Starting phenix.real_space_refine on Fri Jul 3 02:18:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehw_48069/07_2026/9ehw_48069.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehw_48069/07_2026/9ehw_48069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ehw_48069/07_2026/9ehw_48069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehw_48069/07_2026/9ehw_48069.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ehw_48069/07_2026/9ehw_48069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehw_48069/07_2026/9ehw_48069.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 115 5.49 5 Mg 2 5.21 5 S 22 5.16 5 C 6693 2.51 5 N 1946 2.21 5 O 2412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11190 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 452 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8738 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 28, 'TRANS': 1032} Chain breaks: 6 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1812 Classifications: {'RNA': 86} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 42} Link IDs: {'rna2p': 10, 'rna3p': 75} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.22, per 1000 atoms: 0.20 Number of scatterers: 11190 At special positions: 0 Unit cell: (77.4876, 109.149, 144.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 22 16.00 P 115 15.00 Mg 2 11.99 O 2412 8.00 N 1946 7.00 C 6693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 657 " distance=2.09 Simple disulfide: pdb=" SG CYS A 460 " - pdb=" SG CYS A 814 " distance=1.99 Simple disulfide: pdb=" SG CYS A 657 " - pdb=" SG CYS A 814 " distance=2.05 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 817 " distance=2.02 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: 0.70 Conformation dependent library (CDL) restraints added in 380.4 milliseconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 46.7% alpha, 13.2% beta 45 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 52 through 82 removed outlier: 4.034A pdb=" N LYS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 311 through 324 Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 349 through 362 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.839A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 4.155A pdb=" N LYS A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.554A pdb=" N GLN A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 487 through 495 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 579 through 587 removed outlier: 4.044A pdb=" N ALA A 585 " --> pdb=" O ASP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 649 through 652 Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 860 through 887 removed outlier: 5.341A pdb=" N GLN A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 881 " --> pdb=" O ASN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1110 removed outlier: 4.099A pdb=" N ALA A1096 " --> pdb=" O GLN A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1127 through 1131 Processing helix chain 'A' and resid 1132 through 1144 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 4.110A pdb=" N LEU A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 Processing helix chain 'A' and resid 1282 through 1292 Processing helix chain 'A' and resid 1293 through 1296 removed outlier: 3.540A pdb=" N VAL A1296 " --> pdb=" O LEU A1293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1293 through 1296' Processing helix chain 'A' and resid 1308 through 1319 removed outlier: 3.734A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.776A pdb=" N ASN A1346 " --> pdb=" O ILE A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1350 Processing helix chain 'A' and resid 1355 through 1364 Processing helix chain 'A' and resid 1375 through 1384 Processing helix chain 'A' and resid 1385 through 1388 Processing helix chain 'A' and resid 1398 through 1410 Processing helix chain 'A' and resid 1416 through 1425 Processing helix chain 'A' and resid 1472 through 1476 Processing helix chain 'A' and resid 1536 through 1543 Processing helix chain 'A' and resid 1569 through 1579 Processing helix chain 'A' and resid 1586 through 1594 removed outlier: 3.946A pdb=" N GLU A1592 " --> pdb=" O ASP A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1624 removed outlier: 3.736A pdb=" N MET A1614 " --> pdb=" O THR A1610 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.693A pdb=" N LYS A 4 " --> pdb=" O HIS A 892 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 6.693A pdb=" N LYS A 4 " --> pdb=" O HIS A 892 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 18 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N SER A1220 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY