Starting phenix.real_space_refine on Fri Jul 3 01:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lcc_23271/07_2026/7lcc_23271.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lcc_23271/07_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_23271/07_2026/7lcc_23271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lcc_23271/07_2026/7lcc_23271.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lcc_23271/07_2026/7lcc_23271.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lcc_23271/07_2026/7lcc_23271.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lcc_23271/07_2026/7lcc_23271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lcc_23271/07_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-dev-6108/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: 2.61, per 1000 atoms: 0.23 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: 0.86 Conformation dependent library (CDL) restraints added in 600.0 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: 1.04 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: 2.07 Time building geometry restraints manager: 1.16 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: 10782 1.51 - 3.02: 4076 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: 0.730 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.990 Find NCS groups from input model: 0.050 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.370 ------------------------------------------------------------------------------- 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 1.52803 / 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 : 0.431 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: 0.1039 time to fit residues: 50.5383 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 : 0.433 ------------------------------------------------------------------------------- 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: 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 = 0.3853 r_free = 0.3853 target = 0.147939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109639 restraints weight = 16844.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114662 restraints weight = 9510.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117734 restraints weight = 5892.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117878 restraints weight = 4738.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118318 restraints weight = 4704.661| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11569 Z= 0.171 Angle : 0.674 13.740 15714 Z= 0.367 Chirality : 0.044 0.225 1727 Planarity : 0.005 0.049 1974 Dihedral : 12.643 86.679 1735 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.37 % Allowed : 12.61 % Favored : 83.02 % 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: 2.14 (0.23), residues: 474 sheet: 2.30 (0.40), residues: 146 loop : -0.22 (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 731 PHE 0.020 0.002 PHE A1369 TRP 0.013 0.001 TRP A 543 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (11565) covalent geometry : angle 0.65478 / 0.37 (15708) hydrogen bonds : bond 0.07552 / 4.95 ( 424) hydrogen bonds : angle 5.39803 / 3.92 ( 1182) metal coordination : bond 0.01370 / 0.70 ( 4) metal coordination : angle 8.17647 / 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 : 0.396 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8704 (mt) cc_final: 0.8335 (tp) REVERT: A 233 LYS cc_start: 0.7728 (tptt) cc_final: 0.7512 (tptp) REVERT: A 306 MET cc_start: 0.8003 (mtt) cc_final: 0.7793 (mtp) REVERT: A 343 ASP cc_start: 0.7863 (t0) cc_final: 0.6967 (p0) REVERT: A 390 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8219 (tp) REVERT: A 487 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8350 (tp) REVERT: A 547 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6859 (mt-10) REVERT: A 665 PHE cc_start: 0.8263 (t80) cc_final: 0.7881 (t80) REVERT: A 676 TYR cc_start: 0.7856 (m-10) cc_final: 0.7355 (m-10) REVERT: A 679 TYR cc_start: 0.7873 (m-80) cc_final: 0.7497 (m-80) REVERT: A 913 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.7941 (pp) REVERT: A 989 ILE cc_start: 0.8752 (mt) cc_final: 0.8399 (mm) REVERT: A 1481 SER cc_start: 0.8489 (t) cc_final: 0.8166 (p) outliers start: 53 outliers final: 34 residues processed: 194 average time/residue: 0.0966 time to fit residues: 28.1030 Evaluate side-chains 161 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 1144 CYS 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 1240 SER Chi-restraints excluded: chain A residue 1371 ILE 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.9882 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.145844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107585 restraints weight = 17050.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.113448 restraints weight = 10089.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115260 restraints weight = 6082.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115594 restraints weight = 5197.