) outliers start: 38 outliers final: 34 residues processed: 149 average time/residue: 0.0858 time to fit residues: 19.8693 Evaluate side-chains 156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 593 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 661 TYR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 698 TRP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 733 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 777 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 931 ASN Chi-restraints excluded: chain A residue 972 HIS Chi-restraints excluded: chain A residue 1054 HIS Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 SER Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1145 THR Chi-restraints excluded: chain A residue 1156 ASP Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1205 VAL Chi-restraints excluded: chain A residue 1395 ILE Chi-restraints excluded: chain A residue 1493 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: [104, 4, 34, 68, 79, 26, 126, 135, 37, 84, 28] chunk 104 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 26 optimal weight: 0.0870 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 overall best weight: 1.0562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.144499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.104507 restraints weight = 17850.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108839 restraints weight = 10862.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111376 restraints weight = 7199.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111566 restraints weight = 6262.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112185 restraints weight = 6059.977| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11569 Z= 0.121 Angle : 0.517 8.189 15714 Z= 0.277 Chirality : 0.041 0.147 1727 Planarity : 0.004 0.037 1974 Dihedral : 11.292 88.552 1705 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.22 % Allowed : 18.38 % Favored : 78.40 % 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: 0.69 (0.22), residues: 1365 helix: 1.58 (0.23), residues: 488 sheet: 1.26 (0.43), residues: 165 loop : -0.53 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1457 TYR 0.022 0.001 TYR A 702 PHE 0.014 0.001 PHE A 865 TRP 0.007 0.001 TRP A 850 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11565) covalent geometry : angle 0.51021 / 0.28 (15708) hydrogen bonds : bond 0.03774 / 2.59 ( 424) hydrogen bonds : angle 4.56392 / 3.32 ( 1182) metal coordination : bond 0.00672 / 0.34 ( 4) metal coordination : angle 4.28583 / 2.25 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1705.97 seconds wall clock time: 30 minutes 10.55 seconds (1810.55 seconds total)