A 38 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS A1222 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL A 40 " --> pdb=" O LYS A1222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 635 removed outlier: 7.518A pdb=" N GLU A 631 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1441 through 1446 removed outlier: 4.621A pdb=" N PHE A1441 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1443 " --> pdb=" O VAL A1371 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.821A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 17.970A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 10.970A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.114A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.716A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1270 through 1272 Processing sheet with id=AA9, first strand: chain 'A' and resid 1276 through 1277 Processing sheet with id=AB1, first strand: chain 'A' and resid 1390 through 1391 Processing sheet with id=AB2, first strand: chain 'A' and resid 1491 through 1496 Processing sheet with id=AB3, first strand: chain 'A' and resid 1531 through 1533 removed outlier: 4.217A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS A1562 " --> pdb=" O ALA A1545 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE A1547 " --> pdb=" O ARG A1560 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG A1560 " --> pdb=" O ILE A1547 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TYR A1549 " --> pdb=" O LYS A1558 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A1558 " --> pdb=" O TYR A1549 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 113 hydrogen bonds 210 hydrogen bond angles 0 basepair planarities 45 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2999 1.34 - 1.46: 3469 1.46 - 1.59: 4941 1.59 - 1.71: 206 1.71 - 1.84: 33 Bond restraints: 11648 Sorted by residual: bond pdb=" C3' DC C 8 " pdb=" C2' DC C 8 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C1' DT D 4 " pdb=" N1 DT D 4 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C3' DG C 3 " pdb=" C2' DG C 3 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC C 7 " pdb=" C2' DC C 7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG D 2 " pdb=" C2' DG D 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.56e+00 ... (remaining 11643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 15973 3.25 - 6.50: 232 6.50 - 9.74: 36 9.74 - 12.99: 7 12.99 - 16.24: 2 Bond angle restraints: 16250 Sorted by residual: angle pdb=" CA GLN A 591 " pdb=" CB GLN A 591 " pdb=" CG GLN A 591 " ideal model delta sigma weight residual 114.10 127.76 -13.66 2.00e+00 2.50e-01 4.67e+01 angle pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sigma weight residual 117.70 124.92 -7.22 1.20e+00 6.94e-01 3.62e+01 angle pdb=" O2 C B 9 " pdb=" C2 C B 9 " pdb=" N3 C B 9 " ideal model delta sigma weight residual 121.90 117.82 4.08 7.00e-01 2.04e+00 3.40e+01 angle pdb=" CB MET A 629 " pdb=" CG MET A 629 " pdb=" SD MET A 629 " ideal model delta sigma weight residual 112.70 128.94 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O4' DT C 9 " pdb=" C1' DT C 9 " pdb=" N1 DT C 9 " ideal model delta sigma weight residual 108.00 111.79 -3.79 7.00e-01 2.04e+00 2.93e+01 ... (remaining 16245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 6570 28.71 - 57.42: 404 57.42 - 86.12: 123 86.12 - 114.83: 4 114.83 - 143.54: 3 Dihedral angle restraints: 7104 sinusoidal: 3952 harmonic: 3152 Sorted by residual: dihedral pdb=" CB CYS A 460 " pdb=" SG CYS A 460 " pdb=" SG CYS A 814 " pdb=" CB CYS A 814 " ideal model delta sinusoidal sigma weight residual -86.00 -6.79 -79.21 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" O4' U B 57 " pdb=" C1' U B 57 " pdb=" N1 U B 57 " pdb=" C2 U B 57 " ideal model delta sinusoidal sigma weight residual 200.00 56.46 143.54 1 1.50e+01 4.44e-03 7.70e+01 dihedral pdb=" O4' U B 66 " pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sinusoidal sigma weight residual 200.00 66.65 133.35 1 1.50e+01 4.44e-03 7.20e+01 ... (remaining 7101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1483 0.070 - 0.141: 299 0.141 - 0.211: 60 0.211 - 0.282: 7 0.282 - 0.352: 2 Chirality restraints: 1851 Sorted by residual: chirality pdb=" C4' G B 90 " pdb=" C5' G B 90 " pdb=" O4' G B 90 " pdb=" C3' G B 90 " both_signs ideal model delta sigma weight residual False -2.50 -2.14 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1' C B 76 " pdb=" O4' C B 76 " pdb=" C2' C B 76 " pdb=" N1 C B 76 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C1' A B 71 " pdb=" O4' A B 71 " pdb=" C2' A B 71 " pdb=" N9 A B 71 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1848 