Starting phenix.real_space_refine on Sun Jun 22 16:08:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mvu_24056/06_2025/7mvu_24056.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mvu_24056/06_2025/7mvu_24056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mvu_24056/06_2025/7mvu_24056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mvu_24056/06_2025/7mvu_24056.map" model { file = "/net/cci-nas-00/data/ceres_data/7mvu_24056/06_2025/7mvu_24056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mvu_24056/06_2025/7mvu_24056.cif" } resolution = 3.77 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= -0.001 sd= 0.025 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: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 8190 2.51 5 N 2169 2.21 5 O 2379 1.98 5 H 12841 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25645 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 24654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 24654 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 58, 'TRANS': 1482} Chain breaks: 16 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 991 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Time building chain proxies: 10.70, per 1000 atoms: 0.42 Number of scatterers: 25645 At special positions: 0 Unit cell: (86.736, 118.428, 195.156, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 O 2379 8.00 N 2169 7.00 C 8190 6.00 H 12841 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 1.8 seconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3076 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 2 sheets defined 77.2% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 27 through 38 removed outlier: 3.830A pdb=" N GLU A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.887A pdb=" N ALA A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.536A pdb=" N ASN A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 108 through 114 removed outlier: 4.245A pdb=" N THR A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 144 removed outlier: 3.632A pdb=" N ARG A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 184 through 212 removed outlier: 3.882A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 252 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.502A pdb=" N PHE A 260 " --> pdb=" O THR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.725A pdb=" N ILE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 299 through 311 removed outlier: 3.519A pdb=" N ARG A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.650A pdb=" N GLY A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 371 Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.604A pdb=" N LYS A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.881A pdb=" N LEU A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 3.986A pdb=" N GLN A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 455 removed outlier: 3.565A pdb=" N LEU A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 475 Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 483 through 488 removed outlier: 4.576A pdb=" N ASP A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 551 through 568 Processing helix chain 'A' and resid 592 through 613 Processing helix chain 'A' and resid 614 through 621 removed outlier: 3.534A pdb=" N ILE A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.909A pdb=" N ARG A 645 " --> pdb=" O PRO A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.734A pdb=" N ASN A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.790A pdb=" N GLU A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 730 Processing helix chain 'A' and resid 758 through 772 removed outlier: 3.647A pdb=" N VAL A 762 " --> pdb=" O ILE A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 799 removed outlier: 3.596A pdb=" N THR A 799 " --> pdb=" O VAL A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 812 Processing helix chain 'A' and resid 820 through 831 Processing helix chain 'A' and resid 832 through 841 Processing helix chain 'A' and resid 842 through 854 removed outlier: 3.632A pdb=" N ILE A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 863 removed outlier: 3.887A pdb=" N LEU A 860 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 894 removed outlier: 5.136A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 928 through 937 removed outlier: 4.073A pdb=" N VAL A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 941 removed outlier: 4.159A pdb=" N GLY A 941 " --> pdb=" O CYS A 938 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 