Starting phenix.real_space_refine on Thu Jul 2 17:53:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtc_30850/07_2026/7dtc_30850.cif" } resolution = 3.3 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= 0.010 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 73 5.16 5 C 6187 2.51 5 N 1467 2.21 5 O 1636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 9363 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 9237 Classifications: {'peptide': 1151} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 1120} Chain breaks: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 1.91, per 1000 atoms: 0.20 Number of scatterers: 9363 At special positions: 0 Unit cell: (134.23, 129.9, 112.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 73 16.00 O 1636 8.00 N 1467 7.00 C 6187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 326 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 341 " distance=2.05 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A1363 " - pdb=" SG CYS A1384 " distance=2.03 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1742 " distance=2.03 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 Links applied NAG-ASN " NAG A2101 " - " ASN A 283 " " NAG A2102 " - " ASN A 288 " " NAG A2103 " - " ASN A 291 " " NAG A2104 " - " ASN A 318 " " NAG A2105 " - " ASN A 328 " " NAG A2106 " - " ASN A1365 " " NAG A2107 " - " ASN A1374 " " NAG A2108 " - " ASN A1380 " " NAG A2109 " - " ASN A1388 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 274.4 milliseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 72.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.530A pdb=" N VAL A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 149 removed outlier: 4.110A pdb=" N ASN A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 177 Processing helix chain 'A' and resid 191 through 207 removed outlier: 4.122A pdb=" N TRP A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 231 removed outlier: 3.917A pdb=" N VAL A 223 " --> pdb=" O THR A 220 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Processing helix chain 'A' and resid 250 through 273 Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 348 through 352 Processing helix chain 'A' and resid 357 through 370 Processing helix chain 'A' and resid 373 through 386 removed outlier: 4.105A pdb=" N LEU A 377 " --> pdb=" O CYS A 373 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 383 " --> pdb=" O GLN A 379 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 384 " --> pdb=" O GLN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 400 removed outlier: 3.633A pdb=" N PHE A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 429 removed outlier: 3.673A pdb=" N ASN A 406 " --> pdb=" O PHE A 402 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 715 removed outlier: 3.992A pdb=" N MET A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 736 removed outlier: 3.734A pdb=" N LEU A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 769 Processing helix chain 'A' and resid 772 through 777 Processing helix chain 'A' and resid 781 through 798 Processing helix chain 'A' and resid 808 through 813 removed outlier: 3.556A pdb=" N LEU A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 820 Processing helix chain 'A' and resid 824 through 837 Processing helix chain 'A' and resid 841 through 870 removed outlier: 6.050A pdb=" N LYS A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ASN A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 866 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 867 " --> pdb=" O LYS A 863 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 868 " --> pdb=" O ASN A 864 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP A 870 " --> pdb=" O SER A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 897 Processing helix chain 'A' and resid 900 through 911 removed outlier: 4.206A pdb=" N VAL A 909 " --> pdb=" O ASP A 905 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 911 " --> pdb=" O MET A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 944 removed outlier: 3.620A pdb=" N CYS A 915 " --> pdb=" O GLY A 911 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 919 " --> pdb=" O CYS A 915 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 944 " --> pdb=" O SER A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1204 removed outlier: 3.554A pdb=" N LYS A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1201 " --> pdb=" O THR A1197 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A1202 " --> pdb=" O CYS A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1204 through 1221 removed outlier: 3.816A pdb=" N GLU A1208 " --> pdb=" O HIS