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116094 restraints weight = 5082.130| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11569 Z= 0.137 Angle : 0.571 9.672 15714 Z= 0.312 Chirality : 0.042 0.184 1727 Planarity : 0.004 0.045 1974 Dihedral : 12.206 87.010 1719 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.79 % Allowed : 14.92 % Favored : 81.29 % 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: 1.00 (0.22), residues: 1365 helix: 1.81 (0.23), residues: 475 sheet: 1.61 (0.40), residues: 165 loop : -0.33 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 973 TYR 0.020 0.002 TYR A1021 PHE 0.015 0.001 PHE A1369 TRP 0.008 0.001 TRP A 850 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11565) covalent geometry : angle 0.56012 / 0.31 (15708) hydrogen bonds : bond 0.05575 / 3.72 ( 424) hydrogen bonds : angle 5.01497 / 3.65 ( 1182) metal coordination : bond 0.01008 / 0.51 ( 4) metal coordination : angle 5.62398 / 2.90 ( 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 179 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8685 (mt) cc_final: 0.8360 (tp) REVERT: A 233 LYS cc_start: 0.7763 (tptt) cc_final: 0.7548 (tptp) REVERT: A 263 MET cc_start: 0.8539 (tpt) cc_final: 0.8283 (tpt) REVERT: A 306 MET cc_start: 0.8324 (mtt) cc_final: 0.7954 (mtp) REVERT: A 343 ASP cc_start: 0.7779 (t0) cc_final: 0.6917 (p0) REVERT: A 390 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8239 (tp) REVERT: A 487 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8381 (mm) REVERT: A 490 MET cc_start: 0.8038 (ttp) cc_final: 0.7663 (ptm) REVERT: A 547 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6689 (mt-10) REVERT: A 665 PHE cc_start: 0.8284 (t80) cc_final: 0.7829 (t80) REVERT: A 679 TYR cc_start: 0.7972 (m-80) cc_final: 0.7658 (m-80) REVERT: A 913 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8074 (pp) REVERT: A 989 ILE cc_start: 0.8774 (mt) cc_final: 0.8457 (mm) REVERT: A 1232 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 1296 GLU cc_start: 0.7820 (tp30) cc_final: 0.7527 (tp30) REVERT: A 1481 SER cc_start: 0.8576 (t) cc_final: 0.8283 (p) outliers start: 46 outliers final: 31 residues processed: 166 average time/residue: 0.0921 time to fit residues: 23.1118 Evaluate side-chains 154 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 390 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS 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 629 LEU 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 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 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 1232 LEU Chi-restraints excluded: chain A residue 1240 SER Chi-restraints excluded: chain A residue 1301 LEU 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: chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 84 optimal weight: 0.0020 chunk 122 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 0.7750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN A 636 ASN ** A 972 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.147048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107436 restraints weight = 17154.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112348 restraints weight = 9693.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115932 restraints weight = 6167.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.115957 restraints weight = 5046.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116566 restraints weight = 4859.680| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11569 Z= 0.122 Angle : 0.532 8.197 15714 Z= 0.290 Chirality : 0.041 0.146 1727 Planarity : 0.004 0.046 1974 Dihedral : 11.973 87.762 1716 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 : 3.96 % Allowed : 15.50 % Favored : 80.54 % 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: 0.99 (0.22), residues: 1365 helix: 1.80 (0.23), residues: 480 sheet: 1.61 (0.41), residues: 165 loop : -0.36 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1375 TYR 0.018 0.001 TYR A 762 PHE 0.011 0.001 PHE A1369 TRP 0.015 0.001 TRP A 956 HIS 0.009 0.001 HIS A 219 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11565) covalent geometry : angle 0.52349 / 0.29 (15708) hydrogen bonds : bond 0.04668 / 3.13 ( 424) hydrogen bonds : angle 4.81454 / 3.50 ( 1182) metal coordination : bond 0.00752 / 0.38 ( 4) metal coordination : angle 4.90445 / 2.55 ( 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 176 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.369 Fit side-chains REVERT: A 142 LYS cc_start: 0.8138 (mttt) cc_final: 0.7583 (mmtm) REVERT: A 169 LEU cc_start: 0.8671 (mt) cc_final: 0.8417 (tp) REVERT: A 233 LYS cc_start: 0.7753 (tptt) cc_final: 0.7541 (tptp) REVERT: A 263 MET cc_start: 0.8522 (tpt) cc_final: 0.8281 (tpt) REVERT: A 306 MET cc_start: 0.8338 (mtt) cc_final: 0.7976 (mtp) REVERT: A 343 ASP cc_start: 0.7757 (t0) cc_final: 0.7109 (p0) REVERT: A 390 ILE cc_start: 0.8579 (tp) cc_final: 0.8297 (tp) REVERT: A 490 MET cc_start: 0.8021 (ttp) cc_final: 0.7805 (ptm) REVERT: A 547 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: A 566 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7867 (t0) REVERT: A 665 PHE cc_start: 0.8301 (t80) cc_final: 0.7846 (t80) REVERT: A 679 TYR cc_start: 0.7884 (m-80) cc_final: 0.7607 (m-80) REVERT: A 913 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8157 (pp) REVERT: A 989 ILE cc_start: 0.8799 (mt) cc_final: 0.8474 (mm) REVERT: A 1232 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8273 (tp) REVERT: A 1296 GLU cc_start: 0.7737 (tp30) cc_final: 0.7445 (tp30) REVERT: A 1481 SER cc_start: 0.8565 (t) cc_final: 0.8288 (p) REVERT: A 1493 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6883 (pt0) outliers start: 48 outliers final: 29 residues processed: 163 average time/residue: 0.0976 time to fit residues: 23.6434 Evaluate side-chains 154 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.445 ------------------------------------------------------------------------------- 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 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 547 GLU Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 582 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 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 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 1205 VAL Chi-restraints excluded: chain A residue 1232 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 120 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 126 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.145948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105277 restraints weight = 17547.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110570 restraints weight = 10094.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113055 restraints weight = 6397.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113210 restraints weight = 5619.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113699 restraints weight = 5441.131| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11569 Z= 0.146 Angle : 0.535 8.487 15714 Z= 0.289 Chirality : 0.041 0.140 1727 Planarity : 0.004 0.042 1974 Dihedral : 11.675 88.739 1708 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.20 % Allowed : 16.24 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.22), residues: 1365 helix: 1.73 (0.23), residues: 474 sheet: 1.52 (0.41), residues: 165 loop : -0.38 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.018 0.001 TYR A 762 PHE 0.013 0.001 PHE A1369 TRP 0.012 0.001 TRP A 837 HIS 0.009 0.001 HIS A1054 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (11565) covalent geometry : angle 0.52632 / 0.29 (15708) hydrogen bonds : bond 0.04602 / 3.10 ( 424) hydrogen bonds : angle 4.76651 / 3.46 ( 1182) metal coordination : bond 0.00917 / 0.46 ( 4) metal coordination : angle 4.88579 / 2.55 ( 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 177 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8745 (mt) cc_final: 0.8482 (tp) REVERT: A 233 LYS cc_start: 0.7759 (tptt) cc_final: 0.7541 (tptp) REVERT: A 306 MET cc_start: 0.8437 (mtt) cc_final: 0.8053 (mtp) REVERT: A 333 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.8033 (m110) REVERT: A 343 ASP cc_start: 0.7735 (t0) cc_final: 0.7126 (p0) REVERT: A 360 MET cc_start: 0.8820 (mmm) cc_final: 0.8606 (mmt) REVERT: A 390 ILE cc_start: 0.8592 (tp) cc_final: 0.8303 (tp) REVERT: A 547 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: A 665 PHE cc_start: 0.8338 (t80) cc_final: 0.7870 (t80) REVERT: A 913 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 989 ILE cc_start: 0.8775 (mt) cc_final: 0.8460 (mm) REVERT: A 1124 ASP cc_start: 0.7688 (m-30) cc_final: 0.7441 (t0) REVERT: A 1232 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8258 (tp) REVERT: A 1296 GLU cc_start: 0.7865 (tp30) cc_final: 0.7555 (tp30) REVERT: A 1481 SER cc_start: 0.8577 (t) cc_final: 0.8283 (p) REVERT: A 1493 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6890 (pt0) outliers start: 51 outliers final: 33 residues processed: 163 average time/residue: 0.0918 time to fit residues: 22.7059 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 : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 THR 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 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 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 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 1232 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN A1054 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105284 restraints weight = 17537.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110171 restraints weight = 10557.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112648 restraints weight = 6723.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112833 restraints weight = 5839.