938 through 941' Processing helix chain 'A' and resid 942 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 987 through 1002 Processing helix chain 'A' and resid 1012 through 1031 Processing helix chain 'A' and resid 1037 through 1044 removed outlier: 3.683A pdb=" N GLN A1041 " --> pdb=" O THR A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1076 Processing helix chain 'A' and resid 1088 through 1107 Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1122 through 1131 Processing helix chain 'A' and resid 1148 through 1153 removed outlier: 4.201A pdb=" N LEU A1152 " --> pdb=" O CYS A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1183 removed outlier: 3.688A pdb=" N ALA A1158 " --> pdb=" O ASP A1154 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1198 removed outlier: 4.130A pdb=" N LYS A1189 " --> pdb=" O ILE A1185 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A1190 " --> pdb=" O PRO A1186 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN A1191 " --> pdb=" O SER A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1217 Processing helix chain 'A' and resid 1257 through 1276 removed outlier: 4.196A pdb=" N ALA A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1264 " --> pdb=" O LYS A1260 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A1276 " --> pdb=" O TYR A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1326 removed outlier: 3.751A pdb=" N PHE A1282 " --> pdb=" O ALA A1278 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU A1284 " --> pdb=" O PRO A1280 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A1295 " --> pdb=" O LYS A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1353 Proline residue: A1348 - end of helix Processing helix chain 'A' and resid 1359 through 1374 removed outlier: 3.920A pdb=" N GLU A1363 " --> pdb=" O ASP A1359 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A1368 " --> pdb=" O LEU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1413 removed outlier: 3.705A pdb=" N GLN A1405 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU A1406 " --> pdb=" O GLN A1402 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A1407 " --> pdb=" O LEU A1403 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1408 " --> pdb=" O PHE A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1417 through 1435 removed outlier: 3.523A pdb=" N ALA A1434 " --> pdb=" O ARG A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1472 removed outlier: 3.778A pdb=" N TYR A1471 " --> pdb=" O ALA A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1482 removed outlier: 3.770A pdb=" N LEU A1476 " --> pdb=" O GLY A1472 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A1478 " --> pdb=" O ARG A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1508 removed outlier: 3.929A pdb=" N THR A1492 " --> pdb=" O THR A1488 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A1508 " --> pdb=" O THR A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 3.728A pdb=" N ASP A1524 " --> pdb=" O CYS A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1530 through 1538 removed outlier: 3.720A pdb=" N VAL A1534 " --> pdb=" O ASN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1546 removed outlier: 3.641A pdb=" N GLU A1545 " --> pdb=" O GLU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1587 removed outlier: 3.582A pdb=" N CYS A1587 " --> pdb=" O LEU A1583 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1599 removed outlier: 3.657A pdb=" N ALA A1593 " --> pdb=" O THR A1589 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS A1594 " --> pdb=" O ARG A1590 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TYR A1595 " --> pdb=" O GLN A1591 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 removed outlier: 3.722A pdb=" N GLN A1607 " --> pdb=" O ARG A1603 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A1608 " --> pdb=" O ALA A1604 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1603 through 1608' Processing helix chain 'A' and resid 1630 through 1654 removed outlier: 4.444A pdb=" N ARG A1653 " --> pdb=" O ALA A1649 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY A1654 " --> pdb=" O VAL A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1657 through 1668 Processing helix chain 'A' and resid 1670 through 1680 removed outlier: 3.533A pdb=" N VAL A1675 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN A1679 " --> pdb=" O VAL A1675 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A1680 " --> pdb=" O LEU A1676 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1734 Processing helix chain 'A' and resid 1734 through 1739 removed outlier: 3.993A pdb=" N TYR A1738 " --> pdb=" O GLY A1734 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 284 removed outlier: 3.599A pdb=" N SER B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 removed outlier: 4.130A pdb=" N TYR B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 1199 through 1200 840 hydrogen bonds defined for protein. 