A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1262 removed outlier: 3.848A pdb=" N LEU A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1268 Processing helix chain 'A' and resid 1271 through 1293 removed outlier: 3.802A pdb=" N LEU A1286 " --> pdb=" O SER A1282 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A1290 " --> pdb=" O LEU A1286 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A1291 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1304 removed outlier: 3.741A pdb=" N ARG A1303 " --> pdb=" O ILE A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1314 removed outlier: 3.588A pdb=" N LEU A1308 " --> pdb=" O LEU A1305 " (cutoff:3.500A) Proline residue: A1310 - end of helix Processing helix chain 'A' and resid 1317 through 1330 removed outlier: 3.588A pdb=" N ALA A1330 " --> pdb=" O ALA A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1331 through 1357 Processing helix chain 'A' and resid 1380 through 1385 Processing helix chain 'A' and resid 1404 through 1418 removed outlier: 3.584A pdb=" N TYR A1409 " --> pdb=" O VAL A1405 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A1410 " --> pdb=" O GLY A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1429 removed outlier: 3.705A pdb=" N ILE A1424 " --> pdb=" O GLY A1420 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1445 No H-bonds generated for 'chain 'A' and resid 1443 through 1445' Processing helix chain 'A' and resid 1446 through 1480 removed outlier: 3.812A pdb=" N PHE A1450 " --> pdb=" O MET A1446 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A1458 " --> pdb=" O ILE A1454 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A1459 " --> pdb=" O ILE A1455 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1499 Processing helix chain 'A' and resid 1515 through 1526 removed outlier: 4.781A pdb=" N ILE A1524 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL A1525 " --> pdb=" O ILE A1521 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A1526 " --> pdb=" O PHE A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1547 removed outlier: 3.592A pdb=" N VAL A1547 " --> pdb=" O VAL A1543 " (cutoff:3.500A) Processing helix chain 'A' and resid 1553 through 1582 removed outlier: 3.848A pdb=" N ASN A1558 " --> pdb=" O PRO A1554 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1559 " --> pdb=" O GLU A1555 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1582 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1609 Processing helix chain 'A' and resid 1621 through 1627 Processing helix chain 'A' and resid 1629 through 1635 removed outlier: 4.186A pdb=" N ILE A1633 " --> pdb=" O ARG A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1638 No H-bonds generated for 'chain 'A' and resid 1636 through 1638' Processing helix chain 'A' and resid 1640 through 1652 removed outlier: 4.278A pdb=" N LEU A1646 " --> pdb=" O GLY A1642 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A1650 " --> pdb=" O LEU A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1653 through 1679 Processing helix chain 'A' and resid 1696 through 1709 removed outlier: 3.573A pdb=" N CYS A1703 " --> pdb=" O ASN A1699 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A1709 " --> pdb=" O PHE A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1712 through 1718 Processing helix chain 'A' and resid 1744 through 1779 removed outlier: 3.502A pdb=" N LEU A1750 " --> pdb=" O ALA A1746 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 1361 through 1362 removed outlier: 3.675A pdb=" N ARG A1362 " --> pdb=" O THR A1396 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1647 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1428 1.31 - 1.44: 2703 1.44 - 1.57: 5336 1.57 - 1.70: 0 1.70 - 1.83: 121 Bond restraints: 9588 Sorted by residual: bond pdb=" C PHE A 402 " pdb=" O PHE A 402 " ideal model delta sigma weight residual 1.236 1.174 0.062 1.26e-02 6.30e+03 2.45e+01 bond pdb=" CA PHE A 402 " pdb=" C PHE A 402 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.35e-02 5.49e+03 7.58e+00 bond pdb=" N LEU A 807 " pdb=" CA LEU A 807 " ideal model delta sigma weight residual 1.459 1.429 0.030 1.19e-02 7.06e+03 6.43e+00 bond pdb=" C LEU A 807 " pdb=" O LEU A 807 " ideal model delta sigma weight residual 1.236 1.209 0.028 1.15e-02 7.56e+03 5.81e+00 bond pdb=" C PHE A 402 " pdb=" N TYR A 403 " ideal model delta sigma weight residual 1.333 1.299 0.033 1.45e-02 4.76e+03 5.31e+00 ... (remaining 9583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 12535 1.64 - 3.29: 390 3.29 - 4.93: 62 4.93 - 6.58: 15 6.58 - 8.22: 4 Bond angle restraints: 13006 Sorted by residual: angle pdb=" N SER A 805 " pdb=" CA SER