Starting phenix.real_space_refine on Tue May 13 01:41:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtc_30850/05_2025/7dtc_30850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtc_30850/05_2025/7dtc_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7dtc_30850/05_2025/7dtc_30850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtc_30850/05_2025/7dtc_30850.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtc_30850/05_2025/7dtc_30850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtc_30850/05_2025/7dtc_30850.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.28, per 1000 atoms: 0.56 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: 2.43 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.89 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: 2.65 Time building geometry restraints manager: 2.77 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: 5099 17.68 - 35.37: 529 35.37 - 53.05: 71 53.05 - 70.73: 17 70.73 - 88.41: 9 Dihedral angle restraints: 5725 sinusoidal: 2368 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 5722 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.840 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 14.146 88.414 3544 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.001 TRP A1421 HIS 0.003 0.001 HIS A 886 PHE 0.019 0.001 PHE A 884 TYR 0.019 0.001 TYR A 378 ARG 0.003 0.000 ARG A1583 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 9) link_NAG-ASN : angle 5.05040 ( 27) hydrogen bonds : bond 0.13086 ( 569) hydrogen bonds : angle 5.89929 ( 1647) SS BOND : bond 0.00766 ( 5) SS BOND : angle 1.79952 ( 10) covalent geometry : bond 0.00404 ( 9588) covalent geometry : angle 0.70184 (13006) *********************** 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 : 0.976 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: 0.8669 (p) REVERT: A 398 PHE cc_start: 0.7904 (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: 0.2069 time to fit residues: 66.6817 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 : 0.991 ------------------------------------------------------------------------------- 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 97 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A1774 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.092322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.072445 restraints weight = 27408.075| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.78 r_work: 0.3138 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9602 Z= 0.147 Angle : 0.706 12.164 13043 Z= 0.348 Chirality : 0.042 0.317 1532 Planarity : 0.004 0.040 1577 Dihedral : 5.796 36.061 1423 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.86 % Favored : 91.88 % Rotamer: Outliers : 2.96 % Allowed : 11.35 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.24), residues: 1145 helix: 0.16 (0.18), residues: 765 sheet: -5.14 (0.72), residues: 20 loop : -3.21 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1191 HIS 0.007 0.001 HIS A1584 PHE 0.025 0.001 PHE A 170 TYR 0.024 0.002 TYR A1767 ARG 0.004 0.000 ARG A1635 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 9) link_NAG-ASN : angle 4.31346 ( 27) hydrogen bonds : bond 0.04120 ( 569) hydrogen bonds : angle 4.54922 ( 1647) SS BOND : bond 0.01004 ( 5) SS BOND : angle 1.59942 ( 10) covalent geometry : bond 0.00313 ( 9588) covalent geometry : angle 0.67769 (13006) *********************** 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 201 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.8950 (mmm) cc_final: 0.8494 (mtt) REVERT: A 399 LEU cc_start: 0.8872 (tt) cc_final: 0.8458 (mp) REVERT: A 417 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8636 (tm-30) REVERT: A 704 MET cc_start: 0.7070 (ptt) cc_final: 0.6678 (mmt) REVERT: A 759 ILE cc_start: 0.8677 (mt) cc_final: 0.8451 (mt) REVERT: A 785 ASP cc_start: 0.9148 (t0) cc_final: 0.8923 (m-30) REVERT: A 794 MET cc_start: 0.7817 (tpt) cc_final: 0.7591 (mmp) REVERT: A 808 ARG cc_start: 0.8952 (mpt-90) cc_final: 0.8717 (mmt180) REVERT: A 821 SER cc_start: 0.8312 (m) cc_final: 0.7916 (p) REVERT: A 1487 MET cc_start: 0.8445 (mtp) cc_final: 0.8187 (mtm) REVERT: A 1498 MET cc_start: 0.8994 (ttp) cc_final: 0.8629 (ttt) REVERT: A 1651 MET cc_start: 0.9283 (ttt) cc_final: 0.8929 (tmm) outliers start: 30 outliers final: 