2502 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: 10.20 Time building geometry restraints manager: 7.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12809 1.03 - 1.23: 32 1.23 - 1.42: 5384 1.42 - 1.62: 7561 1.62 - 1.81: 100 Bond restraints: 25886 Sorted by residual: bond pdb=" N PRO A1186 " pdb=" CD PRO A1186 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.43e+00 bond pdb=" N GLY A 757 " pdb=" CA GLY A 757 " ideal model delta sigma weight residual 1.449 1.465 -0.016 1.45e-02 4.76e+03 1.18e+00 ... (remaining 25881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.02: 46851 7.02 - 14.03: 0 14.03 - 21.05: 0 21.05 - 28.06: 0 28.06 - 35.08: 3 Bond angle restraints: 46854 Sorted by residual: angle pdb=" C SER A1187 " pdb=" CA SER A1187 " pdb=" HA SER A1187 " ideal model delta sigma weight residual 109.00 73.92 35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" N SER A1187 " pdb=" CA SER A1187 " pdb=" HA SER A1187 " ideal model delta sigma weight residual 110.00 75.50 34.50 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB SER A1187 " pdb=" CA SER A1187 " pdb=" HA SER A1187 " ideal model delta sigma weight residual 109.00 74.86 34.14 3.00e+00 1.11e-01 1.29e+02 angle pdb=" N LYS A 978 " pdb=" CA LYS A 978 " pdb=" C LYS A 978 " ideal model delta sigma weight residual 114.56 110.92 3.64 1.27e+00 6.20e-01 8.23e+00 angle pdb=" N LEU A1283 " pdb=" CA LEU A1283 " pdb=" C LEU A1283 " ideal model delta sigma weight residual 111.02 107.89 3.13 1.22e+00 6.72e-01 6.58e+00 ... (remaining 46849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.12: 11355 12.12 - 24.24: 515 24.24 - 36.36: 99 36.36 - 48.48: 49 48.48 - 60.60: 61 Dihedral angle restraints: 12079 sinusoidal: 6584 harmonic: 5495 Sorted by residual: dihedral pdb=" C SER A1187 " pdb=" N SER A1187 " pdb=" CA SER A1187 " pdb=" CB SER A1187 " ideal model delta harmonic sigma weight residual -122.60 -131.33 8.73 0 2.50e+00 1.60e-01 1.22e+01 dihedral pdb=" N SER A1187 " pdb=" C SER A1187 " pdb=" CA SER A1187 " pdb=" CB SER A1187 " ideal model delta harmonic sigma weight residual 122.80 130.62 -7.82 0 2.50e+00 1.60e-01 9.78e+00 dihedral pdb=" N LEU B 279 " pdb=" CA LEU B 279 " pdb=" CB LEU B 279 " pdb=" CG LEU B 279 " ideal model delta sinusoidal sigma weight residual -60.00 -98.85 38.85 3 1.50e+01 4.44e-03 6.86e+00 ... (remaining 12076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1907 0.067 - 0.135: 120 0.135 - 0.202: 1 0.202 - 0.269: 0 0.269 - 0.337: 1 Chirality restraints: 2029 Sorted by residual: chirality pdb=" CA SER A1187 " pdb=" N SER A1187 " pdb=" C SER A1187 " pdb=" CB SER A1187 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE A 167 " pdb=" N ILE A 167 " pdb=" C ILE A 167 " pdb=" CB ILE A 167 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA ILE A 404 " pdb=" N ILE A 404 " pdb=" C ILE A 404 " pdb=" CB ILE A 404 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 2026 not shown) Planarity restraints: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 759 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO A 760 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 760 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 760 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1307 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C LEU A1307 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU A1307 " -0.006 2.00e-02 2.50e+03 pdb=" N THR A1308 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1294 " 0.005 2.00e-02 2.50e+03 9.54e-03 9.10e-01 pdb=" C ILE A1294 " -0.016 2.00e-02 2.50e+03 pdb=" O ILE A1294 " 0.006 2.00e-02 2.50e+03 pdb=" N GLU A1295 " 0.005 2.00e-02 2.50e+03 ... (remaining 3779 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1271 2.21 - 2.81: 54868 2.81 - 3.41: 68510 3.41 - 4.00: 83955 4.00 - 4.60: 135333 Nonbonded interactions: 343937 Sorted by model distance: nonbonded pdb=" HA SER A1187 " pdb=" HB3 SER A1187 " model vdw 1.618 1.952 nonbonded pdb=" OE1 GLN A 460 " pdb=" H GLN A 460 " model vdw 1.650 2.450 nonbonded pdb=" OE1 GLU A1013 " pdb=" H GLU A1013 " model vdw 1.653 2.450 nonbonded