Starting phenix.real_space_refine on Sat May 2 23:51:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vrd_65284/05_2026/9vrd_65284.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vrd_65284/05_2026/9vrd_65284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vrd_65284/05_2026/9vrd_65284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vrd_65284/05_2026/9vrd_65284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vrd_65284/05_2026/9vrd_65284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vrd_65284/05_2026/9vrd_65284.map" } resolution = 3.03 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= 0.015 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 6 5.49 5 S 52 5.16 5 C 5738 2.51 5 N 1503 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8938 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 8902 Classifications: {'peptide': 1136} Link IDs: {'PTRANS': 45, 'TRANS': 1090} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 8938 At special positions: 0 Unit cell: (78.28, 112.888, 139.256, 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 52 16.00 P 6 15.00 O 1639 8.00 N 1503 7.00 C 5738 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: 0.92 Conformation dependent library (CDL) restraints added in 343.0 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 71.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.953A pdb=" N ALA A 234 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.564A pdb=" N VAL A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 270 through 289 removed outlier: 3.619A pdb=" N ARG A 289 " --> pdb=" O GLN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.668A pdb=" N GLY A 338 " --> pdb=" O ASP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 392 removed outlier: 3.523A pdb=" N ILE A 348 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 400 removed outlier: 3.762A pdb=" N SER A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.727A pdb=" N MET A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.601A pdb=" N PHE A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 448 through 494 removed outlier: 3.787A pdb=" N VAL A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Proline residue: A 465 - end of helix removed outlier: 3.627A pdb=" N GLU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 503 through 554 removed outlier: 3.843A pdb=" N LYS A 520 " --> pdb=" O ASN A 516 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TRP A 521 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Proline residue: A 540 - end of helix Processing helix chain 'A' and resid 559 through 579 removed outlier: 4.371A pdb=" N ARG A 571 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Proline residue: A 576 - end of helix removed outlier: 3.913A pdb=" N ASN A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 602 Processing helix chain 'A' and resid 664 through 673 removed outlier: 4.213A pdb=" N ILE A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.706A pdb=" N ARG A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 732 Processing helix chain 'A' and resid 735 through 738 removed outlier: 3.679A pdb=" N GLN A 738 " --> pdb=" O TYR A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 735 through 738' Processing helix chain 'A' and resid 749 through 765 removed outlier: 3.592A pdb=" N GLN A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 926 through 935 removed outlier: 4.017A pdb=" N TYR A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 940 Processing helix chain 'A' and resid 941 through 968 removed outlier: 3.689A pdb=" N LEU A 945 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 956 " --> pdb=" O MET A 952 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN A 968 " --> pdb=" O MET A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1025 Processing helix chain 'A' and resid 1028 through 1035 removed outlier: 3.592A pdb=" N PHE A1032 " --> pdb=" O PRO A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1054 removed outlier: 3.837A pdb=" N ILE A1040 " --> pdb=" O PRO A1036 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A1047 " --> pdb=" O ARG A1043 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1080 removed outlier: 4.038A pdb=" N VAL A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A1080 " --> pdb=" O MET A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1116 removed outlier: 4.064A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1088 " --> pdb=" O LEU A1084 " (cutoff:3.500A) Proline residue: A1089 - end of