20 residues processed: 191 average time/residue: 0.1757 time to fit residues: 49.8139 Evaluate side-chains 173 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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 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 1732 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 18 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.089730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069614 restraints weight = 27931.953| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.86 r_work: 0.3074 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9602 Z= 0.174 Angle : 0.699 11.820 13043 Z= 0.348 Chirality : 0.042 0.323 1532 Planarity : 0.004 0.038 1577 Dihedral : 5.665 35.123 1423 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.95 % Favored : 91.88 % Rotamer: Outliers : 3.36 % Allowed : 14.51 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.25), residues: 1145 helix: 0.63 (0.18), residues: 768 sheet: -4.72 (0.83), residues: 20 loop : -3.07 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1191 HIS 0.004 0.001 HIS A 886 PHE 0.028 0.001 PHE A1530 TYR 0.037 0.002 TYR A1767 ARG 0.006 0.000 ARG A1303 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 9) link_NAG-ASN : angle 4.19334 ( 27) hydrogen bonds : bond 0.04216 ( 569) hydrogen bonds : angle 4.46901 ( 1647) SS BOND : bond 0.01032 ( 5) SS BOND : angle 1.74534 ( 10) covalent geometry : bond 0.00389 ( 9588) covalent geometry : angle 0.67139 (13006) *********************** 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 195 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.9065 (mmm) cc_final: 0.8693 (mmt) REVERT: A 759 ILE cc_start: 0.8753 (mt) cc_final: 0.8523 (mt) REVERT: A 794 MET cc_start: 0.7906 (tpt) cc_final: 0.7579 (mmp) REVERT: A 808 ARG cc_start: 0.8946 (mpt-90) cc_final: 0.8580 (mmt180) REVERT: A 821 SER cc_start: 0.8346 (m) cc_final: 0.8009 (p) REVERT: A 1213 PHE cc_start: 0.8816 (t80) cc_final: 0.8097 (m-10) REVERT: A 1233 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8612 (mttm) REVERT: A 1485 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8394 (mp) outliers start: 34 outliers final: 20 residues processed: 182 average time/residue: 0.1677 time to fit residues: 45.3722 Evaluate side-chains 169 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 315 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 870 ASP 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 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 1634 LEU 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 112 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3641 r_free = 0.3641 target = 0.090472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.070433 restraints weight = 27650.152| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.89 r_work: 0.3095 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9602 Z= 0.136 Angle : 0.678 11.572 13043 Z= 0.334 Chirality : 0.042 0.323 1532 Planarity : 0.004 0.054 1577 Dihedral : 5.394 35.953 1421 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.31 % Rotamer: Outliers : 3.36 % Allowed : 15.70 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.25), residues: 1145 helix: 0.84 (0.19), residues: 762 sheet: -4.57 (0.80), residues: 20 loop : -2.95 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1395 HIS 0.002 0.001 HIS A 278 PHE 0.028 0.001 PHE A1530 TYR 0.044 0.002 TYR A1767 ARG 0.002 0.000 ARG A1303 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 9) link_NAG-ASN : angle 4.05008 ( 27) hydrogen bonds : bond 0.03995 ( 569) hydrogen bonds : angle 4.35096 ( 1647) SS BOND : bond 0.01179 ( 5) SS BOND : angle 1.98087 ( 10) covalent geometry : bond 0.00293 ( 9588) covalent geometry : angle 0.65147 (13006) *********************** 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 196 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.9010 (mmm) cc_final: 0.8791 (mmt) REVERT: A 759 ILE cc_start: 0.8729 (mt) cc_final: 0.8497 (mt) REVERT: A 785 ASP cc_start: 0.9163 (t0) cc_final: 0.8953 (m-30) REVERT: A 794 MET cc_start: 0.7815 (tpt) cc_final: 0.7472 (mmp) REVERT: A 808 ARG cc_start: 0.8936 (mpt-90) cc_final: 0.8532 (mmt180) REVERT: A 821 SER cc_start: 0.8344 (m) cc_final: 0.8021 (p) REVERT: A 829 ILE cc_start: 0.6523 (mm) cc_final: 0.6314 (mm) REVERT: A 1213 PHE cc_start: 0.8797 (t80) cc_final: 0.8058 (m-10) REVERT: A 1254 MET cc_start: 0.9025 (ttp) cc_final: 0.8815 (tmm) outliers start: 34 outliers final: 22 residues processed: 185 average time/residue: 0.1697 time to fit residues: 46.5060 Evaluate side-chains 171 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 395 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 870 ASP 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 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 1770 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** A1765 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.089312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.069378 restraints weight = 27876.146| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.84 r_work: 0.3075 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9602 Z= 0.159 Angle : 0.686 11.520 13043 Z= 0.343 Chirality : 0.043 0.330 1532 Planarity : 0.004 0.048 1577 Dihedral : 5.391 35.525 1421 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.77 % Favored : 92.05 % Rotamer: Outliers : 3.75 % Allowed : 17.18 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1145 helix: 1.00 (0.19), residues: 758 sheet: -3.60 (1.28), residues: 10 loop : -2.91 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1191 HIS 0.003 0.001 HIS A 278 PHE 0.025 0.001 PHE A1530 TYR 0.048 0.002 TYR A1767 ARG 0.004 0.000 ARG A1303 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 9) link_NAG-ASN : angle 4.01193 ( 27) hydrogen bonds : bond 0.04091 ( 569) hydrogen bonds : angle 4.36969 ( 1647) SS BOND : bond 0.00735 ( 5) SS BOND : angle 2.33319 ( 10) covalent geometry : bond 0.00354 ( 9588) covalent geometry : angle 0.65885 (13006) *********************** 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 187 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 MET cc_start: 0.9007 (mmm) cc_final: 0.8767 (mmt) REVERT: A 417 GLU cc_start: 0.8872 (tp30) cc_final: 0.8401 (tm-30) REVERT: A 419 GLN cc_start: 0.8934 (tt0) cc_final: 0.8711 (pp30) REVERT: A 759 ILE cc_start: 0.8771 (mt) cc_final: 0.8531 (mt) REVERT: A 794 MET cc_start: 0.7887 (tpt) cc_final: 0.7564 (mmp) REVERT: A 808 ARG cc_start: 0.8971 (mpt-90) cc_final: 0.8566 (mmt180) REVERT: A 821 SER cc_start: 0.8294 (m) cc_final: 0.7973 (p) REVERT: A 1213 PHE cc_start: 0.8806 (t80) cc_final: 0.8045 (m-10) outliers start: 38 outliers final: 29 residues processed: 173 average time/residue: 0.1673 time to fit residues: 43.7108 Evaluate side-chains 169 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 395 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 870 ASP 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 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 1341 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1464 LEU 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 1576 ILE 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 24 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.089854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.069974 restraints weight = 27607.005| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.87 r_work: 0.3086 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3882 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= 0.130 Angle : 0.674 11.334 13043 Z= 0.330 Chirality : 0.042 0.324 1532 Planarity : 0.004 0.040 1577 Dihedral : 5.190 34.520 1421 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 3.26 % Allowed : 19.74 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1145 helix: 1.11 (0.19), residues: 756 sheet: -4.15 (0.82), residues: 20 loop : -2.83 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1258 HIS 0.002 0.000 HIS A 278 PHE 0.031 0.001 PHE A 170 TYR 0.046 0.002 TYR A1767 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00677 ( 9) link_NAG-ASN : angle 3.91632 ( 27) hydrogen bonds : bond 0.03827 ( 569) hydrogen bonds : angle 4.31985 ( 1647) SS BOND : bond 0.00305 ( 5) SS BOND : angle 2.55850 ( 10) covalent geometry : bond 0.00283 ( 9588) covalent geometry : angle 0.64707 (13006) *********************** 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 182 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 254 MET cc_start: 0.9051 (mmm) cc_final: 0.8776 (mmt) REVERT: A 417 GLU cc_start: 0.8860 (tp30) cc_final: 0.8501 (tm-30) REVERT: A 419 GLN cc_start: 0.8942 (tt0) cc_final: 0.8712 (pp30) REVERT: A 711 LYS cc_start: 0.8297 (tptp) cc_final: 0.7792 (pttt) REVERT: A 759 ILE cc_start: 0.8653 (mt) cc_final: 0.8404 (mt) REVERT: A 794 MET cc_start: 0.7956 (tpt) cc_final: 0.7702 (mmp) REVERT: A 808 ARG cc_start: 0.8935 (mpt-90) cc_final: 0.8508 (mmt180) REVERT: A 1213 PHE cc_start: 0.8787 (t80) cc_final: 0.8011 (m-10) REVERT: A 1484 ASP cc_start: 0.7777 (t0) cc_final: 0.7160 (t0) outliers start: 33 outliers final: 23 residues processed: 172 average time/residue: 0.1708 time to fit residues: 43.5726 Evaluate side-chains 162 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 261 LEU 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 1464 LEU 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 1704 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.0470 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3644 r_free = 0.3644 target = 0.090662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070877 restraints weight = 27758.421| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.86 r_work: 0.3113 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4057 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= 0.125 Angle : 0.679 11.112 13043 Z= 0.332 Chirality : 0.042 0.324 1532 Planarity : 0.004 0.038 1577 Dihedral : 5.068 32.804 1421 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.16 % Favored : 92.66 % Rotamer: Outliers : 2.76 % Allowed : 20.63 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1145 helix: 1.14 (0.19), residues: 758 sheet: -5.09 (1.03), residues: 10 loop : -2.75 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1191 HIS 0.002 0.001 HIS A 278 PHE 0.030 0.001 PHE A1530 TYR 0.048 0.002 TYR A1767 ARG 0.007 0.000 ARG A 869 Details of bonding type rmsd link_NAG-ASN : bond 0.00680 ( 9) link_NAG-ASN : angle 3.80922 ( 27) hydrogen bonds : bond 0.03775 ( 569) hydrogen bonds : angle 4.28127 ( 1647) SS BOND : bond 0.00753 ( 5) SS BOND : angle 2.96372 ( 10) covalent geometry : bond 0.00268 ( 9588) covalent geometry : angle 0.65202 (13006) *********************** 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 182 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8976 (tp) cc_final: 0.8677 (tp) REVERT: A 254 MET cc_start: 0.9048 (mmm) cc_final: 0.8767 (mmt) REVERT: A 417 GLU cc_start: 0.8894 (tp30) cc_final: 0.8490 (tm-30) REVERT: A 419 GLN cc_start: 0.8877 (tt0) cc_final: 0.8676 (pp30) REVERT: A 704 MET cc_start: 0.6741 (mmm) cc_final: 0.6504 (tpp) REVERT: A 711 LYS cc_start: 0.8306 (tptp) cc_final: 0.7814 (pttp) REVERT: A 759 ILE cc_start: 0.8657 (mt) cc_final: 0.8406 (mt) REVERT: A 794 MET cc_start: 0.7888 (tpt) cc_final: 0.7641 (mmp) REVERT: A 808 ARG cc_start: 0.8954 (mpt-90) cc_final: 0.8557 (mmt180) REVERT: A 1213 PHE cc_start: 0.8770 (t80) cc_final: 0.8042 (m-10) REVERT: A 1546 MET cc_start: 0.8987 (mmt) cc_final: 0.8742 (mmm) outliers start: 28 outliers final: 26 residues processed: 173 average time/residue: 0.1790 time to fit residues: 45.9792 Evaluate side-chains 165 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 240 VAL Chi-restraints excluded: chain A residue 261 LEU 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 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 1464 LEU 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 1704 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 0.2980 chunk 55 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** A1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.091406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071701 restraints weight = 28341.671| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.90 r_work: 0.3123 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 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 : 0.003 0.032 9602 Z= 0.121 Angle : 0.690 10.914 13043 Z= 0.336 Chirality : 0.042 0.321 1532 Planarity : 0.004 0.045 1577 Dihedral : 4.983 32.378 1421 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.07 % Favored : 92.84 % Rotamer: Outliers : 2.76 % Allowed : 21.82 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1145 helix: 1.19 (0.19), residues: 759 sheet: -5.18 (1.05), residues: 10 loop : -2.71 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1191 HIS 0.002 0.000 HIS A 278 PHE 0.028 0.001 PHE A 784 TYR 0.046 