pdb=" O SER A 421 " pdb=" HD1 HIS A 425 " model vdw 1.661 2.450 nonbonded pdb=" OE1 GLN A 702 " pdb=" H GLN A 702 " model vdw 1.662 2.450 ... (remaining 343932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.420 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 52.090 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.002 0.046 13045 Z= 0.088 Angle : 0.363 5.941 17658 Z= 0.209 Chirality : 0.032 0.337 2029 Planarity : 0.002 0.037 2254 Dihedral : 6.378 60.596 4824 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.33 (0.21), residues: 1568 helix: 0.62 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.59 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A1296 HIS 0.001 0.000 HIS A1068 PHE 0.005 0.000 PHE A 745 TYR 0.009 0.001 TYR A1089 ARG 0.001 0.000 ARG A1430 Details of bonding type rmsd hydrogen bonds : bond 0.11117 ( 840) hydrogen bonds : angle 4.72338 ( 2502) covalent geometry : bond 0.00153 (13045) covalent geometry : angle 0.36333 (17658) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.9104 (tt0) cc_final: 0.8644 (tp30) REVERT: A 471 ILE cc_start: 0.8770 (mt) cc_final: 0.8444 (mt) REVERT: A 675 MET cc_start: 0.7012 (mmm) cc_final: 0.5909 (mmm) REVERT: A 1173 ILE cc_start: 0.9086 (mt) cc_final: 0.8789 (tp) REVERT: A 1369 LYS cc_start: 0.8446 (tttt) cc_final: 0.8092 (tppt) REVERT: A 1636 TYR cc_start: 0.9147 (m-80) cc_final: 0.8818 (m-10) REVERT: A 1727 MET cc_start: 0.7813 (ttp) cc_final: 0.7373 (tpt) REVERT: B 290 GLN cc_start: 0.8858 (tt0) cc_final: 0.8369 (tm-30) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.7057 time to fit residues: 299.0688 Evaluate side-chains 186 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 238 GLN A 677 ASN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.071668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.053447 restraints weight = 217031.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.056079 restraints weight = 122052.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.057901 restraints weight = 80224.285| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13045 Z= 0.190 Angle : 0.557 7.033 17658 Z= 0.297 Chirality : 0.035 0.347 2029 Planarity : 0.004 0.044 2254 Dihedral : 2.533 11.822 1716 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.15 % Allowed : 7.18 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.22), residues: 1568 helix: 1.76 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : -2.06 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 552 HIS 0.006 0.001 HIS A1255 PHE 0.017 0.001 PHE A1067 TYR 0.016 0.001 TYR A1431 ARG 0.004 0.000 ARG A1669 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 840) hydrogen bonds : angle 3.79796 ( 2502) covalent geometry : bond 0.00389 (13045) covalent geometry : angle 0.55658 (17658) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9452 (mmm) cc_final: 0.9158 (mmm) REVERT: A 191 GLU cc_start: 0.9561 (tt0) cc_final: 0.9061 (tp30) REVERT: A 462 MET cc_start: 0.8510 (mmm) cc_final: 0.8265 (mmm) REVERT: A 467 PHE cc_start: 0.9344 (t80) cc_final: 0.9071 (t80) REVERT: A 471 ILE cc_start: 0.9235 (mt) cc_final: 0.9024 (mt) REVERT: A 598 MET cc_start: 0.9221 (ttp) cc_final: 0.8739 (tmm) REVERT: A 794 MET cc_start: 0.8954 (tpp) cc_final: 0.8711 (tpp) REVERT: A 837 MET cc_start: 0.9033 (mmm) cc_final: 0.8641 (mmm) REVERT: A 1127 MET cc_start: 0.8928 (mmm) cc_final: 0.8664 (mmm) REVERT: A 1190 ARG cc_start: 0.9486 (ttm170) cc_final: 0.9188 (tpp-160) REVERT: A 1636 TYR cc_start: 0.9534 (m-80) cc_final: 0.9199 (m-10) REVERT: A 1727 MET cc_start: 0.8138 (ttp) cc_final: 0.7580 (tpt) REVERT: B 247 ASP cc_start: 0.8477 (t70) cc_final: 0.8031 (t70) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 0.7412 time to fit residues: 189.3565 Evaluate side-chains 172 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 159 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.068470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.050474 restraints weight = 221495.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.052995 restraints weight = 123234.