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113563 restraints weight = 5723.597| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11569 Z= 0.118 Angle : 0.517 8.159 15714 Z= 0.279 Chirality : 0.040 0.137 1727 Planarity : 0.004 0.041 1974 Dihedral : 11.554 89.583 1707 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.12 % Allowed : 16.32 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.22), residues: 1365 helix: 1.70 (0.23), residues: 480 sheet: 1.54 (0.42), residues: 165 loop : -0.43 (0.21), residues: 720 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 A1369 TRP 0.011 0.001 TRP A 956 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11565) covalent geometry : angle 0.50951 / 0.28 (15708) hydrogen bonds : bond 0.04180 / 2.83 ( 424) hydrogen bonds : angle 4.68635 / 3.40 ( 1182) metal coordination : bond 0.00701 / 0.35 ( 4) metal coordination : angle 4.61404 / 2.41 ( 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 175 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.281 Fit side-chains REVERT: A 142 LYS cc_start: 0.8022 (mttt) cc_final: 0.7441 (mmtm) REVERT: A 169 LEU cc_start: 0.8721 (mt) cc_final: 0.8471 (tp) REVERT: A 233 LYS cc_start: 0.7721 (tptt) cc_final: 0.7403 (tptp) REVERT: A 306 MET cc_start: 0.8420 (mtt) cc_final: 0.8038 (mtp) REVERT: A 343 ASP cc_start: 0.7720 (t0) cc_final: 0.7114 (p0) REVERT: A 390 ILE cc_start: 0.8529 (tp) cc_final: 0.8263 (tp) REVERT: A 547 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6895 (mt-10) REVERT: A 665 PHE cc_start: 0.8288 (t80) cc_final: 0.7791 (t80) REVERT: A 913 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8259 (pp) REVERT: A 989 ILE cc_start: 0.8766 (mt) cc_final: 0.8462 (mm) REVERT: A 1124 ASP cc_start: 0.7677 (m-30) cc_final: 0.7431 (t0) REVERT: A 1296 GLU cc_start: 0.7879 (tp30) cc_final: 0.7656 (tp30) REVERT: A 1481 SER cc_start: 0.8557 (t) cc_final: 0.8279 (p) REVERT: A 1493 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6983 (pt0) outliers start: 50 outliers final: 37 residues processed: 160 average time/residue: 0.0868 time to fit residues: 21.0064 Evaluate side-chains 158 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 308 ILE 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 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 733 TYR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 751 HIS Chi-restraints excluded: chain A residue 775 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 1229 LEU 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: chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 333 ASN A 421 HIS A 646 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.146345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.107819 restraints weight = 16972.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111761 restraints weight = 10173.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115201 restraints weight = 6657.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115329 restraints weight = 5370.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116049 restraints weight = 5226.709| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11569 Z= 0.102 Angle : 0.508 8.042 15714 Z= 0.273 Chirality : 0.040 0.154 1727 Planarity : 0.003 0.040 1974 Dihedral : 11.429 89.697 1707 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.38 % Allowed : 17.07 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.22), residues: 1365 helix: 1.69 (0.23), residues: 486 sheet: 1.50 (0.42), residues: 165 loop : -0.49 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1375 TYR 0.023 0.001 TYR A 209 PHE 0.013 0.001 PHE A 191 TRP 0.009 0.001 TRP A 956 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (11565) covalent geometry : angle 0.50140 / 0.27 (15708) hydrogen bonds : bond 0.03736 / 2.55 ( 424) hydrogen bonds : angle 4.58152 / 3.32 ( 1182) metal coordination : bond 0.00512 / 0.26 ( 4) metal coordination : angle 4.34997 / 2.28 ( 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 165 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.458 Fit side-chains REVERT: A 142 LYS cc_start: 0.8002 (mttt) cc_final: 0.7462 (mmtm) REVERT: A 169 LEU cc_start: 0.8761 (mt) cc_final: 0.8461 (tp) REVERT: A 233 LYS cc_start: 0.7800 (tptt) cc_final: 0.7482 (tptp) REVERT: A 306 MET cc_start: 0.8353 (mtt) cc_final: 0.8055 (mtp) REVERT: A 343 ASP cc_start: 0.7648 (t0) cc_final: 0.7127 (p0) REVERT: A 390 ILE cc_start: 0.8535 (tp) cc_final: 0.8265 (tp) REVERT: A 547 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6839 (mt-10) REVERT: A 637 MET cc_start: 0.7957 (mtm) cc_final: 0.7751 (mtt) REVERT: A 665 PHE cc_start: 0.8266 (t80) cc_final: 0.7731 (t80) REVERT: A 913 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8278 (pp) REVERT: A 989 ILE cc_start: 0.8784 (mt) cc_final: 0.8499 (mm) REVERT: A 1252 HIS cc_start: 0.7149 (p-80) cc_final: 0.6342 (t70) REVERT: A 1367 THR cc_start: 0.9085 (m) cc_final: 0.8844 (m) REVERT: A 1481 SER cc_start: 0.8646 (t) cc_final: 0.8407 (p) REVERT: A 1493 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.7011 (pt0) outliers start: 41 outliers final: 31 residues processed: 154 average time/residue: 0.0747 time to fit residues: 17.4664 Evaluate side-chains 152 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 412 VAL 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 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 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 986 LEU 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 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 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: chunk 21 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 113 optimal weight: 0.0030 chunk 18 optimal weight: 9.9990 overall best weight: 1.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.103687 restraints weight = 17113.