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 8 " -0.043 2.00e-02 2.50e+03 2.34e-02 1.24e+01 pdb=" N1 DC C 8 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DC C 8 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DC C 8 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DC C 8 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC C 8 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC C 8 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC C 8 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC C 8 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 591 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C GLN A 591 " 0.059 2.00e-02 2.50e+03 pdb=" O GLN A 591 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 592 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 46 " -0.038 2.00e-02 2.50e+03 2.27e-02 1.16e+01 pdb=" N1 C B 46 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C B 46 " -0.002 2.00e-02 2.50e+03 pdb=" O2 C B 46 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C B 46 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 46 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 46 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C B 46 " -0.026 2.00e-02 2.50e+03 pdb=" C6 C B 46 " 0.034 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 6462 3.05 - 3.51: 11421 3.51 - 3.97: 19699 3.97 - 4.44: 22979 4.44 - 4.90: 32947 Nonbonded interactions: 93508 Sorted by model distance: nonbonded pdb=" N LYS A 578 " pdb=" N LYS A 579 " model vdw 2.585 2.560 nonbonded pdb=" N1 G B 36 " pdb=" C4 G B 36 " model vdw 2.586 2.672 nonbonded pdb=" N1 G B 62 " pdb=" C4 G B 62 " model vdw 2.590 2.672 nonbonded pdb=" N1 G B 31 " pdb=" C4 G B 31 " model vdw 2.590 2.672 nonbonded pdb=" N1 G B 48 " pdb=" C4 G B 48 " model vdw 2.593 2.672 ... (remaining 93503 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 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.930 Find NCS groups from input model: 0.040 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:8.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 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 : 0.005 0.056 11652 Z= 0.313 Angle : 1.071 21.992 16258 Z= 0.690 Chirality : 0.061 0.352 1851 Planarity : 0.010 0.101 1656 Dihedral : 18.444 143.540 5050 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.94 % Allowed : 13.51 % Favored : 85.55 % Cbeta Deviations : 0.10 % 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: -0.39 (0.24), residues: 1047 helix: -0.57 (0.21), residues: 463 sheet: -0.06 (0.42), residues: 135 loop : 0.30 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.004 ARG A1474 TYR 0.024 0.003 TYR A1329 PHE 0.046 0.002 PHE A1095 TRP 0.022 0.002 TRP A1459 HIS 0.014 0.002 HIS A1177 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.31 (11648) covalent geometry : angle 1.04322 / 0.68 (16250) SS BOND : bond 0.03716 / 3.48 ( 4) SS BOND : angle 11.06728 / 20.02 ( 8) hydrogen bonds : bond 0.13581 / 16.02 ( 499) hydrogen bonds : angle 5.64048 / 7.74 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.361 Fit side-chains REVERT: A 370 LYS cc_start: 0.8771 (tppt) cc_final: 0.8290 (mtpp) REVERT: A 407 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8196 (tp-100) REVERT: A 452 ASN cc_start: 0.8351 (p0) cc_final: 0.8133 (p0) REVERT: A 515 GLU cc_start: 0.8908 (tt0) cc_final: 0.8500 (tt0) REVERT: A 516 TYR cc_start: 0.8679 (m-80) cc_final: 0.7762 (m-80) REVERT: A 521 GLN cc_start: 0.8882 (tp40) cc_final: 0.8525 (tp40) REVERT: A 522 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: A 849 ARG cc_start: 0.9184 (mtp85) cc_final: 0.8750 (mtt90) REVERT: A 1167 MET cc_start: 0.8308 (mtm) cc_final: 0.8003 (mtp) REVERT: A 1171 CYS cc_start: 0.9116 (m) cc_final: 0.8888 (m) REVERT: A 1260 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8486 (mp0) REVERT: A 1274 LYS cc_start: 0.8545 (tmtt) cc_final: 0.8301 (tmtt) REVERT: A 1416 ASP cc_start: 0.8326 (t0) cc_final: 0.7967 (t0) REVERT: A 1442 SER cc_start: 0.9031 (p) cc_final: 0.8689 (t) REVERT: A 1491 GLU cc_start: 0.8355 (tt0) cc_final: 0.7957 (mt-10) REVERT: A 1539 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 1540 ARG cc_start: 0.9018 (mmm160) cc_final: 0.8780 (tpp80) REVERT: A 1544 ILE cc_start: 0.9358 (mt) cc_final: 0.8997 (pp) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 0.5294 time to fit residues: 54.2862 Evaluate side-chains 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1539 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.085448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.065566 restraints weight = 24751.039| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.76 r_work: 0.2795 