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.054726 restraints weight = 81038.424| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13045 Z= 0.184 Angle : 0.531 6.703 17658 Z= 0.282 Chirality : 0.034 0.352 2029 Planarity : 0.004 0.034 2254 Dihedral : 2.650 13.631 1716 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 8.18 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.22), residues: 1568 helix: 2.02 (0.15), residues: 1170 sheet: None (None), residues: 0 loop : -1.96 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 287 HIS 0.012 0.001 HIS A 239 PHE 0.023 0.001 PHE A1404 TYR 0.015 0.001 TYR B 251 ARG 0.003 0.000 ARG A1259 Details of bonding type rmsd hydrogen bonds : bond 0.02855 ( 840) hydrogen bonds : angle 3.79913 ( 2502) covalent geometry : bond 0.00371 (13045) covalent geometry : angle 0.53104 (17658) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.9558 (tt0) cc_final: 0.9056 (tp30) REVERT: A 462 MET cc_start: 0.8522 (mmm) cc_final: 0.8150 (mmm) REVERT: A 471 ILE cc_start: 0.9246 (mt) cc_final: 0.8865 (mt) REVERT: A 515 MET cc_start: 0.9019 (ttp) cc_final: 0.8612 (ttp) REVERT: A 598 MET cc_start: 0.9193 (ttp) cc_final: 0.8682 (tmm) REVERT: A 837 MET cc_start: 0.9049 (mmm) cc_final: 0.8819 (mmm) REVERT: A 1086 MET cc_start: 0.8183 (mmt) cc_final: 0.7472 (mtm) REVERT: A 1101 LEU cc_start: 0.9724 (OUTLIER) cc_final: 0.8963 (mt) REVERT: A 1372 LEU cc_start: 0.9530 (tp) cc_final: 0.9286 (tp) REVERT: A 1437 ASP cc_start: 0.6370 (p0) cc_final: 0.6082 (p0) REVERT: A 1636 TYR cc_start: 0.9540 (m-80) cc_final: 0.9206 (m-10) REVERT: A 1727 MET cc_start: 0.8136 (ttp) cc_final: 0.7837 (tpp) REVERT: B 247 ASP cc_start: 0.8622 (t70) cc_final: 0.8210 (t70) outliers start: 22 outliers final: 13 residues processed: 177 average time/residue: 0.6713 time to fit residues: 162.2592 Evaluate side-chains 162 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.062837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.045551 restraints weight = 226697.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047867 restraints weight = 124029.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049454 restraints weight = 81100.447| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 13045 Z= 0.235 Angle : 0.586 6.344 17658 Z= 0.319 Chirality : 0.035 0.325 2029 Planarity : 0.004 0.039 2254 Dihedral : 3.062 17.390 1716 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.44 % Allowed : 8.54 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.21), residues: 1568 helix: 1.79 (0.15), residues: 1174 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1105 HIS 0.012 0.002 HIS A 239 PHE 0.019 0.002 PHE A1282 TYR 0.015 0.002 TYR B 251 ARG 0.004 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 840) hydrogen bonds : angle 4.05832 ( 2502) covalent geometry : bond 0.00458 (13045) covalent geometry : angle 0.58627 (17658) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9617 (mmm) cc_final: 0.9304 (mmm) REVERT: A 191 GLU cc_start: 0.9637 (tt0) cc_final: 0.9099 (tp30) REVERT: A 462 MET cc_start: 0.8370 (mmm) cc_final: 0.8094 (mmm) REVERT: A 515 MET cc_start: 0.9183 (ttp) cc_final: 0.8932 (ttp) REVERT: A 837 MET cc_start: 0.9160 (mmm) cc_final: 0.8881 (mmm) REVERT: A 1101 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9550 (mt) REVERT: A 1127 MET cc_start: 0.9160 (mmm) cc_final: 0.8676 (mmm) REVERT: A 1607 GLN cc_start: 0.9399 (mm-40) cc_final: 0.9196 (mm110) REVERT: A 1636 TYR cc_start: 0.9605 (m-80) cc_final: 0.9207 (m-10) REVERT: A 1727 MET cc_start: 0.8453 (ttp) cc_final: 0.8104 (tpp) REVERT: B 247 ASP cc_start: 0.8794 (t70) cc_final: 0.8486 (t70) REVERT: B 269 GLU cc_start: 0.9490 (tm-30) cc_final: 0.9088 (tm-30) REVERT: B 273 ARG cc_start: 0.9616 (ptm160) cc_final: 0.9055 (ttp80) outliers start: 20 outliers final: 15 residues processed: 164 average time/residue: 0.6917 time to fit residues: 155.7498 Evaluate side-chains 153 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 155 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.064220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.046561 restraints weight = 223341.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.048972 restraints weight = 121222.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.050621 restraints weight = 79196.544| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13045 Z= 0.110 Angle : 0.498 6.374 17658 Z= 0.255 Chirality : 0.034 0.340 2029 Planarity : 0.003 0.038 2254 Dihedral : 2.876 14.057 1716 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.08 % Allowed : 9.98 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.22), residues: 1568 helix: 2.29 (0.15), residues: 1173 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 287 HIS 0.007 0.001 HIS A 239 PHE 0.016 0.001 PHE A1404 TYR 0.017 0.001 TYR B 251 ARG 0.003 0.000 ARG A 772 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 840) hydrogen bonds : angle 3.63409 ( 2502) covalent geometry : bond 0.00235 (13045) covalent geometry : angle 0.49758 (17658) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9620 (mmm) cc_final: 0.9397 (mmm) REVERT: A 191 GLU cc_start: 0.9634 (tt0) cc_final: 0.9099 (tp30) REVERT: A 515 MET cc_start: 0.9200 (ttp) cc_final: 0.8913 (ttp) REVERT: A 598 MET cc_start: 0.9241 (ttp) cc_final: 0.8583 (tmm) REVERT: A 837 MET cc_start: 0.9200 (mmm) cc_final: 0.8907 (mmm) REVERT: A 1086 MET cc_start: 0.8165 (mmt) cc_final: 0.7674 (mtm) REVERT: A 1127 MET cc_start: 0.9124 (mmm) cc_final: 0.8689 (mmm) REVERT: A 1541 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8817 (mp0) REVERT: B 247 ASP cc_start: 0.8739 (t70) cc_final: 0.8460 (t70) outliers start: 15 outliers final: 12 residues processed: 158 average time/residue: 0.7044 time to fit residues: 153.0781 Evaluate side-chains 152 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 141 optimal weight: 7.9990 chunk 83 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.064166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.046621 restraints weight = 219349.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.049036 restraints weight = 118995.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.050699 restraints weight = 77510.771| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13045 Z= 0.098 Angle : 0.492 6.960 17658 Z= 0.248 Chirality : 0.034 0.340 2029 Planarity : 0.003 0.041 2254 Dihedral : 2.800 13.221 1716 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.93 % Allowed : 10.62 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.42 (0.22), residues: 1568 helix: 2.54 (0.15), residues: 1173 sheet: None (None), residues: 0 loop : -1.45 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 287 HIS 0.007 0.001 HIS A 239 PHE 0.024 0.001 PHE A1282 TYR 0.018 0.001 TYR B 251 ARG 0.002 0.000 ARG A 188 Details of bonding type rmsd hydrogen bonds : bond 0.02596 ( 840) hydrogen bonds : angle 3.47225 ( 2502) covalent geometry : bond 0.00214 (13045) covalent geometry : angle 0.49203 (17658) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9605 (mmm) cc_final: 0.9368 (mmm) REVERT: A 191 GLU cc_start: 0.9629 (tt0) cc_final: 0.9100 (tp30) REVERT: A 515 MET cc_start: 0.9201 (ttp) cc_final: 0.8913 (ttp) REVERT: A 1086 MET cc_start: 0.8152 (mmt) cc_final: 0.7664 (mtm) REVERT: A 1282 PHE cc_start: 0.7970 (t80) cc_final: 0.7729 (t80) REVERT: B 247 ASP cc_start: 0.8691 (t70) cc_final: 0.8414 (t70) outliers start: 13 outliers final: 11 residues processed: 154 average time/residue: 0.7285 time to fit residues: 154.5557 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 136 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 51 optimal weight: 0.0670 chunk 119 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.064233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.046658 restraints weight = 220434.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.049089 restraints weight = 119048.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.050779 restraints weight = 77183.989| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13045 Z= 0.095 Angle : 0.500 7.076 17658 Z= 0.250 Chirality : 0.034 0.338 2029 Planarity : 0.003 0.043 2254 Dihedral : 2.754 13.131 1716 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.01 % Allowed : 11.13 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.63 (0.22), residues: 1568 helix: 2.66 (0.15), residues: 1180 sheet: None (None), residues: 0 loop : -1.33 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 287 HIS 0.006 0.001 HIS A 239 PHE 0.016 0.001 PHE A1282 TYR 0.015 0.001 TYR B 251 ARG 0.011 0.000 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.02563 ( 840) hydrogen bonds : angle 3.41446 ( 2502) covalent geometry : bond 0.00211 (13045) covalent geometry : angle 0.50016 (17658) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9610 (mmm) cc_final: 0.9373 (mmm) REVERT: A 191 GLU cc_start: 0.9627 (tt0) cc_final: 0.9104 (tp30) REVERT: A 515 MET cc_start: 0.9129 (ttp) cc_final: 0.8835 (ttp) REVERT: A 837 MET cc_start: 0.8846 (mmm) cc_final: 0.8522 (mmm) REVERT: A 951 LYS cc_start: 0.9399 (tppt) cc_final: 0.9114 (tppt) REVERT: A 1086 MET cc_start: 0.8069 (mmt) cc_final: 0.7475 (mtm) REVERT: A 1282 PHE cc_start: 0.8010 (t80) cc_final: 0.7726 (t80) REVERT: A 1541 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8807 (mp0) REVERT: B 247 ASP cc_start: 0.8658 (t70) cc_final: 0.8373 (t70) outliers start: 14 outliers final: 11 residues processed: 151 average time/residue: 0.6700 time to fit residues: 141.7757 Evaluate side-chains 149 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 57 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN A 627 ASN A 771 ASN A1574 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.060524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.043481 restraints weight = 230202.