Starting phenix.real_space_refine on Wed Aug 5 16:23:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qgt_18390/08_2026/8qgt_18390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qgt_18390/08_2026/8qgt_18390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qgt_18390/08_2026/8qgt_18390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qgt_18390/08_2026/8qgt_18390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qgt_18390/08_2026/8qgt_18390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qgt_18390/08_2026/8qgt_18390.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 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 P 12 5.49 5 S 57 5.16 5 C 6797 2.51 5 N 1790 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10635 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1289, 10376 Classifications: {'peptide': 1289} Link IDs: {'PTRANS': 41, 'TRANS': 1247} Chain breaks: 9 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 259 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 8} Time building chain proxies: 2.61, per 1000 atoms: 0.25 Number of scatterers: 10635 At special positions: 0 Unit cell: (91.451, 104.036, 124.172, 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 57 16.00 P 12 15.00 O 1979 8.00 N 1790 7.00 C 6797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 411.8 milliseconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 60.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.727A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.591A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 429 Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.782A pdb=" N GLN A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 489 removed outlier: 3.871A pdb=" N HIS A 474 " --> pdb=" O THR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' Processing helix chain 'A' and resid 564 through 572 removed outlier: 3.611A pdb=" N ILE A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 614 Processing helix chain 'A' and resid 616 through 635 removed outlier: 3.580A pdb=" N ARG A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 654 through 673 Processing helix chain 'A' and resid 712 through 725 removed outlier: 3.918A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 removed outlier: 4.233A pdb=" N HIS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 759 Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.951A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.666A pdb=" N SER A 823 " --> pdb=" O PRO A 820 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 824 " --> pdb=" O TYR A 821 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N THR A 825 " --> pdb=" O PHE A 822 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG A 826 " --> pdb=" O SER A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 858 Processing helix chain 'A' and resid 864 through 873 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 928 through 947 removed outlier: 4.079A pdb=" N ILE A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 933 " --> pdb=" O GLU A 929 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 992 removed outlier: 4.137A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1011 Processing helix chain 'A' and resid 1020 through 1030 removed outlier: 3.621A pdb=" N MET A1030 " --> pdb=" O TYR A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1042 Processing helix chain 'A' and resid 1061 through 1084 removed outlier: 3.564A pdb=" N SER A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1126 removed outlier: 3.625A pdb=" N LEU A1118 " --> pdb=" O THR A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1135 removed outlier: 3.637A pdb=" N SER A1133 " --> pdb=" O HIS A1130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A1135 " --> pdb=" O PHE A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.860A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1179 Processing helix chain 'A' and resid 1184 through 1192 removed outlier: 3.836A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1219 Processing helix chain 'A' and resid 1221 through 1241 Processing helix chain 'A' and resid 1249 through 1253 Processing helix chain 'A' and resid 1272 through 1280 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1301 through 1320 removed outlier: 4.280A pdb=" N ILE A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1308 " --> pdb=" O MET A1304 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A1309 " --> pdb=" O LEU A1305 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A1310 " --> pdb=" O TYR A1306 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A1311 " --> pdb=" O ILE A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 4.371A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1396 Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 