A 805 " pdb=" C SER A 805 " ideal model delta sigma weight residual 111.14 117.48 -6.34 1.08e+00 8.57e-01 3.45e+01 angle pdb=" N PHE A 402 " pdb=" CA PHE A 402 " pdb=" C PHE A 402 " ideal model delta sigma weight residual 111.82 116.76 -4.94 1.16e+00 7.43e-01 1.82e+01 angle pdb=" N ARG A 367 " pdb=" CA ARG A 367 " pdb=" C ARG A 367 " ideal model delta sigma weight residual 111.28 107.01 4.27 1.09e+00 8.42e-01 1.54e+01 angle pdb=" N LEU A 807 " pdb=" CA LEU A 807 " pdb=" C LEU A 807 " ideal model delta sigma weight residual 111.07 106.98 4.09 1.07e+00 8.73e-01 1.46e+01 angle pdb=" C PHE A 402 " pdb=" CA PHE A 402 " pdb=" CB PHE A 402 " ideal model delta sigma weight residual 110.67 103.47 7.20 1.92e+00 2.71e-01 1.41e+01 ... (remaining 13001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4938 17.68 - 35.37: 511 35.37 - 53.05: 63 53.05 - 70.73: 15 70.73 - 88.41: 9 Dihedral angle restraints: 5536 sinusoidal: 2179 harmonic: 3357 Sorted by residual: dihedral pdb=" CB CYS A 280 " pdb=" SG CYS A 280 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual 93.00 179.80 -86.80 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS A 335 " pdb=" SG CYS A 335 " pdb=" SG CYS A 341 " pdb=" CB CYS A 341 " ideal model delta sinusoidal sigma weight residual -86.00 -9.77 -76.23 1 1.00e+01 1.00e-02 7.31e+01 dihedral pdb=" CB CYS A1363 " pdb=" SG CYS A1363 " pdb=" SG CYS A1384 " pdb=" CB CYS A1384 " ideal model delta sinusoidal sigma weight residual -86.00 -161.37 75.37 1 1.00e+01 1.00e-02 7.18e+01 ... (remaining 5533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1332 0.060 - 0.120: 189 0.120 - 0.181: 6 0.181 - 0.241: 2 0.241 - 0.301: 3 Chirality restraints: 1532 Sorted by residual: chirality pdb=" C1 NAG A2107 " pdb=" ND2 ASN A1374 " pdb=" C2 NAG A2107 " pdb=" O5 NAG A2107 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 NAG A2102 " pdb=" ND2 ASN A 288 " pdb=" C2 NAG A2102 " pdb=" O5 NAG A2102 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C1 NAG A2105 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG A2105 " pdb=" O5 NAG A2105 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1529 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 804 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.22e+00 pdb=" C LEU A 804 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 804 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 805 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1513 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C PRO A1513 " -0.033 2.00e-02 2.50e+03 pdb=" O PRO A1513 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU A1514 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A1309 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A1310 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1310 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1310 " -0.025 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 957 2.74 - 3.28: 10285 3.28 - 3.82: 15237 3.82 - 4.36: 17867 4.36 - 4.90: 30049 Nonbonded interactions: 74395 Sorted by model distance: nonbonded pdb=" O LEU A1342 " pdb=" OH TYR A1409 " model vdw 2.201 3.040 nonbonded pdb=" OD1 ASP A 197 " pdb=" NZ LYS A 228 " model vdw 2.216 3.120 nonbonded pdb=" OE1 GLN A 371 " pdb=" OG SER A 401 " model vdw 2.228 3.040 nonbonded pdb=" OE1 GLU A 795 " pdb=" CD1 LEU A 807 " model vdw 2.240 3.460 nonbonded pdb=" ND2 ASN A1379 " pdb=" O6 NAG A2108 " model vdw 2.252 3.120 ... (remaining 74390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.650 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9602 Z= 0.202 Angle : 0.739 13.062 13043 Z= 0.403 Chirality : 0.043 0.301 1532 Planarity : 0.004 0.045 1577 Dihedral : 14.148 88.414 3355 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.95 % Favored : 91.62 % Rotamer: Outliers : 0.49 % Allowed : 5.82 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -3.34 (0.21), residues: 1145 helix: -1.32 (0.16), residues: 756 sheet: -5.84 (0.91), residues: 10 loop : -3.88 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1583 TYR 0.019 0.001 TYR A 378 PHE 0.019 0.001 PHE A 884 TRP 0.019 0.001 TRP A1421 HIS 0.003 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 ( 9588) covalent geometry : angle 0.70184 / 0.40 (13006) SS BOND : bond 0.00766 / 0.53 ( 5) SS BOND : angle 1.79952 / 0.79 ( 10) hydrogen bonds : bond 0.13086 / 8.79 ( 569) hydrogen bonds : angle 5.89929 / 4.28 ( 1647) link_NAG-ASN : bond 0.00691 / 0.50 ( 9) link_NAG-ASN : angle 5.05040 / 2.89 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 226 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9041 (tt) cc_final: 0.8758 (tt) REVERT: A 232 VAL cc_start: 0.8883 (p) cc_final: 0.8668 (p) REVERT: A 398 PHE cc_start: 0.7903 (t80) cc_final: 0.7687 (m-10) REVERT: A 399 LEU cc_start: 0.8730 (tt) cc_final: 0.8341 (mp) REVERT: A 417 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 704 MET cc_start: 0.7112 (ptt) cc_final: 0.6688 (mmt) REVERT: A 748 MET cc_start: 0.8971 (tmm) cc_final: 0.8709 (tmm) REVERT: A 759 ILE cc_start: 0.8671 (mt) cc_final: 0.8404 (mt) REVERT: A 794 MET cc_start: 0.7801 (tpt) cc_final: 0.7472 (mmp) REVERT: A 808 ARG cc_start: 0.8686 (mpt-90) cc_final: 0.8299 (mmt180) REVERT: A 821 SER cc_start: 0.8293 (m) cc_final: 0.7790 (p) REVERT: A 1280 ASP cc_start: 0.9097 (m-30) cc_final: 0.8823 (m-30) REVERT: A 1530 PHE cc_start: 0.7811 (t80) cc_final: 0.7539 (t80) REVERT: A 1579 LEU cc_start: 0.8699 (mt) cc_final: 0.8476 (mt) REVERT: A 1651 MET cc_start: 0.8697 (ttt) cc_final: 0.8322 (ttt) REVERT: A 1777 VAL cc_start: 0.9076 (p) cc_final: 0.8867 (m) outliers start: 5 outliers final: 1 residues processed: 231 average time/residue: 0.0867 time to fit residues: 28.5619 Evaluate side-chains 158 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1757 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 HIS A 194 ASN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN A 371 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 ASN A 880 HIS A1354 ASN A1483 GLN A1491 GLN A1584 HIS A1613 GLN A1659 ASN A1699 ASN A1736 ASN A1765 ASN A1774 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.092152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071950 restraints weight = 27757.379| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.85 r_work: 0.3130 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9602 Z= 0.148 Angle : 0.711 11.990 13043 Z= 0.348 Chirality : 0.041 0.317 1532 Planarity : 0.004 0.040 1577 Dihedral : 5.303 32.609 1234 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 3.06 % Allowed : 11.45 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.52 (0.24), residues: 1145 helix: 0.12 (0.18), residues: 767 sheet: -5.12 (0.74), residues: 20 loop : -3.25 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1635 TYR 0.024 0.002 TYR A1767 PHE 0.024 0.001 PHE A 170 TRP 0.009 0.001 TRP A 156 HIS 0.006 0.001 HIS A1584 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 9588) covalent geometry : angle 0.68535 / 0.34 (13006) SS BOND : bond 0.00575 / 0.40 ( 5) SS BOND : angle 1.49392 / 0.85 ( 10) hydrogen bonds : bond 0.04213 / 2.82 ( 569) hydrogen bonds : angle 4.59512 / 3.29 ( 1647) link_NAG-ASN : bond 0.00666 / 0.49 ( 9) link_NAG-ASN : angle 4.13768 / 2.42 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8938 (mmm) cc_final: 0.8483 (mtt) REVERT: A 365 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8915 (tt) REVERT: A 399 LEU cc_start: 0.8894 (tt) cc_final: 0.8468 (mp) REVERT: A 417 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8671 (tm-30) REVERT: A 704 MET cc_start: 0.7069 (ptt) cc_final: 0.6672 (mmt) REVERT: A 759 ILE cc_start: 0.8687 (mt) cc_final: 0.8460 (mt) REVERT: A 785 ASP cc_start: 0.9152 (t0) cc_final: 0.8928 (m-30) REVERT: A 794 MET cc_start: 0.7849 (tpt) cc_final: 0.7618 (mmp) REVERT: A 808 ARG cc_start: 0.8964 (mpt-90) cc_final: 0.8719 (mmt180) REVERT: A 821 SER cc_start: 0.8303 (m) cc_final: 0.7908 (p) REVERT: A 1213 PHE cc_start: 0.8837 (t80) cc_final: 0.8078 (m-10) REVERT: A 1214 MET cc_start: 0.9183 (mmm) cc_final: 0.8955 (tpp) REVERT: A 1487 MET cc_start: 0.8445 (mtp) cc_final: 0.8208 (mtm) REVERT: A 1498 MET cc_start: 0.9021 (ttp) cc_final: 0.8649 (ttp) REVERT: A 1586 TYR cc_start: 0.6660 (t80) cc_final: 0.6217 (t80) REVERT: A 1651 MET cc_start: 0.9281 (ttt) cc_final: 0.8929 (tmm) outliers start: 31 outliers final: 21 residues processed: 188 average time/residue: 0.0681 time to fit residues: 19.4793 Evaluate side-chains 172 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1465 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1757 ILE Chi-restraints excluded: chain A residue 1770 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 HIS A1443 ASN A1765 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.088855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068654 restraints weight = 27707.615| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.84 r_work: 0.3055 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9602 Z= 0.194 Angle : 0.725 11.733 13043 Z= 0.360 Chirality : 0.043 0.338 1532 Planarity : 0.004 0.039 1577 Dihedral : 5.233 31.737 1234 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.30 % Favored : 91.53 % Rotamer: Outliers : 3.46 % Allowed : 14.71 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.94 (0.25), residues: 1145 helix: 0.60 (0.18), residues: 765 