0.001 TYR A1767 ARG 0.007 0.000 ARG A 869 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 9) link_NAG-ASN : angle 3.71780 ( 27) hydrogen bonds : bond 0.03717 ( 569) hydrogen bonds : angle 4.26229 ( 1647) SS BOND : bond 0.00390 ( 5) SS BOND : angle 2.99759 ( 10) covalent geometry : bond 0.00260 ( 9588) covalent geometry : angle 0.66474 (13006) *********************** 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 181 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8969 (tp) cc_final: 0.8660 (tp) REVERT: A 417 GLU cc_start: 0.8908 (tp30) cc_final: 0.8467 (tm-30) REVERT: A 704 MET cc_start: 0.6755 (mmm) cc_final: 0.6545 (tpp) REVERT: A 711 LYS cc_start: 0.8328 (tptp) cc_final: 0.7822 (pttt) REVERT: A 759 ILE cc_start: 0.8623 (mt) cc_final: 0.8370 (mt) REVERT: A 794 MET cc_start: 0.7745 (tpt) cc_final: 0.7509 (mmp) REVERT: A 808 ARG cc_start: 0.8940 (mpt-90) cc_final: 0.8555 (mmt180) REVERT: A 1213 PHE cc_start: 0.8761 (t80) cc_final: 0.8015 (m-10) REVERT: A 1484 ASP cc_start: 0.7640 (t0) cc_final: 0.6853 (t0) REVERT: A 1528 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8005 (tm-30) outliers start: 28 outliers final: 24 residues processed: 171 average time/residue: 0.1710 time to fit residues: 43.5369 Evaluate side-chains 169 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 240 VAL Chi-restraints excluded: chain A residue 261 LEU 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 1464 LEU Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1528 GLN Chi-restraints excluded: chain A residue 1704 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 83 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1592 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 = 0.3653 r_free = 0.3653 target = 0.091244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.071360 restraints weight = 27498.053| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.87 r_work: 0.3121 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9602 Z= 0.129 Angle : 0.717 10.792 13043 Z= 0.347 Chirality : 0.042 0.321 1532 Planarity : 0.004 0.042 1577 Dihedral : 4.995 31.795 1421 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.34 % Favored : 92.58 % Rotamer: Outliers : 2.96 % Allowed : 22.21 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1145 helix: 1.18 (0.19), residues: 759 sheet: -5.20 (0.94), residues: 10 loop : -2.74 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1713 HIS 0.002 0.000 HIS A 278 PHE 0.026 0.001 PHE A1276 TYR 0.051 0.001 TYR A1767 ARG 0.004 0.000 ARG A 869 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 9) link_NAG-ASN : angle 3.67321 ( 27) hydrogen bonds : bond 0.03787 ( 569) hydrogen bonds : angle 4.26355 ( 1647) SS BOND : bond 0.00381 ( 5) SS BOND : angle 3.18869 ( 10) covalent geometry : bond 0.00288 ( 9588) covalent geometry : angle 0.69291 (13006) *********************** 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 185 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8971 (tp) cc_final: 0.8664 (tp) REVERT: A 254 MET cc_start: 0.8702 (mmm) cc_final: 0.8453 (mmt) REVERT: A 417 GLU cc_start: 0.8898 (tp30) cc_final: 0.8435 (tm-30) REVERT: A 704 MET cc_start: 0.6868 (mmm) cc_final: 0.6647 (tpp) REVERT: A 711 LYS cc_start: 0.8363 (tptp) cc_final: 0.7845 (pttt) REVERT: A 759 ILE cc_start: 0.8624 (mt) cc_final: 0.8372 (mt) REVERT: A 785 ASP cc_start: 0.9197 (t0) cc_final: 0.8996 (m-30) REVERT: A 808 ARG cc_start: 0.8947 (mpt-90) cc_final: 0.8571 (mmt180) REVERT: A 810 PHE cc_start: 0.8446 (m-80) cc_final: 0.7821 (m-80) REVERT: A 821 SER cc_start: 0.8341 (m) cc_final: 0.8141 (p) REVERT: A 1213 PHE cc_start: 0.8777 (t80) cc_final: 0.8047 (m-10) REVERT: A 1484 ASP cc_start: 0.7509 (t0) cc_final: 0.7050 (t0) REVERT: A 1528 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8006 (tm-30) outliers start: 30 outliers final: 26 residues processed: 173 average time/residue: 0.1813 time to fit residues: 46.7531 Evaluate side-chains 175 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 334 THR 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 1341 CYS Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1528 GLN Chi-restraints excluded: chain A residue 1653 SER Chi-restraints excluded: chain A residue 1704 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 A1515 ASN ** A1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1765 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.092397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.072613 restraints weight = 28275.970| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.92 r_work: 0.3145 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9602 Z= 0.121 Angle : 0.719 10.660 13043 Z= 0.345 Chirality : 0.042 0.318 1532 Planarity : 0.004 0.043 1577 Dihedral : 4.936 31.391 1421 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.16 % Favored : 92.75 % Rotamer: Outliers : 2.67 % Allowed : 23.40 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1145 helix: 1.28 (0.19), residues: 756 sheet: -5.40 (0.81), residues: 10 loop : -2.73 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1713 HIS 0.002 0.000 HIS A 738 PHE 0.025 0.001 PHE A 784 TYR 0.056 0.001 TYR A1767 ARG 0.003 0.000 ARG A 869 Details of bonding type rmsd link_NAG-ASN : bond 0.00686 ( 9) link_NAG-ASN : angle 3.59836 ( 27) hydrogen bonds : bond 0.03697 ( 569) hydrogen bonds : angle 4.23400 ( 1647) SS BOND : bond 0.00445 ( 5) SS BOND : angle 2.74990 ( 10) covalent geometry : bond 0.00263 ( 9588) covalent geometry : angle 0.69727 (13006) ********************** 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 182 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8947 (tp) cc_final: 0.8628 (tp) REVERT: A 417 GLU cc_start: 0.8915 (tp30) cc_final: 0.8475 (tm-30) REVERT: A 704 MET cc_start: 0.6902 (mmm) cc_final: 0.6677 (tpp) REVERT: A 711 LYS cc_start: 0.8345 (tptp) cc_final: 0.7830 (pttt) REVERT: A 808 ARG cc_start: 0.8928 (mpt-90) cc_final: 0.8532 (mmt180) REVERT: A 810 PHE cc_start: 0.8423 (m-80) cc_final: 0.7835 (m-80) REVERT: A 821 SER cc_start: 0.8346 (m) cc_final: 0.8120 (p) REVERT: A 1213 PHE cc_start: 0.8783 (t80) cc_final: 0.8064 (m-10) REVERT: A 1528 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8007 (tm-30) outliers start: 27 outliers final: 24 residues processed: 171 average time/residue: 0.1654 time to fit residues: 42.5034 Evaluate side-chains 172 residues out of total 1013 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 240 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 334 THR 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 1338 LEU Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1485 ILE Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1517 TYR Chi-restraints excluded: chain A residue 1522 PHE Chi-restraints excluded: chain A residue 1528 GLN Chi-restraints excluded: chain A residue 1653 SER Chi-restraints excluded: chain A residue 1704 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2522 > 50: distance: 70 - 88: 5.730 distance: 74 - 99: 8.941 distance: 84 - 88: 5.119 distance: 85 - 115: 9.437 distance: 88 - 89: 3.301 distance: 89 - 90: 4.023 distance: 90 - 91: 7.771 distance: 90 - 99: 10.511 distance: 91 - 122: 15.726 distance: 99 - 100: 7.876 distance: 100 - 101: 4.758 distance: 100 - 103: 6.688 distance: 101 - 107: 4.686 distance: 102 - 129: 23.869 distance: 103 - 104: 4.356 distance: 104 - 105: 4.751 distance: 107 - 108: 3.948 distance: 108 - 109: 3.851 distance: 109 - 110: 7.287 distance: 109 - 115: 8.943 distance: 110 - 137: 8.793 distance: 115 - 116: 8.804 distance: 116 - 117: 13.207 distance: 116 - 119: 6.727 distance: 117 - 118: 5.881 distance: 117 - 122: 13.773 distance: 118 - 145: 5.484 distance: 119 - 120: 6.990 distance: 119 - 121: 7.540 distance: 122 - 123: 15.475 distance: 123 - 124: 5.076 distance: 123 - 126: 6.625 distance: 124 - 125: 6.719 distance: 124 - 129: 19.625 distance: 125 - 157: 9.832 distance: 126 - 127: 14.949 distance: 126 - 128: 5.822 distance: 129 - 130: 37.635 distance: 130 - 131: 26.578 distance: 130 - 133: 43.473 distance: 131 - 132: 10.551 distance: 131 - 137: 12.047 distance: 132 - 165: 8.930 distance: 133 - 134: 33.975 distance: 134 - 135: 21.962 distance: 134 - 136: 31.119 distance: 137 - 138: 6.279 distance: 138 - 139: 4.396 distance: 138 - 141: 3.254 distance: 139 - 140: 4.211 distance: 139 - 145: 5.465 distance: 141 - 142: 5.158 distance: 157 - 158: 3.060 distance: 158 - 159: 4.267 distance: 159 - 160: 3.721 distance: 159 - 165: 6.555 distance: 160 - 185: 4.057 distance: 161 - 162: 4.062 distance: 162 - 164: 3.628 distance: 166 - 169: 6.538 distance: 167 - 170: 3.061 distance: 168 - 191: 4.258