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 11652 Z= 0.271 Angle : 0.670 14.797 16258 Z= 0.378 Chirality : 0.046 0.305 1851 Planarity : 0.004 0.045 1656 Dihedral : 19.208 148.682 2837 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.41 % Allowed : 11.41 % Favored : 86.18 % 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 (0.25), residues: 1047 helix: 0.63 (0.23), residues: 465 sheet: 0.53 (0.41), residues: 139 loop : 0.48 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 665 TYR 0.013 0.002 TYR A1329 PHE 0.019 0.002 PHE A 75 TRP 0.015 0.002 TRP A 477 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.27 (11648) covalent geometry : angle 0.64707 / 0.37 (16250) SS BOND : bond 0.02427 / 2.45 ( 4) SS BOND : angle 7.79563 / 14.95 ( 8) hydrogen bonds : bond 0.05209 / 5.76 ( 499) hydrogen bonds : angle 4.56449 / 6.33 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.379 Fit side-chains REVERT: A 370 LYS cc_start: 0.8896 (tppt) cc_final: 0.8428 (mtpp) REVERT: A 407 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8310 (tp-100) REVERT: A 515 GLU cc_start: 0.8883 (tt0) cc_final: 0.8526 (tt0) REVERT: A 516 TYR cc_start: 0.8719 (m-80) cc_final: 0.8148 (m-80) REVERT: A 521 GLN cc_start: 0.8922 (tp40) cc_final: 0.8529 (tp40) REVERT: A 849 ARG cc_start: 0.9215 (mtp85) cc_final: 0.8676 (mtt90) REVERT: A 1167 MET cc_start: 0.8350 (mtm) cc_final: 0.7964 (mtp) REVERT: A 1260 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8556 (mp0) REVERT: A 1416 ASP cc_start: 0.8274 (t0) cc_final: 0.7945 (t0) REVERT: A 1442 SER cc_start: 0.9081 (p) cc_final: 0.8730 (t) REVERT: A 1491 GLU cc_start: 0.7993 (tt0) cc_final: 0.7681 (mt-10) REVERT: A 1540 ARG cc_start: 0.9018 (mmm160) cc_final: 0.8778 (tpp80) REVERT: A 1544 ILE cc_start: 0.9395 (mt) cc_final: 0.9042 (pp) REVERT: A 1570 ASP cc_start: 0.8849 (p0) cc_final: 0.8531 (t70) outliers start: 23 outliers final: 6 residues processed: 93 average time/residue: 0.5081 time to fit residues: 51.8018 Evaluate side-chains 74 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1567 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 97 optimal weight: 0.0020 chunk 18 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.087954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067971 restraints weight = 24779.925| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.78 r_work: 0.2843 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11652 Z= 0.123 Angle : 0.552 10.553 16258 Z= 0.319 Chirality : 0.041 0.280 1851 Planarity : 0.004 0.040 1656 Dihedral : 19.043 149.050 2830 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.26 % Allowed : 12.88 % Favored : 85.86 % 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: 1.22 (0.26), residues: 1047 helix: 1.12 (0.24), residues: 467 sheet: 0.77 (0.42), residues: 138 loop : 0.69 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.013 0.001 TYR A1329 PHE 0.017 0.001 PHE A1576 TRP 0.010 0.001 TRP A 477 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (11648) covalent geometry : angle 0.53569 / 0.31 (16250) SS BOND : bond 0.01530 / 1.46 ( 4) SS BOND : angle 5.97472 / 11.93 ( 8) hydrogen bonds : bond 0.04411 / 4.92 ( 499) hydrogen bonds : angle 4.10113 / 5.73 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.355 Fit side-chains REVERT: A 370 LYS cc_start: 0.8855 (tppt) cc_final: 0.8364 (mtpp) REVERT: A 407 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8290 (tp-100) REVERT: A 515 GLU cc_start: 0.8839 (tt0) cc_final: 0.8519 (tt0) REVERT: A 516 TYR cc_start: 0.8721 (m-80) cc_final: 0.8146 (m-80) REVERT: A 521 GLN cc_start: 0.8880 (tp40) cc_final: 0.8482 (tp40) REVERT: A 849 ARG cc_start: 0.9209 (mtp85) cc_final: 0.8973 (mtp85) REVERT: A 1115 ASP cc_start: 0.8709 (m-30) cc_final: 0.8169 (m-30) REVERT: A 1135 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 1260 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8611 (mp0) REVERT: A 1416 ASP cc_start: 0.8248 (t0) cc_final: 0.7863 (t0) REVERT: A 1442 SER cc_start: 0.9076 (p) cc_final: 0.8783 (t) REVERT: A 1491 GLU cc_start: 0.7898 (tt0) cc_final: 0.7603 (mt-10) REVERT: A 1540 ARG cc_start: 0.8987 (mmm160) cc_final: 0.8739 (tpp80) REVERT: A 1544 ILE cc_start: 0.9413 (mt) cc_final: 0.9021 (pp) REVERT: A 1570 ASP cc_start: 0.8839 (p0) cc_final: 0.8504 (t70) REVERT: A 1577 MET cc_start: 0.9297 (tpp) cc_final: 0.9094 (mmt) REVERT: A 1624 ASN cc_start: 0.8122 (p0) cc_final: 0.7864 (p0) outliers start: 12 outliers final: 6 residues processed: 83 average time/residue: 0.5079 time to fit residues: 46.2236 Evaluate side-chains 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1092 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.086282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.066370 