4.210A pdb=" N PHE A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1407 " --> pdb=" O GLN A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1439 Processing helix chain 'A' and resid 1444 through 1457 Processing helix chain 'A' and resid 1463 through 1470 removed outlier: 3.699A pdb=" N PHE A1467 " --> pdb=" O ALA A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1512 Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1552 through 1560 removed outlier: 3.591A pdb=" N MET A1556 " --> pdb=" O LEU A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1592 Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 503 removed outlier: 5.378A pdb=" N THR A 529 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA6, first strand: chain 'A' and resid 832 through 837 removed outlier: 5.037A pdb=" N SER A 834 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER A 846 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN A 836 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 893 through 897 removed outlier: 7.040A pdb=" N ALA A 877 " --> pdb=" O ASP A1016 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N PHE A1018 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 879 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 952 Processing sheet with id=AA9, first strand: chain 'A' and resid 949 through 952 removed outlier: 3.537A pdb=" N THR A1163 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 1474 through 1476 removed outlier: 4.758A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1489 594 hydrogen bonds defined for protein. 1701 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.23 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2240 1.33 - 1.45: 2542 1.45 - 1.57: 5995 1.57 - 1.69: 23 1.69 - 1.81: 95 Bond restraints: 10895 Sorted by residual: bond pdb=" N ILE A1372 " pdb=" CA ILE A1372 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.76e+01 bond pdb=" N ASP A1112 " pdb=" CA ASP A1112 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.80e+00 bond pdb=" N ILE A1333 " pdb=" CA ILE A1333 " ideal model delta sigma weight residual 1.464 1.495 -0.031 1.13e-02 7.83e+03 7.53e+00 bond pdb=" N PHE A1330 " pdb=" CA PHE A1330 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.50e+00 bond pdb=" N ILE A1371 " pdb=" CA ILE A1371 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.39e+00 ... (remaining 10890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 14586 2.19 - 4.37: 165 4.37 - 6.56: 20 6.56 - 8.74: 3 8.74 - 10.93: 1 Bond angle restraints: 14775 Sorted by residual: angle pdb=" C3' A C 8 " pdb=" O3' A C 8 " pdb=" P G C 9 " ideal model delta sigma weight residual 119.70 108.77 10.93 1.20e+00 6.94e-01 8.29e+01 angle pdb=" C3' U C 7 " pdb=" O3' U C 7 " pdb=" P A C 8 " ideal model delta sigma weight residual 119.70 111.31 8.39 1.20e+00 6.94e-01 4.89e+01 angle pdb=" N PRO A 978 " pdb=" CA PRO A 978 " pdb=" C PRO A 978 " ideal model delta sigma weight residual 114.20 107.89 6.31 1.20e+00 6.94e-01 2.76e+01 angle pdb=" N SER A 252 " pdb=" CA SER A 252 " pdb=" C SER A 252 " ideal model delta sigma weight residual 113.28 108.84 4.44 1.22e+00 6.72e-01 1.33e+01 angle pdb=" CA THR A 328 " pdb=" C THR A 328 " pdb=" O THR A 328 " ideal model delta sigma weight residual 121.08 117.99 3.09 8.90e-01 1.26e+00 1.21e+01 ... (remaining 14770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 6243 32.25 - 64.50: 272 64.50 - 96.75: 17 96.75 - 129.00: 1 129.00 - 161.26: 1 Dihedral angle restraints: 6534 sinusoidal: 2742 harmonic: 3792 Sorted by residual: dihedral pdb=" O4' U C 7 " pdb=" C1' U C 7 " pdb=" N1 U C 7 " pdb=" C2 U C 7 " ideal model delta sinusoidal sigma weight residual 200.00 38.74 161.26 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" CA LEU A1152 " pdb=" C LEU A1152 " pdb=" N GLY A1153 " pdb=" CA GLY A1153 " ideal model delta harmonic sigma weight residual 180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CB GLU A 909 " pdb=" CG GLU A 909 " pdb=" CD GLU A 909 " pdb=" OE1 GLU A 909 " ideal model delta sinusoidal sigma weight residual 0.00 -85.52 85.52 1 3.00e+01 1.11e-03 9.83e+00 ... (remaining 6531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1546 0.082 - 0.164: 100 0.164 - 0.246: 6 0.246 - 0.328: 0 0.328 - 0.409: 3 Chirality restraints: 1655 Sorted by residual: chirality pdb=" P U C 7 " pdb=" OP1 U C 7 " pdb=" OP2 U C 7 " pdb=" O5' U C 7 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" P A C 8 " pdb=" OP1 A C 8 " pdb=" OP2 A C 8 " pdb=" O5' A C 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" P G C 9 " pdb=" OP1 G C 9 " pdb=" OP2 G C 9 " pdb=" O5' G C 9 " both_signs ideal model delta sigma weight residual True 2.41 -2.76 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1652 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 286 " 0.166 9.50e-02 