sheet: -4.73 (0.81), residues: 20 loop : -3.11 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1303 TYR 0.037 0.002 TYR A1767 PHE 0.027 0.002 PHE A1530 TRP 0.017 0.001 TRP A1191 HIS 0.006 0.001 HIS A 886 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 9588) covalent geometry : angle 0.70102 / 0.35 (13006) SS BOND : bond 0.01047 / 0.74 ( 5) SS BOND : angle 1.82648 / 1.01 ( 10) hydrogen bonds : bond 0.04365 / 2.92 ( 569) hydrogen bonds : angle 4.52366 / 3.23 ( 1647) link_NAG-ASN : bond 0.00678 / 0.47 ( 9) link_NAG-ASN : angle 3.95672 / 2.32 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.9041 (mmm) cc_final: 0.8646 (mmt) REVERT: A 417 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 759 ILE cc_start: 0.8787 (mt) cc_final: 0.8559 (mt) REVERT: A 785 ASP cc_start: 0.9211 (t0) cc_final: 0.8973 (m-30) REVERT: A 794 MET cc_start: 0.7913 (tpt) cc_final: 0.7586 (mmp) REVERT: A 808 ARG cc_start: 0.8960 (mpt-90) cc_final: 0.8618 (mmt180) REVERT: A 821 SER cc_start: 0.8359 (m) cc_final: 0.8024 (p) REVERT: A 917 LEU cc_start: 0.9348 (tp) cc_final: 0.9086 (tp) REVERT: A 1213 PHE cc_start: 0.8824 (t80) cc_final: 0.8065 (m-10) REVERT: A 1233 LYS cc_start: 0.8832 (ttpt) cc_final: 0.8605 (mttm) REVERT: A 1487 MET cc_start: 0.8649 (mtp) cc_final: 0.8393 (mtm) REVERT: A 1586 TYR cc_start: 0.6638 (t80) cc_final: 0.6064 (t80) outliers start: 35 outliers final: 20 residues processed: 178 average time/residue: 0.0666 time to fit residues: 18.1430 Evaluate side-chains 160 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1465 PHE Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1770 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.091245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070745 restraints weight = 28228.131| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.92 r_work: 0.3105 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9602 Z= 0.139 Angle : 0.680 11.519 13043 Z= 0.337 Chirality : 0.042 0.333 1532 Planarity : 0.004 0.057 1577 Dihedral : 5.022 35.992 1232 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.60 % Favored : 92.23 % Rotamer: Outliers : 3.06 % Allowed : 16.29 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1145 helix: 0.82 (0.19), residues: 765 sheet: -4.62 (0.82), residues: 20 loop : -2.98 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1303 TYR 0.038 0.002 TYR A1767 PHE 0.030 0.001 PHE A1530 TRP 0.013 0.001 TRP A1191 HIS 0.002 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9588) covalent geometry : angle 0.65538 / 0.33 (13006) SS BOND : bond 0.01139 / 0.81 ( 5) SS BOND : angle 1.94046 / 1.15 ( 10) hydrogen bonds : bond 0.04059 / 2.72 ( 569) hydrogen bonds : angle 4.39184 / 3.11 ( 1647) link_NAG-ASN : bond 0.00682 / 0.49 ( 9) link_NAG-ASN : angle 3.91430 / 2.29 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8615 (mmm) cc_final: 0.7902 (mmm) REVERT: A 254 MET cc_start: 0.8971 (mmm) cc_final: 0.8747 (mmt) REVERT: A 421 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8679 (tp-100) REVERT: A 759 ILE cc_start: 0.8746 (mt) cc_final: 0.8513 (mt) REVERT: A 785 ASP cc_start: 0.9172 (t0) cc_final: 0.8948 (m-30) REVERT: A 794 MET cc_start: 0.7809 (tpt) cc_final: 0.7541 (mmp) REVERT: A 808 ARG cc_start: 0.8911 (mpt-90) cc_final: 0.8521 (mmt180) REVERT: A 821 SER cc_start: 0.8302 (m) cc_final: 0.7991 (p) REVERT: A 917 LEU cc_start: 0.9310 (tp) cc_final: 0.9109 (tp) REVERT: A 1213 PHE cc_start: 0.8813 (t80) cc_final: 0.7995 (m-10) REVERT: A 1465 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.8170 (m-80) outliers start: 31 outliers final: 22 residues processed: 179 average time/residue: 0.0654 time to fit residues: 17.6415 Evaluate side-chains 166 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1465 PHE Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1770 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 9.9990 chunk 100 optimal weight: 0.4980 chunk 85 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.090073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070100 restraints weight = 27767.094| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.90 r_work: 0.3090 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9602 Z= 0.136 Angle : 0.676 11.299 13043 Z= 0.335 Chirality : 0.042 0.340 1532 Planarity : 0.004 0.045 1577 Dihedral : 4.898 35.628 1232 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.31 % Rotamer: Outliers : 3.55 % Allowed : 17.67 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.35 (0.25), residues: 1145 helix: 1.02 (0.19), residues: 757 sheet: -3.80 (1.24), residues: 10 loop : -2.84 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 869 TYR 0.041 0.002 TYR A1767 