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107766 restraints weight = 10375.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111023 restraints weight = 6748.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111220 restraints weight = 5430.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111945 restraints weight = 5347.457| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11569 Z= 0.162 Angle : 0.558 8.935 15714 Z= 0.299 Chirality : 0.042 0.137 1727 Planarity : 0.004 0.061 1974 Dihedral : 11.399 89.876 1705 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.96 % Allowed : 17.48 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.22), residues: 1365 helix: 1.60 (0.23), residues: 475 sheet: 1.51 (0.42), residues: 169 loop : -0.51 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 589 TYR 0.020 0.002 TYR A 702 PHE 0.014 0.001 PHE A 574 TRP 0.008 0.001 TRP A 956 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (11565) covalent geometry : angle 0.54926 / 0.30 (15708) hydrogen bonds : bond 0.04433 / 3.01 ( 424) hydrogen bonds : angle 4.70329 / 3.41 ( 1182) metal coordination : bond 0.00952 / 0.48 ( 4) metal coordination : angle 4.97123 / 2.59 ( 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 165 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 117 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8706 (mt) cc_final: 0.8430 (tp) REVERT: A 188 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7921 (t0) REVERT: A 233 LYS cc_start: 0.7830 (tptt) cc_final: 0.7514 (tptp) REVERT: A 343 ASP cc_start: 0.7627 (t0) cc_final: 0.7133 (p0) REVERT: A 390 ILE cc_start: 0.8572 (tp) cc_final: 0.8301 (tp) REVERT: A 547 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6915 (mt-10) REVERT: A 589 ARG cc_start: 0.7082 (mtp180) cc_final: 0.6875 (mtp85) REVERT: A 637 MET cc_start: 0.8070 (mtm) cc_final: 0.7864 (mtt) REVERT: A 665 PHE cc_start: 0.8328 (t80) cc_final: 0.7842 (t80) REVERT: A 913 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8433 (pp) REVERT: A 989 ILE cc_start: 0.8766 (mt) cc_final: 0.8463 (mm) REVERT: A 1117 GLU cc_start: 0.7309 (pt0) cc_final: 0.7097 (pt0) REVERT: A 1252 HIS cc_start: 0.7211 (p-80) cc_final: 0.6431 (t70) REVERT: A 1481 SER cc_start: 0.8603 (t) cc_final: 0.8369 (p) REVERT: A 1493 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7066 (pt0) outliers start: 48 outliers final: 38 residues processed: 154 average time/residue: 0.0834 time to fit residues: 20.0750 Evaluate side-chains 156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE 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 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 487 ILE 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 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 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 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 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 1229 LEU 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: chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS A 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103867 restraints weight = 17111.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107963 restraints weight = 10220.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111310 restraints weight = 6694.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111363 restraints weight = 5463.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111934 restraints weight = 5287.455| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11569 Z= 0.138 Angle : 0.534 8.423 15714 Z= 0.286 Chirality : 0.041 0.137 1727 Planarity : 0.003 0.038 1974 Dihedral : 11.363 89.911 1705 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.63 % Allowed : 17.56 % Favored : 78.81 % 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: 1.54 (0.23), residues: 481 sheet: 1.40 (0.43), residues: 163 loop : -0.53 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 589 TYR 0.020 0.001 TYR A 702 PHE 0.013 0.001 PHE A 630 TRP 0.009 0.001 TRP A 956 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (11565) covalent geometry : angle 0.52568 / 0.29 (15708) hydrogen bonds : bond 0.04138 / 2.82 ( 424) hydrogen bonds : angle 4.65329 / 3.38 ( 1182) metal coordination : bond 0.00809 / 0.40 ( 4) metal coordination : angle 4.70145 / 2.46 ( 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 163 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8723 (mt) cc_final: 0.8378 (tp) REVERT: A 188 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7942 (t0) REVERT: A 233 LYS cc_start: 0.7832 (tptt) cc_final: 0.7515 (tptp) REVERT: A 343 ASP cc_start: 0.7594 (t0) cc_final: 0.7145 (p0) REVERT: A 390 ILE cc_start: 0.8571 (tp) cc_final: 0.8316 (tp) REVERT: A 547 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: A 589 ARG cc_start: 0.7112 (mtp180) cc_final: 0.6807 (mtp85) REVERT: A 665 PHE cc_start: 0.8351 (t80) cc_final: 0.7905 (t80) REVERT: A 913 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8436 (pp) REVERT: A 989 ILE cc_start: 0.8764 (mt) cc_final: 0.8471 (mm) REVERT: A 1117 GLU cc_start: 0.7425 (pt0) cc_final: 0.7201 (pt0) REVERT: A 1252 HIS cc_start: 0.7255 (p-80) cc_final: 0.6529 (t70) REVERT: A 1481 SER cc_start: 0.8598 (t) cc_final: 0.8349 (p) REVERT: A 1493 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7075 (pt0) outliers start: 44 outliers final: 36 residues processed: 154 average time/residue: 0.0891 time to fit residues: 20.6597 Evaluate side-chains 156 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 1229 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 94 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 104 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 421 HIS ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.145302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105539 restraints weight = 17601.