1.11e+02 7.42e-02 3.42e+00 pdb=" NE ARG A 286 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 286 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 286 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 286 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1467 " -0.009 2.00e-02 2.50e+03 1.32e-02 3.06e+00 pdb=" CG PHE A1467 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A1467 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A1467 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A1467 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A1467 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1467 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 253 " -0.142 9.50e-02 1.11e+02 6.36e-02 2.48e+00 pdb=" NE ARG A 253 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 253 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 253 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 253 " -0.005 2.00e-02 2.50e+03 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1402 2.75 - 3.29: 10249 3.29 - 3.83: 18362 3.83 - 4.36: 22568 4.36 - 4.90: 37901 Nonbonded interactions: 90482 Sorted by model distance: nonbonded pdb=" O ILE A 717 " pdb=" OG1 THR A 721 " model vdw 2.214 3.040 nonbonded pdb=" O GLU A 765 " pdb=" OH TYR A 785 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A1306 " pdb=" OD1 ASN A1434 " model vdw 2.224 3.040 nonbonded pdb=" OE2 GLU A 738 " pdb=" OG SER A1020 " model vdw 2.229 3.040 nonbonded pdb=" OG SER A 297 " pdb=" O ARG A 532 " model vdw 2.235 3.040 ... (remaining 90477 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10895 Z= 0.208 Angle : 0.567 10.928 14775 Z= 0.345 Chirality : 0.044 0.409 1655 Planarity : 0.004 0.074 1813 Dihedral : 16.976 161.255 4076 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.88 % Allowed : 21.42 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.23), residues: 1269 helix: 1.53 (0.19), residues: 703 sheet: 0.22 (0.49), residues: 103 loop : -0.57 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 707 TYR 0.012 0.001 TYR A 912 PHE 0.030 0.002 PHE A1467 TRP 0.013 0.001 TRP A 976 HIS 0.005 0.001 HIS A1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.21 (10895) covalent geometry : angle 0.56693 / 0.35 (14775) hydrogen bonds : bond 0.14887 / 10.05 ( 580) hydrogen bonds : angle 5.75603 / 4.05 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.471 Fit side-chains REVERT: A 299 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7392 (mp) REVERT: A 520 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7962 (t) REVERT: A 951 PHE cc_start: 0.8211 (m-80) cc_final: 0.7916 (m-80) REVERT: A 961 ARG cc_start: 0.7478 (ptm160) cc_final: 0.7217 (ttp80) REVERT: A 1587 ARG cc_start: 0.7446 (mtt90) cc_final: 0.7055 (mtt90) outliers start: 10 outliers final: 5 residues processed: 183 average time/residue: 0.6019 time to fit residues: 118.8447 Evaluate side-chains 149 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1259 THR Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1481 VAL Chi-restraints excluded: chain A residue 1524 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 ASN A 598 GLN A 842 HIS A1036 HIS ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1287 ASN A1399 GLN A1413 HIS A1577 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.159054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.125991 restraints weight = 12331.947| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.37 r_work: 0.3117 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10895 Z= 0.212 Angle : 0.594 6.738 14775 Z= 0.321 Chirality : 0.043 0.158 1655 Planarity : 0.005 0.045 1813 Dihedral : 10.072 149.558 1576 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.65 % Allowed : 20.19 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.23), residues: 1269 helix: 1.34 (0.19), residues: 712 sheet: 0.02 (0.50), residues: 104 loop : -0.79 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 707 TYR 0.023 0.002 TYR A 912 PHE 0.035 0.002 PHE A1313 TRP 0.010 0.002 TRP A 817 HIS 0.008 0.001 HIS A1258 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (10895) covalent geometry : angle 0.59356 / 0.32 (14775) hydrogen bonds : bond 0.05541 / 3.56 ( 580) hydrogen bonds : angle 4.63561 / 3.31 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 153 time to evaluate : 0.414 Fit side-chains REVERT: A 269 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7772 (mm-30) REVERT: A 346 ARG cc_start: 0.7724 (ppt90) cc_final: 0.7517 (ptm-80) REVERT: A 645 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8473 (tt0) REVERT: A 729 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8387 (mttt) REVERT: A 761 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7636 (tp30) REVERT: A 1010 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7995 (mttt) REVERT: A 1287 ASN cc_start: 0.7898 (m110) cc_final: 0.7599 (m-40) REVERT: A 1305 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6277 (pp) REVERT: A 1372 ILE cc_start: 0.8006 (tt) cc_final: 0.7785 (tt) REVERT: A 1538 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6175 (mtm) outliers start: 53 outliers final: 13 residues processed: 189 average time/residue: 0.5480 time to fit residues: 112.3605 Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1577 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN A 457 ASN A 565 ASN ** A 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1413 HIS A1577 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.160004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.126385 restraints weight = 12429.618| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.33 r_work: 0.3124 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10895 Z= 0.141 Angle : 0.497 6.744 14775 Z= 0.268 Chirality : 0.039 0.145 1655 Planarity : 0.004 0.042 1813 Dihedral : 9.980 150.499 1568 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 21.51 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.23), residues: 1269 helix: 1.63 (0.19), residues: 713 sheet: -0.12 (0.50), residues: 104 loop : -0.69 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 707 TYR 0.014 0.001 TYR A 912 PHE 0.024 0.002 PHE A1313 TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A 861 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (10895) covalent geometry : angle 0.49701 / 0.27 (14775) hydrogen bonds : bond 0.04594 / 2.95 ( 580) hydrogen bonds : angle 4.37634 / 3.13 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.366 Fit side-chains REVERT: A 346 ARG cc_start: 0.7719 (ppt90) cc_final: 0.7513 (ptm-80) REVERT: A 729 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (mttt) REVERT: A 761 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7615 (tp30) REVERT: A 1010 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8007 (mttt) REVERT: A 1275 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: A 1287 ASN cc_start: 0.7902 (m110) cc_final: 0.7591 (m-40) REVERT: A 1312 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.6915 (mmtt) REVERT: A 1538 MET cc_start: 0.6402 (OUTLIER) cc_final: 0.6011 (mtm) outliers start: 38 outliers final: 12 residues processed: 169 average time/residue: 0.4970 time to fit residues: 90.8476 Evaluate side-chains 152 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 729 LYS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 128 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN A 504 ASN A 625 ASN A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.158023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125003 restraints weight = 12440.202| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.34 r_work: 0.3112 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10895 Z= 0.193 Angle : 0.535 6.534 14775 Z= 0.288 Chirality : 0.041 0.161 1655 Planarity : 0.004 0.042 1813 Dihedral : 10.025 149.706 1568 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.86 % Allowed : 21.51 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.23), residues: 1269 helix: 1.54 (0.19), residues: 713 sheet: -0.14 (0.50), residues: 104 loop : -0.78 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 707 TYR 0.017 0.002 TYR A 912 PHE 0.024 0.002 PHE A1313 TRP 0.011 0.001 TRP A 817 HIS 0.006 0.001 HIS A 861 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (10895) covalent geometry : angle 0.53470 / 0.29 (14775) hydrogen bonds : bond 0.05022 / 3.23 ( 580) hydrogen bonds : angle 4.37380 / 3.13 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.391 Fit side-chains REVERT: A 346 ARG cc_start: 0.7678 (ppt90) cc_final: 0.7463 (ptm-80) REVERT: A 363 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7979 (tm-30) REVERT: A 761 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: A 778 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 833 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8137 (ttt) REVERT: A 1010 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7995 (mttt) REVERT: A 1287 ASN cc_start: 0.7888 (m110) cc_final: 0.7568 (m-40) REVERT: A 1312 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.6825 (mmtt) REVERT: A 1538 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6038 (mtm) outliers start: 44 outliers final: 16 residues processed: 171 average time/residue: 0.4790 time to fit residues: 88.6999 Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1377 ASP Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1538 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 68 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 HIS A1413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.159205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.125841 