PHE 0.025 0.001 PHE A1530 TRP 0.012 0.001 TRP A1191 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 9588) covalent geometry : angle 0.65084 / 0.33 (13006) SS BOND : bond 0.00690 / 0.49 ( 5) SS BOND : angle 2.31487 / 1.43 ( 10) hydrogen bonds : bond 0.03965 / 2.66 ( 569) hydrogen bonds : angle 4.33520 / 3.06 ( 1647) link_NAG-ASN : bond 0.00684 / 0.49 ( 9) link_NAG-ASN : angle 3.85208 / 2.25 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.9020 (mmm) cc_final: 0.8769 (mmt) REVERT: A 759 ILE cc_start: 0.8731 (mt) cc_final: 0.8497 (mt) REVERT: A 785 ASP cc_start: 0.9147 (t0) cc_final: 0.8940 (m-30) REVERT: A 794 MET cc_start: 0.7922 (tpt) cc_final: 0.7599 (mmp) REVERT: A 808 ARG cc_start: 0.8960 (mpt-90) cc_final: 0.8553 (mmt180) REVERT: A 1213 PHE cc_start: 0.8815 (t80) cc_final: 0.8029 (m-10) outliers start: 36 outliers final: 25 residues processed: 173 average time/residue: 0.0643 time to fit residues: 17.0214 Evaluate side-chains 166 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1545 MET Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1767 TYR Chi-restraints excluded: chain A residue 1770 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.087203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067307 restraints weight = 27981.330| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.84 r_work: 0.3022 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9602 Z= 0.208 Angle : 0.724 11.471 13043 Z= 0.362 Chirality : 0.044 0.352 1532 Planarity : 0.004 0.039 1577 Dihedral : 5.077 35.619 1232 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.03 % Favored : 91.79 % Rotamer: Outliers : 3.46 % Allowed : 20.04 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.39 (0.25), residues: 1145 helix: 0.98 (0.19), residues: 762 sheet: -4.25 (0.81), residues: 20 loop : -2.79 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 869 TYR 0.039 0.002 TYR A1767 PHE 0.032 0.002 PHE A 170 TRP 0.018 0.001 TRP A1191 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 ( 9588) covalent geometry : angle 0.69989 / 0.36 (13006) SS BOND : bond 0.00688 / 0.47 ( 5) SS BOND : angle 2.63557 / 1.55 ( 10) hydrogen bonds : bond 0.04274 / 2.86 ( 569) hydrogen bonds : angle 4.48100 / 3.18 ( 1647) link_NAG-ASN : bond 0.00677 / 0.47 ( 9) link_NAG-ASN : angle 3.86402 / 2.27 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.9075 (mmm) cc_final: 0.8814 (mmt) REVERT: A 417 GLU cc_start: 0.8816 (tp30) cc_final: 0.8503 (tm-30) REVERT: A 419 GLN cc_start: 0.8990 (tt0) cc_final: 0.8718 (pp30) REVERT: A 706 ILE cc_start: 0.7158 (mm) cc_final: 0.6940 (pt) REVERT: A 733 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8373 (m-80) REVERT: A 759 ILE cc_start: 0.8756 (mt) cc_final: 0.8509 (mt) REVERT: A 794 MET cc_start: 0.8030 (tpt) cc_final: 0.7779 (mmp) REVERT: A 808 ARG cc_start: 0.8955 (mpt-90) cc_final: 0.8538 (mmt180) REVERT: A 821 SER cc_start: 0.8317 (m) cc_final: 0.7999 (p) REVERT: A 1213 PHE cc_start: 0.8802 (t80) cc_final: 0.8006 (m-10) REVERT: A 1484 ASP cc_start: 0.7794 (t0) cc_final: 0.7562 (t0) outliers start: 35 outliers final: 25 residues processed: 162 average time/residue: 0.0674 time to fit residues: 16.6471 Evaluate side-chains 156 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1770 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 81 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 GLN A1765 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.090757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071116 restraints weight = 27642.820| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.81 r_work: 0.3117 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9602 Z= 0.127 Angle : 0.695 11.262 13043 Z= 0.338 Chirality : 0.042 0.334 1532 Planarity : 0.004 0.038 1577 Dihedral : 4.858 33.725 1232 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.16 % Favored : 92.66 % Rotamer: Outliers : 2.67 % Allowed : 21.42 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.19 (0.25), residues: 1145 helix: 1.15 (0.19), residues: 759 sheet: -4.21 (0.82), residues: 20 loop : -2.71 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 869 TYR 0.047 0.002 TYR A1767 PHE 0.029 0.001 PHE A1530 TRP 0.012 0.001 TRP A1191 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 9588) covalent geometry : angle 0.66836 / 0.33 (13006) SS BOND : bond 0.00425 / 0.30 ( 5) SS BOND : angle 2.93073 / 1.88 ( 10) hydrogen bonds : bond 0.03888 / 2.62 ( 569) hydrogen bonds : angle 4.30126 / 3.04 ( 1647) link_NAG-ASN : bond 0.00701 / 0.50 ( 9) link_NAG-ASN : angle 3.82853 / 2.24 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8666 (mmm) cc_final: 0.8460 (mmm) REVERT: A 159 TYR