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109800 restraints weight = 10659.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112945 restraints weight = 7105.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112843 restraints weight = 6011.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.113403 restraints weight = 5832.535| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11569 Z= 0.108 Angle : 0.521 8.876 15714 Z= 0.277 Chirality : 0.040 0.139 1727 Planarity : 0.003 0.040 1974 Dihedral : 11.293 89.954 1705 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.89 % Allowed : 18.14 % 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: 0.74 (0.22), residues: 1365 helix: 1.64 (0.24), residues: 481 sheet: 1.34 (0.43), residues: 165 loop : -0.51 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.023 0.001 TYR A 702 PHE 0.015 0.001 PHE A 865 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 0.00242 / 0.11 (11565) covalent geometry : angle 0.51411 / 0.28 (15708) hydrogen bonds : bond 0.03700 / 2.55 ( 424) hydrogen bonds : angle 4.57492 / 3.33 ( 1182) metal coordination : bond 0.00552 / 0.28 ( 4) metal coordination : angle 4.29846 / 2.26 ( 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 157 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.8823 (mt) cc_final: 0.8477 (tp) REVERT: A 209 TYR cc_start: 0.5508 (t80) cc_final: 0.5245 (t80) REVERT: A 233 LYS cc_start: 0.7810 (tptt) cc_final: 0.7500 (tptp) REVERT: A 306 MET cc_start: 0.8440 (mtt) cc_final: 0.7962 (mtp) REVERT: A 343 ASP cc_start: 0.7601 (t0) cc_final: 0.7149 (p0) REVERT: A 360 MET cc_start: 0.8558 (mmm) cc_final: 0.7971 (mtm) REVERT: A 390 ILE cc_start: 0.8541 (tp) cc_final: 0.8287 (tp) REVERT: A 547 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6889 (mt-10) REVERT: A 589 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6712 (mtp85) REVERT: A 665 PHE cc_start: 0.8352 (t80) cc_final: 0.7866 (t80) REVERT: A 913 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8480 (pp) REVERT: A 989 ILE cc_start: 0.8771 (mt) cc_final: 0.8493 (mm) REVERT: A 1117 GLU cc_start: 0.7344 (pt0) cc_final: 0.7120 (pt0) REVERT: A 1252 HIS cc_start: 0.7199 (p-80) cc_final: 0.6405 (t70) REVERT: A 1367 THR cc_start: 0.9165 (m) cc_final: 0.8893 (m) REVERT: A 1481 SER cc_start: 0.8641 (t) cc_final: 0.8385 (p) REVERT: A 1493 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7107 (pt0) outliers start: 35 outliers final: 31 residues processed: 149 average time/residue: 0.0926 time to fit residues: 20.8124 Evaluate side-chains 150 residues out of total 1213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 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 487 ILE Chi-restraints excluded: chain A residue 526 THR 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 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 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 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 1229 LEU 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: chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105737 restraints weight = 17236.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110616 restraints weight = 10317.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113713 restraints weight = 6445.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113706 restraints weight = 5255.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114274 restraints weight = 5226.042| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11569 Z= 0.107 Angle : 0.513 8.065 15714 Z= 0.273 Chirality : 0.040 0.152 1727 Planarity : 0.003 0.038 1974 Dihedral : 11.253 89.972 1705 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.97 % Allowed : 18.05 % 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: 0.79 (0.22), residues: 1365 helix: 1.67 (0.24), residues: 481 sheet: 1.39 (0.43), residues: 165 loop : -0.47 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1375 TYR 0.020 0.001 TYR A 702 PHE 0.017 0.001 PHE A 865 TRP 0.007 0.001 TRP A 956 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11565) covalent geometry : angle 0.50615 / 0.27 (15708) hydrogen bonds : bond 0.03572 / 2.45 ( 424) hydrogen bonds : angle 4.54261 / 3.31 ( 1182) metal coordination : bond 0.00558 / 0.28 ( 4) metal coordination : angle 4.16340 / 2.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.36 seconds wall clock time: 30 minutes 59.79 seconds (1859.79 seconds total)