restraints weight = 12392.216| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.33 r_work: 0.3122 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10895 Z= 0.158 Angle : 0.508 8.669 14775 Z= 0.272 Chirality : 0.039 0.147 1655 Planarity : 0.004 0.043 1813 Dihedral : 9.963 150.462 1568 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.07 % Allowed : 22.56 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.23), residues: 1269 helix: 1.63 (0.19), residues: 713 sheet: -0.17 (0.50), residues: 104 loop : -0.74 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 707 TYR 0.016 0.002 TYR A 912 PHE 0.026 0.002 PHE A1313 TRP 0.012 0.001 TRP A 976 HIS 0.004 0.001 HIS A 861 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10895) covalent geometry : angle 0.50836 / 0.27 (14775) hydrogen bonds : bond 0.04603 / 2.95 ( 580) hydrogen bonds : angle 4.27886 / 3.07 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.383 Fit side-chains REVERT: A 346 ARG cc_start: 0.7675 (ppt90) cc_final: 0.7460 (ptm-80) REVERT: A 363 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: A 526 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (mtt180) REVERT: A 761 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: A 778 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: A 833 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7899 (ttp) REVERT: A 1010 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7984 (mttt) REVERT: A 1275 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: A 1287 ASN cc_start: 0.7877 (m110) cc_final: 0.7568 (m-40) REVERT: A 1312 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6724 (mmtt) REVERT: A 1538 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.6014 (mtm) outliers start: 35 outliers final: 13 residues processed: 158 average time/residue: 0.5190 time to fit residues: 88.3081 Evaluate side-chains 150 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 526 ARG Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126510 restraints weight = 12403.931| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.34 r_work: 0.3143 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10895 Z= 0.132 Angle : 0.485 7.409 14775 Z= 0.260 Chirality : 0.038 0.143 1655 Planarity : 0.004 0.050 1813 Dihedral : 9.876 151.095 1568 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.69 % Allowed : 22.04 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1269 helix: 1.70 (0.19), residues: 719 sheet: -0.16 (0.50), residues: 104 loop : -0.69 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 707 TYR 0.016 0.001 TYR A 912 PHE 0.023 0.002 PHE A1313 TRP 0.012 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10895) covalent geometry : angle 0.48531 / 0.26 (14775) hydrogen bonds : bond 0.04265 / 2.72 ( 580) hydrogen bonds : angle 4.18634 / 3.00 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 130 time to evaluate : 0.394 Fit side-chains REVERT: A 303 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8418 (mptp) REVERT: A 346 ARG cc_start: 0.7612 (ppt90) cc_final: 0.7409 (ptm-80) REVERT: A 363 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: A 761 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: A 778 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: A 833 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7859 (ttp) REVERT: A 1010 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7946 (mttt) REVERT: A 1275 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: A 1287 ASN cc_start: 0.7871 (m110) cc_final: 0.7562 (m-40) REVERT: A 1305 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6313 (pp) REVERT: A 1312 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7102 (mmmt) REVERT: A 1372 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7423 (mt) REVERT: A 1538 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5964 (mtm) outliers start: 42 outliers final: 18 residues processed: 164 average time/residue: 0.4975 time to fit residues: 88.4472 Evaluate side-chains 153 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 565 ASN A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.157883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.123977 restraints weight = 12278.835| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.36 r_work: 0.3106 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10895 Z= 0.196 Angle : 0.538 7.815 14775 Z= 0.288 Chirality : 0.041 0.159 1655 Planarity : 0.004 0.053 1813 Dihedral : 9.939 150.168 1568 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.69 % Allowed : 22.12 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.23), residues: 1269 helix: 1.54 (0.19), residues: 720 sheet: -0.18 (0.50), residues: 104 loop : -0.78 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 707 TYR 0.016 0.002 TYR A 912 PHE 0.022 0.002 PHE