helix removed outlier: 3.720A pdb=" N ALA A1103 " --> pdb=" O ARG A1099 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER A1104 " --> pdb=" O TYR A1100 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A1110 " --> pdb=" O ARG A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1129 Processing helix chain 'A' and resid 1129 through 1137 Processing helix chain 'A' and resid 1138 through 1188 Proline residue: A1156 - end of helix Processing helix chain 'A' and resid 1195 through 1207 Processing helix chain 'A' and resid 1208 through 1227 Processing helix chain 'A' and resid 1227 through 1236 Processing helix chain 'A' and resid 1303 through 1310 removed outlier: 4.346A pdb=" N GLN A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1330 No H-bonds generated for 'chain 'A' and resid 1328 through 1330' Processing helix chain 'A' and resid 1331 through 1337 Processing helix chain 'A' and resid 1353 through 1358 Processing helix chain 'A' and resid 1364 through 1375 Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1386 through 1389 Processing helix chain 'A' and resid 1393 through 1397 Processing helix chain 'A' and resid 1400 through 1416 removed outlier: 3.722A pdb=" N LYS A1415 " --> pdb=" O ARG A1411 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A1416 " --> pdb=" O ALA A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1445 Processing helix chain 'A' and resid 1456 through 1462 removed outlier: 3.536A pdb=" N ASP A1462 " --> pdb=" O PRO A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1486 removed outlier: 3.544A pdb=" N LEU A1483 " --> pdb=" O THR A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1497 removed outlier: 3.529A pdb=" N GLN A1493 " --> pdb=" O SER A1489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 646 through 648 removed outlier: 4.019A pdb=" N LEU A 646 " --> pdb=" O ILE A 625 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 623 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN A 624 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 683 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 681 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.529A pdb=" N TYR A 769 " --> pdb=" O ILE A 801 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 700 through 701 Processing sheet with id=AA4, first strand: chain 'A' and resid 1285 through 1286 removed outlier: 4.433A pdb=" N LEU A1267 " --> pdb=" O GLY A1317 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY A1317 " --> pdb=" O LEU A1267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1340 through 1342 removed outlier: 6.842A pdb=" N SER A1340 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASP A1423 " --> pdb=" O SER A1340 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A1342 " --> pdb=" O ASP A1423 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A1420 " --> pdb=" O CYS A1451 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A1453 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A1422 " --> pdb=" O ILE A1453 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A1478 " --> pdb=" O VAL A1466 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A1476 " --> pdb=" O VAL A1468 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER A1470 " --> pdb=" O ILE A1474 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A1474 " --> pdb=" O SER A1470 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1351 through 1352 567 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2851 1.34 - 1.46: 1943 1.46 - 1.58: 4232 1.58 - 1.70: 6 1.70 - 1.81: 85 Bond restraints: 9117 Sorted by residual: bond pdb=" O15 IHP A1601 " pdb=" P5 IHP A1601 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O13 IHP A1601 " pdb=" P3 IHP A1601 " ideal model delta sigma weight residual 1.669 1.605 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O12 IHP A1601 " pdb=" P2 IHP A1601 " ideal model delta sigma weight residual 1.675 1.611 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O16 IHP A1601 " pdb=" P6 IHP A1601 " ideal model delta sigma weight residual 1.672 1.609 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O14 IHP A1601 " pdb=" P4 IHP A1601 " ideal model delta sigma weight residual 1.671 1.610 0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 9112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12013 1.77 - 3.53: 283 3.53 - 5.30: 72 5.30 - 7.07: 4 7.07 - 8.83: 4 Bond angle restraints: 12376 Sorted by residual: angle pdb=" C SER A1254 " pdb=" CA SER A1254 " pdb=" CB SER A1254 " ideal model delta