cc_start: 0.5635 (t80) cc_final: 0.5266 (t80) REVERT: A 189 LEU cc_start: 0.8974 (tp) cc_final: 0.8669 (tp) REVERT: A 230 ILE cc_start: 0.9445 (tp) cc_final: 0.9155 (tp) REVERT: A 417 GLU cc_start: 0.8837 (tp30) cc_final: 0.8484 (tm-30) REVERT: A 419 GLN cc_start: 0.8945 (tt0) cc_final: 0.8664 (pp30) REVERT: A 759 ILE cc_start: 0.8724 (mt) cc_final: 0.8473 (mt) REVERT: A 794 MET cc_start: 0.7890 (tpt) cc_final: 0.7678 (mmp) REVERT: A 1213 PHE cc_start: 0.8768 (t80) cc_final: 0.8016 (m-10) REVERT: A 1484 ASP cc_start: 0.7799 (t0) cc_final: 0.7239 (t0) outliers start: 27 outliers final: 22 residues processed: 168 average time/residue: 0.0662 time to fit residues: 17.3224 Evaluate side-chains 155 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1765 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 47 optimal weight: 0.0370 chunk 60 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.089510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.069670 restraints weight = 27722.424| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.82 r_work: 0.3084 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9602 Z= 0.145 Angle : 0.716 10.962 13043 Z= 0.349 Chirality : 0.043 0.339 1532 Planarity : 0.004 0.045 1577 Dihedral : 4.872 33.751 1232 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.42 % Favored : 92.40 % Rotamer: Outliers : 2.86 % Allowed : 21.92 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.18 (0.25), residues: 1145 helix: 1.14 (0.19), residues: 759 sheet: -4.24 (0.84), residues: 20 loop : -2.65 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.056 0.002 TYR A1767 PHE 0.038 0.001 PHE A 170 TRP 0.023 0.001 TRP A 703 HIS 0.002 0.001 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9588) covalent geometry : angle 0.69044 / 0.34 (13006) SS BOND : bond 0.00653 / 0.46 ( 5) SS BOND : angle 3.36955 / 2.21 ( 10) hydrogen bonds : bond 0.03985 / 2.65 ( 569) hydrogen bonds : angle 4.35837 / 3.08 ( 1647) link_NAG-ASN : bond 0.00673 / 0.48 ( 9) link_NAG-ASN : angle 3.71403 / 2.18 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.8667 (mmm) cc_final: 0.8441 (mmm) REVERT: A 159 TYR cc_start: 0.5582 (t80) cc_final: 0.5347 (t80) REVERT: A 189 LEU cc_start: 0.8967 (tp) cc_final: 0.8666 (tp) REVERT: A 230 ILE cc_start: 0.9442 (tp) cc_final: 0.9142 (tp) REVERT: A 254 MET cc_start: 0.8681 (mmm) cc_final: 0.8422 (mmt) REVERT: A 417 GLU cc_start: 0.8877 (tp30) cc_final: 0.8470 (tm-30) REVERT: A 419 GLN cc_start: 0.8945 (tt0) cc_final: 0.8712 (pp30) REVERT: A 759 ILE cc_start: 0.8733 (mt) cc_final: 0.8486 (mt) REVERT: A 794 MET cc_start: 0.7923 (tpt) cc_final: 0.7708 (mmp) REVERT: A 808 ARG cc_start: 0.8915 (mpt-90) cc_final: 0.8559 (mmt180) REVERT: A 810 PHE cc_start: 0.8382 (m-80) cc_final: 0.7858 (m-80) REVERT: A 869 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.6778 (mmm-85) REVERT: A 1213 PHE cc_start: 0.8790 (t80) cc_final: 0.8079 (m-10) REVERT: A 1484 ASP cc_start: 0.7766 (t0) cc_final: 0.6870 (t0) outliers start: 29 outliers final: 24 residues processed: 165 average time/residue: 0.0696 time to fit residues: 17.7676 Evaluate side-chains 161 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1486 PHE Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1545 MET Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Chi-restraints excluded: chain A residue 1770 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.0030 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.090735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070330 restraints weight = 27502.854| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.02 r_work: 0.3079 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9602 Z= 0.122 Angle : 0.722 11.930 13043 Z= 0.346 Chirality : 0.043 0.329 1532 Planarity : 0.004 0.047 1577 Dihedral : 4.792 32.731 1232 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.25 % Favored : 92.66 % Rotamer: Outliers : 2.17 % Allowed : 23.10 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.08 (0.25), residues: 1145 helix: 1.36 (0.19), residues: 739 sheet: -4.13 (0.85), residues: 20 loop : -2.42 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.051 0.001 TYR A1767 PHE 0.025 0.001 PHE A 784 TRP 0.021 0.001 TRP A 703 HIS 0.002 0.000 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9588) covalent geometry : angle 0.69893 / 0.34 (13006) SS BOND : bond 0.00509 / 0.36 ( 5) SS BOND : angle 2.80920 / 1.91 ( 10) hydrogen bonds : bond 0.03773 / 2.53 ( 569) hydrogen bonds : angle 4.28128 / 3.02 ( 1647) link_NAG-ASN : bond 0.00691 / 0.50 ( 9) link_NAG-ASN : angle 3.67261 / 2.