restraints weight = 25094.404| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.76 r_work: 0.2833 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11652 Z= 0.148 Angle : 0.538 9.171 16258 Z= 0.310 Chirality : 0.041 0.264 1851 Planarity : 0.003 0.039 1656 Dihedral : 18.954 149.870 2830 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.05 % Allowed : 13.93 % Favored : 85.03 % 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: 1.37 (0.26), residues: 1047 helix: 1.36 (0.24), residues: 464 sheet: 0.78 (0.43), residues: 138 loop : 0.66 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 665 TYR 0.012 0.001 TYR A1329 PHE 0.019 0.001 PHE A1209 TRP 0.009 0.001 TRP A 79 HIS 0.006 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (11648) covalent geometry : angle 0.52431 / 0.30 (16250) SS BOND : bond 0.01507 / 1.48 ( 4) SS BOND : angle 5.41422 / 11.00 ( 8) hydrogen bonds : bond 0.04261 / 4.69 ( 499) hydrogen bonds : angle 3.97256 / 5.57 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8892 (tppt) cc_final: 0.8431 (mtpp) REVERT: A 407 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8329 (tp-100) REVERT: A 515 GLU cc_start: 0.8809 (tt0) cc_final: 0.8458 (tt0) REVERT: A 516 TYR cc_start: 0.8723 (m-80) cc_final: 0.8174 (m-80) REVERT: A 521 GLN cc_start: 0.8919 (tp40) cc_final: 0.8532 (tp40) REVERT: A 1115 ASP cc_start: 0.8720 (m-30) cc_final: 0.8197 (m-30) REVERT: A 1127 ILE cc_start: 0.8781 (mm) cc_final: 0.8507 (pp) REVERT: A 1135 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 1260 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8613 (mp0) REVERT: A 1416 ASP cc_start: 0.8239 (t0) cc_final: 0.7922 (t0) REVERT: A 1442 SER cc_start: 0.9069 (p) cc_final: 0.8793 (t) REVERT: A 1491 GLU cc_start: 0.7926 (tt0) cc_final: 0.7619 (mt-10) REVERT: A 1540 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8736 (tpp80) REVERT: A 1544 ILE cc_start: 0.9404 (mt) cc_final: 0.9146 (pp) REVERT: A 1570 ASP cc_start: 0.8810 (p0) cc_final: 0.8488 (t70) REVERT: A 1577 MET cc_start: 0.9327 (tpp) cc_final: 0.9058 (mmt) outliers start: 10 outliers final: 5 residues processed: 76 average time/residue: 0.5652 time to fit residues: 46.7693 Evaluate side-chains 71 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1133 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 16 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 522 GLN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.067885 restraints weight = 24709.094| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.69 r_work: 0.2850 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11652 Z= 0.127 Angle : 0.516 9.559 16258 Z= 0.298 Chirality : 0.040 0.245 1851 Planarity : 0.003 0.050 1656 Dihedral : 18.920 150.652 2828 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.99 % Allowed : 13.82 % Favored : 84.19 % 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: 1.52 (0.26), residues: 1047 helix: 1.54 (0.24), residues: 463 sheet: 0.87 (0.43), residues: 138 loop : 0.65 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.011 0.001 TYR A1329 PHE 0.020 0.001 PHE A1209 TRP 0.009 0.001 TRP A 79 HIS 0.008 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (11648) covalent geometry : angle 0.50444 / 0.29 (16250) SS BOND : bond 0.01328 / 1.29 ( 4) SS BOND : angle 4.94090 / 10.11 ( 8) hydrogen bonds : bond 0.04080 / 4.47 ( 499) hydrogen bonds : angle 3.83503 / 5.37 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8889 (tppt) cc_final: 0.8442 (mtpp) REVERT: A 407 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8370 (tp-100) REVERT: A 515 GLU cc_start: 0.8767 (tt0) cc_final: 0.8419 (tt0) REVERT: A 516 TYR cc_start: 0.8680 (m-80) cc_final: 0.8121 (m-80) REVERT: A 521 GLN cc_start: 0.8879 (tp40) cc_final: 0.8472 (tp40) REVERT: A 522 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: A 596 GLN cc_start: 0.8480 (pm20) cc_final: 0.7984 (pp30) REVERT: A 1115 ASP cc_start: 0.8722 (m-30) cc_final: 0.8215 (m-30) REVERT: A 1127 ILE cc_start: 0.8767 (mm) cc_final: 0.8524 (pp) REVERT: A 1416 ASP cc_start: 0.8213 (t0) cc_final: 0.7977 (t0) REVERT: A 1419 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8797 (mm-30) REVERT: A 1442 SER cc_start: 0.9049 (p) cc_final: 0.8844 (t) REVERT: A 1491 GLU cc_start: 0.7921 (tt0) cc_final: 0.7608 (mt-10) REVERT: A 1544 ILE cc_start: 0.9416 (mt) cc_final: 0.9144 (pp) REVERT: A 1570 ASP cc_start: 0.8755 (p0) cc_final: 0.8464 (t70) REVERT: A 1577 MET cc_start: 0.9341 (tpp) cc_final: 0.9088 (mmt) outliers start: 19 outliers final: 6 residues processed: 89 average time/residue: 0.5126 time to fit residues: 49.9104 Evaluate side-chains 71 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 