sigma weight residual 115.79 111.59 4.20 1.19e+00 7.06e-01 1.25e+01 angle pdb=" C TRP A1256 " pdb=" N PRO A1257 " pdb=" CA PRO A1257 " ideal model delta sigma weight residual 121.65 118.29 3.36 1.01e+00 9.80e-01 1.10e+01 angle pdb=" CB GLN A1344 " pdb=" CG GLN A1344 " pdb=" CD GLN A1344 " ideal model delta sigma weight residual 112.60 117.58 -4.98 1.70e+00 3.46e-01 8.56e+00 angle pdb=" CB LEU A1086 " pdb=" CG LEU A1086 " pdb=" CD2 LEU A1086 " ideal model delta sigma weight residual 110.70 119.47 -8.77 3.00e+00 1.11e-01 8.55e+00 angle pdb=" N ARG A1215 " pdb=" CA ARG A1215 " pdb=" C ARG A1215 " ideal model delta sigma weight residual 111.07 108.12 2.95 1.07e+00 8.73e-01 7.62e+00 ... (remaining 12371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 5038 23.68 - 47.37: 413 47.37 - 71.05: 47 71.05 - 94.74: 7 94.74 - 118.42: 12 Dihedral angle restraints: 5517 sinusoidal: 2213 harmonic: 3304 Sorted by residual: dihedral pdb=" C4 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" C3 IHP A1601 " pdb=" O12 IHP A1601 " ideal model delta sinusoidal sigma weight residual 60.90 179.32 -118.42 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C6 IHP A1601 " pdb=" C1 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" O12 IHP A1601 " ideal model delta sinusoidal sigma weight residual 61.05 179.32 -118.27 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" O15 IHP A1601 " pdb=" C5 IHP A1601 " pdb=" C6 IHP A1601 " pdb=" O16 IHP A1601 " ideal model delta sinusoidal sigma weight residual 54.28 -62.62 116.90 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 1438 0.997 - 1.994: 0 1.994 - 2.991: 0 2.991 - 3.987: 0 3.987 - 4.984: 4 Chirality restraints: 1442 Sorted by residual: chirality pdb=" C2 IHP A1601 " pdb=" C1 IHP A1601 " pdb=" C3 IHP A1601 " pdb=" O12 IHP A1601 " both_signs ideal model delta sigma weight residual False -2.52 2.47 -4.98 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" C5 IHP A1601 " pdb=" C4 IHP A1601 " pdb=" C6 IHP A1601 " pdb=" O15 IHP A1601 " both_signs ideal model delta sigma weight residual False -2.42 2.51 -4.92 2.00e-01 2.50e+01 6.06e+02 chirality pdb=" C3 IHP A1601 " pdb=" C2 IHP A1601 " pdb=" C4 IHP A1601 " pdb=" O13 IHP A1601 " both_signs ideal model delta sigma weight residual False -2.34 2.50 -4.84 2.00e-01 2.50e+01 5.86e+02 ... (remaining 1439 not shown) Planarity restraints: 1541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 325 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO A 326 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1181 " 0.010 2.00e-02 2.50e+03 1.28e-02 2.89e+00 pdb=" CG PHE A1181 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE A1181 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A1181 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A1181 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1181 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A1181 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 734 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" CD GLN A 734 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLN A 734 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 734 " -0.009 2.00e-02 2.50e+03 ... (remaining 1538 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 4080 2.94 - 3.43: 9787 3.43 - 3.92: 14458 3.92 - 4.41: 16672 4.41 - 4.90: 26735 Nonbonded interactions: 71732 Sorted by model distance: nonbonded pdb=" O VAL A1073 " pdb=" OG SER A1077 " model vdw 2.451 3.040 nonbonded pdb=" OG1 THR A 452 " pdb=" OG1 THR A 547 " model vdw 2.471 3.040 nonbonded pdb=" O SER A1030 " pdb=" OD1 ASP A1033 " model vdw 2.515 3.040 nonbonded pdb=" O ASP A1471 " pdb=" OD1 ASP A1471 " model vdw 2.530 3.040 nonbonded pdb=" O THR A1080 " pdb=" OG1 THR A1080 " model vdw 2.530 3.040 ... (remaining 71727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 0.064 9117 Z= 0.198 Angle : 0.693 8.834 12376 Z= 0.359 Chirality : 0.260 4.984 1442 Planarity : 0.004 0.057 1541 Dihedral : 17.532 118.420 3381 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.82 % Allowed : 22.29 % Favored : 76.89 % 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: 1.46 (0.26), residues: 1130 helix: 1.24 (0.19), residues: 751 sheet: -1.07 (0.73), residues: 42 loop : 0.94 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 653 TYR 0.015 0.001 TYR A 331 PHE 0.029 0.002 PHE A1181 TRP 0.010 0.001 TRP A1096 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9117) covalent geometry : angle 0.69350 (12376) hydrogen bonds : bond 0.15501 ( 567) hydrogen