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.045741 restraints weight = 124061.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.047301 restraints weight = 80620.974| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 13045 Z= 0.197 Angle : 0.558 6.710 17658 Z= 0.300 Chirality : 0.035 0.330 2029 Planarity : 0.004 0.048 2254 Dihedral : 3.072 13.682 1716 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.15 % Allowed : 11.70 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.21), residues: 1568 helix: 2.16 (0.15), residues: 1190 sheet: None (None), residues: 0 loop : -1.42 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 748 HIS 0.006 0.001 HIS A 661 PHE 0.014 0.001 PHE A1282 TYR 0.011 0.002 TYR A1471 ARG 0.009 0.001 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 840) hydrogen bonds : angle 3.90396 ( 2502) covalent geometry : bond 0.00391 (13045) covalent geometry : angle 0.55761 (17658) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9549 (mmm) cc_final: 0.9325 (mmm) REVERT: A 191 GLU cc_start: 0.9622 (tt0) cc_final: 0.9162 (tp30) REVERT: A 515 MET cc_start: 0.9253 (ttp) cc_final: 0.8992 (ttp) REVERT: A 837 MET cc_start: 0.9133 (mmm) cc_final: 0.8702 (mmm) REVERT: A 951 LYS cc_start: 0.9469 (tppt) cc_final: 0.9196 (tppt) REVERT: A 1001 MET cc_start: 0.9579 (mmm) cc_final: 0.9319 (mmm) REVERT: A 1282 PHE cc_start: 0.8049 (t80) cc_final: 0.7737 (t80) REVERT: A 1636 TYR cc_start: 0.9489 (m-10) cc_final: 0.9281 (m-10) outliers start: 16 outliers final: 16 residues processed: 146 average time/residue: 0.7032 time to fit residues: 145.7384 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 269 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 135 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.061653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.044417 restraints weight = 224667.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.046765 restraints weight = 119677.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.048362 restraints weight = 77348.935| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13045 Z= 0.102 Angle : 0.515 7.234 17658 Z= 0.260 Chirality : 0.034 0.338 2029 Planarity : 0.003 0.037 2254 Dihedral : 2.930 14.134 1716 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.08 % Allowed : 11.56 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.22), residues: 1568 helix: 2.57 (0.15), residues: 1187 sheet: None (None), residues: 0 loop : -1.27 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 748 HIS 0.004 0.001 HIS A1068 PHE 0.012 0.001 PHE A1282 TYR 0.011 0.001 TYR A1089 ARG 0.009 0.000 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.02632 ( 840) hydrogen bonds : angle 3.53158 ( 2502) covalent geometry : bond 0.00225 (13045) covalent geometry : angle 0.51512 (17658) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9564 (mmm) cc_final: 0.9327 (mmm) REVERT: A 191 GLU cc_start: 0.9626 (tt0) cc_final: 0.9158 (tp30) REVERT: A 515 MET cc_start: 0.9262 (ttp) cc_final: 0.8979 (ttp) REVERT: A 598 MET cc_start: 0.9286 (ttp) cc_final: 0.8572 (tmm) REVERT: A 708 MET cc_start: 0.9402 (mtm) cc_final: 0.8815 (mtm) REVERT: A 837 MET cc_start: 0.9060 (mmm) cc_final: 0.8587 (mmm) REVERT: A 951 LYS cc_start: 0.9464 (tppt) cc_final: 0.9193 (tppt) REVERT: A 1086 MET cc_start: 0.8172 (mmt) cc_final: 0.7902 (mtm) REVERT: A 1282 PHE cc_start: 0.8009 (t80) cc_final: 0.7668 (t80) REVERT: A 1541 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8956 (mp0) REVERT: A 1636 TYR cc_start: 0.9491 (m-10) cc_final: 0.9283 (m-10) REVERT: B 273 ARG cc_start: 0.9578 (ptm160) cc_final: 0.9203 (ttp80) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.6910 time to fit residues: 140.7728 Evaluate side-chains 148 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1541 GLU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 150 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.060579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.043598 restraints weight = 228634.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.045911 restraints weight = 120947.