112 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.087653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.067757 restraints weight = 24763.956| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.77 r_work: 0.2846 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11652 Z= 0.129 Angle : 0.524 10.234 16258 Z= 0.301 Chirality : 0.040 0.232 1851 Planarity : 0.003 0.048 1656 Dihedral : 18.904 151.071 2828 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.94 % Allowed : 15.92 % Favored : 83.14 % 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: 1.57 (0.26), residues: 1047 helix: 1.62 (0.24), residues: 463 sheet: 0.90 (0.43), residues: 138 loop : 0.62 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 665 TYR 0.010 0.001 TYR A1329 PHE 0.015 0.001 PHE A1209 TRP 0.009 0.001 TRP A 79 HIS 0.007 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (11648) covalent geometry : angle 0.51379 / 0.30 (16250) SS BOND : bond 0.01287 / 1.24 ( 4) SS BOND : angle 4.72653 / 9.72 ( 8) hydrogen bonds : bond 0.04032 / 4.41 ( 499) hydrogen bonds : angle 3.77903 / 5.30 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8874 (tppt) cc_final: 0.8409 (mtpp) REVERT: A 407 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8338 (tp-100) REVERT: A 515 GLU cc_start: 0.8775 (tt0) cc_final: 0.8416 (tt0) REVERT: A 516 TYR cc_start: 0.8671 (m-80) cc_final: 0.8075 (m-80) REVERT: A 521 GLN cc_start: 0.8713 (tp40) cc_final: 0.8231 (tp40) REVERT: A 579 LYS cc_start: 0.9093 (tmtt) cc_final: 0.8852 (tptt) REVERT: A 596 GLN cc_start: 0.8489 (pm20) cc_final: 0.7984 (pp30) REVERT: A 1115 ASP cc_start: 0.8767 (m-30) cc_final: 0.8252 (m-30) REVERT: A 1127 ILE cc_start: 0.8699 (mm) cc_final: 0.8401 (pp) REVERT: A 1135 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 1416 ASP cc_start: 0.8184 (t0) cc_final: 0.7842 (t0) REVERT: A 1442 SER cc_start: 0.9093 (p) cc_final: 0.8856 (t) REVERT: A 1491 GLU cc_start: 0.7907 (tt0) cc_final: 0.7593 (mt-10) REVERT: A 1544 ILE cc_start: 0.9430 (mt) cc_final: 0.9157 (pp) REVERT: A 1570 ASP cc_start: 0.8782 (p0) cc_final: 0.8500 (t70) REVERT: A 1577 MET cc_start: 0.9298 (tpp) cc_final: 0.9039 (mmt) outliers start: 9 outliers final: 9 residues processed: 71 average time/residue: 0.4824 time to fit residues: 37.7857 Evaluate side-chains 70 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 660 LYS Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1567 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 327 ASN A 522 GLN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.066429 restraints weight = 24718.721| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.74 r_work: 0.2815 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11652 Z= 0.174 Angle : 0.541 11.281 16258 Z= 0.306 Chirality : 0.041 0.229 1851 Planarity : 0.003 0.052 1656 Dihedral : 18.921 151.263 2828 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.88 % Allowed : 15.18 % Favored : 82.93 % 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: 1.52 (0.26), residues: 1047 helix: 1.58 (0.24), residues: 470 sheet: 0.92 (0.43), residues: 138 loop : 0.55 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 32 TYR 0.014 0.001 TYR A 24 PHE 0.018 0.001 PHE A1095 TRP 0.008 0.001 TRP A 477 HIS 0.005 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (11648) covalent geometry : angle 0.53083 / 0.30 (16250) SS BOND : bond 0.01406 / 1.37 ( 4) SS BOND : angle 4.74639 / 9.74 ( 8) hydrogen bonds : bond 0.04248 / 4.63 ( 499) hydrogen bonds : angle 3.82147 / 5.36 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8885 (tppt) cc_final: 0.8420 (mtpp) REVERT: A 407 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8364 (tp-100) REVERT: A 515 GLU cc_start: 0.8784 (tt0) cc_final: 0.8493 (tt0) REVERT: A 516 TYR cc_start: 0.8671 (m-80) cc_final: 0.8194 (m-80) REVERT: A 521 GLN cc_start: 0.8870 (tp40) cc_final: 0.8459 (tp40) REVERT: A 579 LYS cc_start: 0.9069 (tmtt) cc_final: 0.8814 (tptt) REVERT: A 596 GLN cc_start: 0.8490 (pm20) cc_final: 0.7980 (pp30) REVERT: A 1115 ASP cc_start: 0.8777 (m-30) cc_final: 0.8250 (m-30) REVERT: A 1127 ILE cc_start: 0.8659 (mm) cc_final: 0.8384 (pp) REVERT: A 1135 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7482 (mm-30) REVERT: A 1358 MET cc_start: 0.8709 (tpp) cc_final: 0.7967 (ttp) REVERT: A 1416 ASP cc_start: 0.8199 (t0) cc_final: 0.7855 (t0) REVERT: A 1442 SER cc_start: 0.9109 (p) cc_final: 0.8865 (t) REVERT: A 1491 GLU cc_start: 0.7928 (tt0) cc_final: 0.7600 (mt-10) REVERT: A 1544 ILE cc_start: 0.9442 (mt) cc_final: 0.9126 (pp) REVERT: A 1570 ASP cc_start: 0.8787 (p0) cc_final: 0.8513 (t70) REVERT: A 1577 MET cc_start: 0.9288 (tpp) cc_final: 0.8983 (mmt) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.4642 time to fit residues: 39.5136 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1598 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 69 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.087010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.067195 restraints weight = 24589.894| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.75 r_work: 0.2833 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11652 Z= 0.129 Angle : 0.522 12.045 16258 Z= 0.296 Chirality : 0.039 0.229 1851 Planarity : 0.003 0.058 1656 Dihedral : 18.959 151.455 2828 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.88 % Allowed : 15.18 % Favored : 82.93 % 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: 1.57 (0.26), residues: 1047 helix: 1.65 (0.24), residues: 470 sheet: 0.91 (0.43), residues: 138 loop : 0.56 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 665 TYR 0.010 0.001 TYR A1329 PHE 0.012 0.001 PHE A1420 TRP 0.009 0.001 TRP A 79 HIS 0.005 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11648) covalent geometry : angle 0.51219 / 0.29 (16250) SS BOND : bond 0.01275 / 1.23 ( 4) SS BOND : angle 4.56697 / 9.39 ( 8) hydrogen bonds : bond 0.04077 / 4.46 ( 499) hydrogen bonds : angle 3.75951 / 5.26 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8873 (tppt) cc_final: 0.8406 (mtpp) REVERT: A 407 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8366 (tp-100) REVERT: A 515 GLU cc_start: 0.8774 (tt0) cc_final: 0.8464 (tt0) REVERT: A 516 TYR cc_start: 0.8667 (m-80) cc_final: 0.8111 (m-80) REVERT: A 521 GLN cc_start: 0.8902 (tp40) cc_final: 0.8546 (tp40) REVERT: A 522 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: A 596 GLN cc_start: 0.8452 (pm20) cc_final: 0.7945 (pp30) REVERT: A 1115 ASP cc_start: 0.8785 (m-30) cc_final: 0.8259 (m-30) REVERT: A 1127 ILE cc_start: 0.8629 (mm) cc_final: 0.8357 (pp) REVERT: A 1135 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 1416 ASP cc_start: 0.8194 (t0) cc_final: 0.7873 (t0) REVERT: A 1442 SER cc_start: 0.9098 (p) cc_final: 0.8867 (t) REVERT: A 1491 GLU cc_start: 0.7930 (tt0) cc_final: 0.7604 (mt-10) REVERT: A 1544 ILE cc_start: 0.9449 (mt) cc_final: 0.9125 (pp) REVERT: A 1570 ASP cc_start: 0.8755 (p0) cc_final: 0.8493 (t70) REVERT: A 1577 MET cc_start: 0.9276 (tpp) cc_final: 0.8971 (mmt) outliers start: 18 outliers final: 11 residues processed: 82 average time/residue: 0.4613 time to fit residues: 41.9867 Evaluate side-chains 75 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1598 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.0870 chunk 93 optimal weight: 0.0370 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.065260 restraints weight = 24762.501| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.75 r_work: 0.2810 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8855 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11652 Z= 0.190 Angle : 0.550 11.247 16258 Z= 0.309 Chirality : 0.041 0.227 1851 Planarity : 0.003 0.048 1656 Dihedral : 18.972 151.433 2828 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.88 % Allowed : 15.60 % Favored : 82.51 % 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: 1.54 (0.26), residues: 1047 helix: 1.63 (0.24), residues: 470 sheet: 0.91 (0.43), residues: 138 loop : 0.53 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 32 TYR 0.011 0.001 TYR A1329 PHE 0.018 0.001 PHE A1095 TRP 0.008 0.001 TRP A 79 HIS 0.007 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (11648) covalent geometry : angle 0.54039 / 0.30 (16250) SS BOND : bond 0.01432 / 1.35 ( 4) SS BOND : angle 4.67495 / 9.61 ( 8) hydrogen bonds : bond 0.04249 / 4.65 ( 499) hydrogen bonds : angle 3.82216 / 5.33 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8899 (tppt) cc_final: 0.8522 (ttpp) REVERT: A 407 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8387 (tp-100) REVERT: A 515 GLU cc_start: 0.8767 (tt0) cc_final: 0.8446 (tt0) REVERT: A 516 TYR cc_start: 0.8659 (m-80) cc_final: 0.8158 (m-80) REVERT: A 521 GLN cc_start: 0.8954 (tp40) cc_final: 0.8614 (tp40) REVERT: A 522 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: A 579 LYS cc_start: 0.9024 (tptm) cc_final: 0.8597 (tptt) REVERT: A 596 GLN cc_start: 0.8469 (pm20) cc_final: 0.7957 (pp30) REVERT: A 1115 ASP cc_start: 0.8755 (m-30) cc_final: 0.8264 (m-30) REVERT: A 1127 ILE cc_start: 0.8658 (mm) cc_final: 0.8402 (pp) REVERT: A 1135 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 1304 ILE cc_start: 0.9171 (tp) cc_final: 0.8911 (pp) REVERT: A 1358 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8228 (ttp) REVERT: A 1416 ASP cc_start: 0.8204 (t0) cc_final: 0.7894 (t0) REVERT: A 1442 SER