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.8657 (mmm) cc_final: 0.8431 (mmm) REVERT: A 159 TYR cc_start: 0.5760 (t80) cc_final: 0.5423 (t80) REVERT: A 189 LEU cc_start: 0.8960 (tp) cc_final: 0.8674 (tp) REVERT: A 230 ILE cc_start: 0.9425 (tp) cc_final: 0.9131 (tp) REVERT: A 417 GLU cc_start: 0.8881 (tp30) cc_final: 0.8451 (tm-30) REVERT: A 419 GLN cc_start: 0.8978 (tt0) cc_final: 0.8697 (pp30) REVERT: A 759 ILE cc_start: 0.8592 (mt) cc_final: 0.8342 (mt) REVERT: A 785 ASP cc_start: 0.9286 (t0) cc_final: 0.8985 (m-30) REVERT: A 794 MET cc_start: 0.7991 (tpt) cc_final: 0.7716 (mmm) REVERT: A 810 PHE cc_start: 0.8527 (m-80) cc_final: 0.8010 (m-80) REVERT: A 869 ARG cc_start: 0.7748 (mmm-85) cc_final: 0.6676 (mmm-85) REVERT: A 1213 PHE cc_start: 0.8806 (t80) cc_final: 0.8012 (m-10) REVERT: A 1546 MET cc_start: 0.9016 (mmt) cc_final: 0.8776 (mmm) outliers start: 22 outliers final: 19 residues processed: 168 average time/residue: 0.0614 time to fit residues: 15.9132 Evaluate side-chains 160 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 105 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.091151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070578 restraints weight = 27510.682| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.05 r_work: 0.3087 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9602 Z= 0.124 Angle : 0.733 11.572 13043 Z= 0.349 Chirality : 0.043 0.329 1532 Planarity : 0.004 0.046 1577 Dihedral : 4.747 32.239 1232 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 2.37 % Allowed : 23.59 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.15 (0.25), residues: 1145 helix: 1.40 (0.19), residues: 739 sheet: -5.32 (0.86), residues: 10 loop : -2.38 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 869 TYR 0.056 0.001 TYR A1767 PHE 0.028 0.001 PHE A1530 TRP 0.031 0.001 TRP A 703 HIS 0.001 0.000 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9588) covalent geometry : angle 0.71107 / 0.34 (13006) SS BOND : bond 0.00515 / 0.36 ( 5) SS BOND : angle 2.81047 / 1.90 ( 10) hydrogen bonds : bond 0.03762 / 2.53 ( 569) hydrogen bonds : angle 4.29743 / 3.03 ( 1647) link_NAG-ASN : bond 0.00692 / 0.50 ( 9) link_NAG-ASN : angle 3.56967 / 2.10 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 TYR cc_start: 0.5759 (t80) cc_final: 0.5475 (t80) REVERT: A 189 LEU cc_start: 0.8965 (tp) cc_final: 0.8673 (tp) REVERT: A 230 ILE cc_start: 0.9436 (tp) cc_final: 0.9144 (tp) REVERT: A 419 GLN cc_start: 0.8994 (tt0) cc_final: 0.8716 (pp30) REVERT: A 759 ILE cc_start: 0.8565 (mt) cc_final: 0.8315 (mt) REVERT: A 785 ASP cc_start: 0.9269 (t0) cc_final: 0.8993 (m-30) REVERT: A 794 MET cc_start: 0.7965 (tpt) cc_final: 0.7691 (mmm) REVERT: A 808 ARG cc_start: 0.8962 (mpt-90) cc_final: 0.8581 (mmt180) REVERT: A 810 PHE cc_start: 0.8569 (m-80) cc_final: 0.8053 (m-80) REVERT: A 1213 PHE cc_start: 0.8811 (t80) cc_final: 0.8021 (m-10) REVERT: A 1546 MET cc_start: 0.8973 (mmt) cc_final: 0.8747 (mmm) outliers start: 24 outliers final: 21 residues processed: 160 average time/residue: 0.0592 time to fit residues: 14.9274 Evaluate side-chains 159 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 906 CYS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 1273 TRP Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1378 VAL Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1727 TYR Chi-restraints excluded: chain A residue 1732 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1474 ASN A1765 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070437 restraints weight = 27289.178| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 3.01 r_work: 0.3082 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9602 Z= 0.131 Angle : 0.736 11.318 13043 Z= 0.352 Chirality : 0.043 0.328 1532 Planarity : 0.004 0.044 1577 Dihedral : 4.758 32.053 1232 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.60 % Favored : 92.31 % Rotamer: Outliers : 2.47 % Allowed : 24.28 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.18 (0.25), residues: 1145 helix: 1.43 (0.19), residues: 739 sheet: -5.33 (0.84), residues: 10 loop : -2.37 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1321 TYR 0.056 0.002 TYR A1767 PHE 0.024 0.001 PHE A1530 TRP 0.034 0.001 TRP A 703 HIS 0.002 0.000 HIS A 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9588) covalent geometry : angle 0.71496 / 0.35 (13006) SS BOND : bond 0.00535 / 0.38 ( 5) SS BOND : angle 2.76880 / 1.85 ( 10) hydrogen bonds : bond 0.03816 / 2.55 ( 569) hydrogen bonds : angle 4.28928 / 3.04 ( 1647) link_NAG-ASN : bond 0.00669 / 0.48 ( 9) link_NAG-ASN : angle 3.53531 / 2.09 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1926.91 seconds wall clock time: 33 minutes 46.92 seconds (2026.92 seconds total)