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.047482 restraints weight = 77950.648| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13045 Z= 0.137 Angle : 0.524 7.707 17658 Z= 0.271 Chirality : 0.035 0.337 2029 Planarity : 0.004 0.085 2254 Dihedral : 2.959 14.767 1716 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.01 % Allowed : 11.41 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.22), residues: 1568 helix: 2.56 (0.15), residues: 1189 sheet: None (None), residues: 0 loop : -1.27 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 748 HIS 0.004 0.001 HIS A1068 PHE 0.015 0.001 PHE A 467 TYR 0.011 0.001 TYR B 251 ARG 0.029 0.001 ARG B 270 Details of bonding type rmsd hydrogen bonds : bond 0.02658 ( 840) hydrogen bonds : angle 3.61790 ( 2502) covalent geometry : bond 0.00282 (13045) covalent geometry : angle 0.52441 (17658) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9565 (mmm) cc_final: 0.9338 (mmm) REVERT: A 191 GLU cc_start: 0.9626 (tt0) cc_final: 0.9197 (tp30) REVERT: A 463 ASP cc_start: 0.8928 (m-30) cc_final: 0.8028 (t0) REVERT: A 515 MET cc_start: 0.9279 (ttp) cc_final: 0.9001 (ttp) REVERT: A 837 MET cc_start: 0.9119 (mmm) cc_final: 0.8641 (mmm) REVERT: A 951 LYS cc_start: 0.9479 (tppt) cc_final: 0.9195 (tppt) REVERT: A 1282 PHE cc_start: 0.8045 (t80) cc_final: 0.7705 (t80) REVERT: B 270 ARG cc_start: 0.9575 (OUTLIER) cc_final: 0.9082 (ptp-110) REVERT: B 273 ARG cc_start: 0.9590 (ptm160) cc_final: 0.9197 (ttp-110) outliers start: 14 outliers final: 13 residues processed: 146 average time/residue: 0.6794 time to fit residues: 137.8813 Evaluate side-chains 149 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 672 GLU Chi-restraints excluded: chain A residue 879 VAL Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1477 ASN Chi-restraints excluded: chain A residue 1497 LEU Chi-restraints excluded: chain A residue 1583 LEU Chi-restraints excluded: chain A residue 1674 HIS Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 270 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 53.0538 > 50: distance: 156 - 201: 4.830 distance: 176 - 244: 5.648 distance: 186 - 254: 6.613 distance: 203 - 225: 3.303 distance: 204 - 269: 7.357 distance: 206 - 208: 3.361 distance: 207 - 209: 3.235 distance: 225 - 233: 7.481 distance: 226 - 227: 3.817 distance: 226 - 229: 3.290 distance: 227 - 244: 3.393 distance: 228 - 286: 6.629 distance: 229 - 230: 5.457 distance: 229 - 231: 3.744 distance: 229 - 235: 3.082 distance: 230 - 236: 8.342 distance: 230 - 237: 4.215 distance: 231 - 238: 4.243 distance: 231 - 239: 4.804 distance: 231 - 240: 4.568 distance: 232 - 241: 3.816 distance: 232 - 243: 3.405 distance: 244 - 245: 12.592 distance: 244 - 249: 18.022 distance: 245 - 246: 11.705 distance: 245 - 248: 8.290 distance: 245 - 250: 9.309 distance: 246 - 247: 10.619 distance: 246 - 254: 18.309 distance: 248 - 251: 15.728 distance: 248 - 252: 7.643 distance: 248 - 253: 15.600 distance: 254 - 255: 6.255 distance: 254 - 263: 28.594 distance: 255 - 256: 6.486 distance: 255 - 258: 7.006 distance: 255 - 264: 3.417 distance: 258 - 259: 4.818 distance: 259 - 267: 5.193 distance: 259 - 268: 9.248 distance: 260 - 261: 5.270 distance: 260 - 262: 7.432 distance: 269 - 270: 3.435 distance: 269 - 279: 7.476 distance: 271 - 272: 4.188 distance: 271 - 286: 4.871 distance: 274 - 276: 3.412 distance: 286 - 294: 3.597 distance: 287 - 288: 3.286 distance: 287 - 290: 4.499 distance: 287 - 295: 3.216 distance: 288 - 289: 8.850 distance: 288 - 300: 4.337 distance: 290 - 291: 3.514 distance: 290 - 296: 3.443 distance: 291 - 292: 3.880 distance: 291 - 293: 4.259 distance: 301 - 302: 3.992 distance: 301 - 305: 4.610 distance: 301 - 306: 4.562 distance: 302 - 307: 3.754 distance: 307 - 308: 3.214 distance: 308 - 309: 3.951 distance: 308 - 319: 3.791 distance: 309 - 327: 4.103 distance: 311 - 320: 3.608 distance: 311 - 321: 3.417 distance: 327 - 328: 5.410 distance: 328 - 329: 4.797 distance: 328 - 331: 8.288 distance: 328 - 340: 3.520 distance: 329 - 330: 5.548 distance: 329 - 348: 3.832 distance: 331 - 332: 5.743 distance: 331 - 341: 7.478 distance: 331 - 342: 11.366 distance: 333 - 343: 4.606 distance: 334 - 344: 3.282 distance: 335 - 337: 3.453 distance: 336 - 346: 3.598 distance: 337 - 338: 4.996 distance: 338 - 347: 4.955 distance: 348 - 349: 3.817 distance: 348 - 356: 7.090 distance: 349 - 352: 6.086 distance: 349 - 357: 6.380 distance: 350 - 351: 5.061 distance: 350 - 367: 4.273 distance: 352 - 353: 6.461 distance: 352 - 358: 6.820 distance: 352 - 359: 6.681 distance: 353 - 354: 7.837 distance: 353 - 355: 8.562 distance: 353 - 360: 4.134 distance: 354 - 361: 5.023 distance: 354 - 362: 3.997 distance: 354 - 363: 5.449 distance: 355 - 364: 7.178 distance: 355 - 366: 4.784