A1313 TRP 0.010 0.001 TRP A 817 HIS 0.005 0.001 HIS A 861 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (10895) covalent geometry : angle 0.53797 / 0.29 (14775) hydrogen bonds : bond 0.04914 / 3.15 ( 580) hydrogen bonds : angle 4.28680 / 3.07 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.353 Fit side-chains REVERT: A 346 ARG cc_start: 0.7593 (ppt90) cc_final: 0.7381 (ptm-80) REVERT: A 761 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7554 (tp30) REVERT: A 778 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: A 833 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7955 (ttt) REVERT: A 873 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7786 (ttt90) REVERT: A 1010 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7959 (mttt) REVERT: A 1287 ASN cc_start: 0.7865 (m110) cc_final: 0.7566 (m-40) REVERT: A 1305 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6348 (pp) REVERT: A 1312 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6703 (mmtt) REVERT: A 1372 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7427 (mt) REVERT: A 1396 MET cc_start: 0.7537 (mtt) cc_final: 0.7168 (mmm) REVERT: A 1538 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5916 (mtm) outliers start: 42 outliers final: 18 residues processed: 156 average time/residue: 0.4853 time to fit residues: 81.9762 Evaluate side-chains 153 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 770 MET Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 124 optimal weight: 9.9990 chunk 35 optimal weight: 0.0070 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.159190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.127637 restraints weight = 12262.010| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.37 r_work: 0.3135 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10895 Z= 0.139 Angle : 0.505 9.311 14775 Z= 0.269 Chirality : 0.039 0.178 1655 Planarity : 0.004 0.056 1813 Dihedral : 9.875 150.789 1568 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.25 % Allowed : 22.21 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1269 helix: 1.69 (0.19), residues: 719 sheet: -0.15 (0.50), residues: 104 loop : -0.68 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 707 TYR 0.016 0.002 TYR A 912 PHE 0.020 0.002 PHE A1313 TRP 0.016 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10895) covalent geometry : angle 0.50498 / 0.27 (14775) hydrogen bonds : bond 0.04359 / 2.78 ( 580) hydrogen bonds : angle 4.18448 / 3.00 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.251 Fit side-chains REVERT: A 346 ARG cc_start: 0.7635 (ppt90) cc_final: 0.7431 (ptm-80) REVERT: A 761 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: A 833 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7868 (ttp) REVERT: A 873 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7735 (ttt90) REVERT: A 1010 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7970 (mttt) REVERT: A 1275 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: A 1287 ASN cc_start: 0.7886 (m110) cc_final: 0.7579 (m-40) REVERT: A 1305 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6320 (pp) REVERT: A 1312 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.7075 (mmmt) REVERT: A 1372 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7431 (mt) REVERT: A 1396 MET cc_start: 0.7557 (mtt) cc_final: 0.7223 (mmm) REVERT: A 1538 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5905 (mtm) outliers start: 37 outliers final: 18 residues processed: 159 average time/residue: 0.5126 time to fit residues: 87.8676 Evaluate side-chains 150 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1227 LEU Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 504 ASN A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.160074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.126193 restraints weight = 12338.781| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.39 r_work: 0.3117 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10895 Z= 0.132 Angle : 0.510 9.815 14775 Z= 0.269 Chirality : 0.038 0.180 1655 Planarity : 0.004 0.059 1813 Dihedral : 9.836 151.310 1568 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.63 % Allowed : 23.00 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1269 helix: 1.78 (0.19), residues: 719 sheet: -0.15 (0.50), residues: 104 loop : -0.65 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 961 TYR 0.017 0.001 TYR A 912 PHE 0.022 0.002 PHE A1467 TRP 0.017 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10895) covalent geometry : angle 0.51009 / 0.27 (14775) hydrogen bonds : bond 0.04183 / 2.66 ( 580) hydrogen bonds : angle 4.14724 / 2.97 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.269 Fit side-chains REVERT: A 363 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: A 761 