cc_start: 0.9104 (p) cc_final: 0.8879 (t) REVERT: A 1491 GLU cc_start: 0.7931 (tt0) cc_final: 0.7602 (mt-10) REVERT: A 1544 ILE cc_start: 0.9470 (mt) cc_final: 0.9149 (pp) REVERT: A 1570 ASP cc_start: 0.8734 (p0) cc_final: 0.8524 (t70) REVERT: A 1577 MET cc_start: 0.9293 (tpp) cc_final: 0.8998 (mmt) outliers start: 18 outliers final: 13 residues processed: 79 average time/residue: 0.4595 time to fit residues: 40.2078 Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1358 MET Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1598 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.065378 restraints weight = 25146.463| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.74 r_work: 0.2816 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11652 Z= 0.158 Angle : 0.542 13.423 16258 Z= 0.304 Chirality : 0.040 0.227 1851 Planarity : 0.003 0.052 1656 Dihedral : 18.991 151.493 2828 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.47 % Allowed : 16.13 % Favored : 82.41 % 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: 1.56 (0.26), residues: 1047 helix: 1.65 (0.24), residues: 470 sheet: 0.93 (0.43), residues: 138 loop : 0.54 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 32 TYR 0.011 0.001 TYR A1329 PHE 0.012 0.001 PHE A1576 TRP 0.008 0.001 TRP A 79 HIS 0.009 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (11648) covalent geometry : angle 0.53239 / 0.30 (16250) SS BOND : bond 0.01348 / 1.27 ( 4) SS BOND : angle 4.61526 / 9.44 ( 8) hydrogen bonds : bond 0.04187 / 4.59 ( 499) hydrogen bonds : angle 3.80063 / 5.30 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8900 (tppt) cc_final: 0.8531 (ttpp) REVERT: A 407 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8393 (tp-100) REVERT: A 515 GLU cc_start: 0.8767 (tt0) cc_final: 0.8449 (tt0) REVERT: A 516 TYR cc_start: 0.8659 (m-80) cc_final: 0.8162 (m-80) REVERT: A 521 GLN cc_start: 0.8957 (tp40) cc_final: 0.8607 (tp40) REVERT: A 522 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: A 579 LYS cc_start: 0.9002 (tptm) cc_final: 0.8520 (tptt) REVERT: A 596 GLN cc_start: 0.8449 (pm20) cc_final: 0.7954 (pp30) REVERT: A 1115 ASP cc_start: 0.8740 (m-30) cc_final: 0.8239 (m-30) REVERT: A 1127 ILE cc_start: 0.8659 (mm) cc_final: 0.8404 (pp) REVERT: A 1135 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7532 (mm-30) REVERT: A 1141 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8174 (mp0) REVERT: A 1304 ILE cc_start: 0.9177 (tp) cc_final: 0.8918 (pp) REVERT: A 1358 MET cc_start: 0.8713 (tpp) cc_final: 0.8194 (ttp) REVERT: A 1416 ASP cc_start: 0.8210 (t0) cc_final: 0.7902 (t0) REVERT: A 1442 SER cc_start: 0.9097 (p) cc_final: 0.8881 (t) REVERT: A 1491 GLU cc_start: 0.7945 (tt0) cc_final: 0.7618 (mt-10) REVERT: A 1544 ILE cc_start: 0.9468 (mt) cc_final: 0.9147 (pp) REVERT: A 1577 MET cc_start: 0.9286 (tpp) cc_final: 0.8989 (mmt) outliers start: 14 outliers final: 11 residues processed: 77 average time/residue: 0.4842 time to fit residues: 41.2530 Evaluate side-chains 77 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 486 LYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 814 CYS Chi-restraints excluded: chain A residue 1102 ASN Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1307 SER Chi-restraints excluded: chain A residue 1458 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 40 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 68 optimal weight: 0.0170 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 522 GLN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.086582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.066745 restraints weight = 24945.325| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.75 r_work: 0.2845 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11652 Z= 0.111 Angle : 0.522 14.215 16258 Z= 0.294 Chirality : 0.039 0.227 1851 Planarity : 0.003 0.050 1656 Dihedral : 18.995 151.711 2828 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.15 % Allowed : 16.44 % Favored : 82.41 % 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: 1.64 (0.26), residues: 1047 helix: 1.73 (0.24), residues: 470 sheet: 0.94 (0.43), residues: 138 loop : 0.58 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 32 TYR 0.010 0.001 TYR A 614 PHE 0.020 0.001 PHE A1095 TRP 0.009 0.001 TRP A 79 HIS 0.006 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (11648) covalent geometry : angle 0.51302 / 0.29 (16250) SS BOND : bond 0.01145 / 1.08 ( 4) SS BOND : angle 4.41838 / 9.01 ( 8) hydrogen bonds : bond 0.03969 / 4.36 ( 499) hydrogen bonds : angle 3.72202 / 5.19 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.93 seconds wall clock time: 47 minutes 20.67 seconds (2840.67 seconds total)