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7627 (tp30) REVERT: A 778 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: A 833 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7851 (ttp) REVERT: A 873 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7720 (ttt90) REVERT: A 1287 ASN cc_start: 0.7891 (m110) cc_final: 0.7582 (m-40) REVERT: A 1305 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.6217 (pp) REVERT: A 1312 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7125 (mmmt) REVERT: A 1372 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7445 (mt) REVERT: A 1396 MET cc_start: 0.7586 (mtt) cc_final: 0.7208 (mmm) REVERT: A 1538 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5940 (mtm) outliers start: 30 outliers final: 18 residues processed: 146 average time/residue: 0.5061 time to fit residues: 80.0313 Evaluate side-chains 149 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 GLN Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 HIS A1413 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.157129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.123775 restraints weight = 12212.879| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.31 r_work: 0.3103 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10895 Z= 0.221 Angle : 0.577 10.279 14775 Z= 0.307 Chirality : 0.042 0.176 1655 Planarity : 0.005 0.063 1813 Dihedral : 9.954 149.837 1568 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.63 % Allowed : 23.09 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1269 helix: 1.56 (0.19), residues: 714 sheet: -0.13 (0.49), residues: 106 loop : -0.74 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 961 TYR 0.016 0.002 TYR A 912 PHE 0.021 0.002 PHE A1143 TRP 0.012 0.002 TRP A 817 HIS 0.006 0.001 HIS A1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (10895) covalent geometry : angle 0.57683 / 0.31 (14775) hydrogen bonds : bond 0.05121 / 3.29 ( 580) hydrogen bonds : angle 4.33430 / 3.10 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.272 Fit side-chains REVERT: A 761 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7552 (tp30) REVERT: A 778 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 810 ASN cc_start: 0.7235 (m-40) cc_final: 0.6947 (m-40) REVERT: A 833 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8061 (ttt) REVERT: A 873 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7685 (ttt90) REVERT: A 1287 ASN cc_start: 0.7791 (m110) cc_final: 0.7486 (m-40) REVERT: A 1305 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6160 (pp) REVERT: A 1312 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6679 (mmtt) REVERT: A 1335 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7722 (mtmt) REVERT: A 1369 ASP cc_start: 0.7523 (t0) cc_final: 0.7293 (t0) REVERT: A 1372 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 1538 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.5963 (mtm) outliers start: 30 outliers final: 17 residues processed: 150 average time/residue: 0.5213 time to fit residues: 84.5845 Evaluate side-chains 147 residues out of total 1139 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 ARG Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1072 MET Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1312 LYS Chi-restraints excluded: chain A residue 1335 LYS Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1416 VAL Chi-restraints excluded: chain A residue 1454 THR Chi-restraints excluded: chain A residue 1457 THR Chi-restraints excluded: chain A residue 1489 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1593 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 10 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 HIS A1122 GLN A1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.159424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.127144 restraints weight = 12296.361| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.33 r_work: 0.3118 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10895 Z= 0.138 Angle : 0.524 9.840 14775 Z= 0.278 Chirality : 0.039 0.199 1655 Planarity : 0.004 0.059 1813 Dihedral : 9.886 150.768 1568 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.55 % Allowed : 23.44 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1269 helix: 1.68 (0.19), residues: 719 sheet: -0.11 (0.50), residues: 104 loop : -0.66 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 961 TYR 0.015 0.001 TYR A 912 PHE 0.023 0.002 PHE A1467 TRP 0.019 0.001 TRP A 976 HIS 0.004 0.001 HIS A1036 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (10895) covalent geometry : angle 0.52378 / 0.28 (14775) hydrogen bonds : bond 0.04342 / 2.77 ( 580) hydrogen bonds : angle 4.18412 / 3.00 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.68 seconds wall clock time: 59 minutes 13.47 seconds (3553.47 seconds total)