bonds : angle 6.23692 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8636 (tpp) cc_final: 0.8165 (tmm) REVERT: A 420 TYR cc_start: 0.8679 (t80) cc_final: 0.8467 (t80) REVERT: A 424 PHE cc_start: 0.8473 (t80) cc_final: 0.8244 (t80) REVERT: A 466 VAL cc_start: 0.9013 (p) cc_final: 0.8748 (m) REVERT: A 478 MET cc_start: 0.7464 (tpp) cc_final: 0.7174 (mtm) REVERT: A 652 MET cc_start: 0.6883 (ppp) cc_final: 0.6536 (tmm) REVERT: A 718 LYS cc_start: 0.9486 (tttt) cc_final: 0.9078 (mmtp) REVERT: A 719 ARG cc_start: 0.8852 (mmm160) cc_final: 0.8002 (mmm160) REVERT: A 722 GLU cc_start: 0.9131 (tt0) cc_final: 0.8856 (tm-30) REVERT: A 733 LEU cc_start: 0.8842 (mt) cc_final: 0.8509 (mt) REVERT: A 738 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7583 (pt0) REVERT: A 934 MET cc_start: 0.8298 (mtt) cc_final: 0.7273 (ptt) REVERT: A 1096 TRP cc_start: 0.6663 (t60) cc_final: 0.6450 (t60) REVERT: A 1423 ASP cc_start: 0.7723 (t70) cc_final: 0.7322 (t70) REVERT: A 1482 ARG cc_start: 0.9056 (mtp85) cc_final: 0.8718 (ttm110) outliers start: 8 outliers final: 7 residues processed: 147 average time/residue: 0.0890 time to fit residues: 18.6570 Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 630 PHE Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1291 LYS Chi-restraints excluded: chain A residue 1333 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN A 574 GLN A1333 HIS A1344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.104309 restraints weight = 16721.565| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.41 r_work: 0.3410 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 9117 Z= 0.277 Angle : 0.683 10.127 12376 Z= 0.338 Chirality : 0.045 0.286 1442 Planarity : 0.004 0.051 1541 Dihedral : 6.039 53.889 1290 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.09 % Allowed : 18.61 % Favored : 77.30 % 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: 1.69 (0.25), residues: 1130 helix: 1.45 (0.19), residues: 767 sheet: -0.45 (0.62), residues: 68 loop : 0.92 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 484 TYR 0.020 0.002 TYR A1205 PHE 0.028 0.002 PHE A 304 TRP 0.014 0.002 TRP A1166 HIS 0.004 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 9117) covalent geometry : angle 0.68335 (12376) hydrogen bonds : bond 0.05307 ( 567) hydrogen bonds : angle 4.50095 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8029 (tp30) REVERT: A 718 LYS cc_start: 0.9528 (tttt) cc_final: 0.8988 (mtpp) REVERT: A 719 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8189 (mmm160) REVERT: A 722 GLU cc_start: 0.9082 (tt0) cc_final: 0.8867 (tm-30) REVERT: A 738 GLN cc_start: 0.8425 (mm-40) cc_final: 0.7641 (pt0) REVERT: A 934 MET cc_start: 0.8666 (mtt) cc_final: 0.7326 (ppp) REVERT: A 1107 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7882 (mp0) REVERT: A 1194 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7572 (pp) REVERT: A 1350 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7984 (mm-30) REVERT: A 1476 GLU cc_start: 0.7357 (mp0) cc_final: 0.7107 (pm20) outliers start: 40 outliers final: 24 residues processed: 174 average time/residue: 0.0748 time to fit residues: 19.2280 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 803 VAL Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1023 CYS Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1291 LYS Chi-restraints excluded: chain A residue 1344 GLN Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 701 ASN ** A1344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.150268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107644 restraints weight = 16506.489| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.37 r_work: 0.3452 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9117 Z= 0.133 Angle : 0.535 8.195 12376 Z= 0.269 Chirality : 0.039 0.134 1442 Planarity : 0.004 0.042 1541 Dihedral : 5.311 57.052 1284 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.66 % Allowed : 19.84 % Favored : 77.51 % 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: 2.27 (0.25), residues: 1130 helix: 1.98 (0.19), residues: 761 sheet: -0.56 (0.67), residues: 58 loop : 0.92 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 653 TYR 0.012 0.001 TYR A1148 PHE 0.011 0.001 PHE A 304 TRP 0.017 0.001 TRP A1166 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9117) covalent geometry : angle 0.53485 (12376) hydrogen bonds : bond 0.04374 ( 567) hydrogen bonds : angle 4.06912 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8805 (tpp) cc_final: 0.8239 (tmm) REVERT: A 405 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8034 (tp30) REVERT: A 652 MET cc_start: 0.6824 (tmm) cc_final: 0.6397 (tmm) REVERT: A 718 LYS cc_start: 0.9540 (tttt) cc_final: 0.8998 (mtpp) REVERT: A 719 ARG cc_start: 0.8977 (mmm160) cc_final: 0.8288 (mmm160) REVERT: A 722 GLU cc_start: 0.9111 (tt0) cc_final: 0.8868 (tm-30) REVERT: A 738 GLN cc_start: 0.8300 (mm-40) cc_final: 0.7690 (pt0) REVERT: A 934 MET cc_start: 0.8570 (mtt) cc_final: 0.7319 (ppp) REVERT: A 1107 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7967 (mp0) REVERT: A 1194 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7726 (pp) REVERT: A 1266 ASP cc_start: 0.9021 (m-30) cc_final: 0.8535 (t0) REVERT: A 1350 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7931 (mm-30) REVERT: A 1471 ASP cc_start: 0.7745 (t0) cc_final: 0.7539 (t0) REVERT: A 1476 GLU cc_start: 0.7326 (mp0) cc_final: 0.7017 (pm20) outliers start: 26 outliers final: 13 residues processed: 148 average time/residue: 0.0876 time to fit residues: 18.6322 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1352 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1068 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.148537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105121 restraints weight = 16737.002| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.40 r_work: 0.3400 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9117 Z= 0.186 Angle : 0.572 9.408 12376 Z= 0.285 Chirality : 0.041 0.148 1442 Planarity : 0.004 0.038 1541 Dihedral : 5.133 55.407 1280 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.27 % Allowed : 20.14 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.24 (0.25), residues: 1130 helix: 1.91 (0.19), residues: 766 sheet: -0.46 (0.70), residues: 56 loop : 1.00 (0.37), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1482 TYR 0.016 0.001 TYR A1205 PHE 0.021 0.002 PHE A1179 TRP 0.017 0.001 TRP A1166 HIS 0.003 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 9117) covalent geometry : angle 0.57219 (12376) hydrogen bonds : bond 0.04519 ( 567) hydrogen bonds : angle 4.06065 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8168 (tp30) REVERT: A 718 LYS cc_start: 0.9550 (tttt) cc_final: 0.9021 (mtpp) REVERT: A 719 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8380 (mmm160) REVERT: A 722 GLU cc_start: 0.9145 (tt0) cc_final: 0.8876 (tm-30) REVERT: A 738 GLN cc_start: 0.8426 (mm-40) cc_final: 0.7818 (pt0) REVERT: A 1107 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8027 (mp0) REVERT: A 1194 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7950 (pp) REVERT: A 1266 ASP cc_start: 0.9119 (m-30) cc_final: 0.8639 (t0) REVERT: A 1471 ASP cc_start: 0.7803 (t0) cc_final: 0.7565 (t0) outliers start: 32 outliers final: 18 residues processed: 154 average time/residue: 0.0841 time to fit residues: 18.5654 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1182 CYS Chi-restraints excluded: chain A residue 1194 ILE Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.144429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.100082 restraints weight = 16595.239| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.42 r_work: 0.3318 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9117 Z= 0.291 Angle : 0.656 9.022 12376 Z= 0.329 Chirality : 0.044 0.179 1442 Planarity : 0.004 0.044 1541 Dihedral : 5.286 52.278 1278 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.60 % Allowed : 18.81 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.25), residues: 1130 helix: 1.60 (0.19), residues: 766 sheet: -0.47 (0.70), residues: 56 loop : 0.96 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 523 TYR 0.022 0.002 TYR A1205 PHE 0.029 0.002 PHE A 304 TRP 0.016 0.002 TRP A1166 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00690 ( 9117) covalent geometry : angle 0.65646 (12376) hydrogen bonds : bond 0.05102 ( 567) hydrogen bonds : angle 4.34802 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.8867 (tpp) cc_final: 0.8343 (tmm) REVERT: A 359 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8664 (mp) REVERT: A 405 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8211 (tp30) REVERT: A 652 MET cc_start: 0.7175 (tmm) cc_final: 0.6861 (tmm) REVERT: A 718 LYS cc_start: 0.9581 (tttt) cc_final: 0.9081 (mmtp) REVERT: A 719 ARG cc_start: 0.9048 (mmm160) cc_final: 0.8692 (mmm160) REVERT: A 738 GLN cc_start: 0.8458 (mm-40) cc_final: 0.7842 (pt0) REVERT: A 1266 ASP cc_start: 0.9177 (m-30) cc_final: 0.8720 (t0) REVERT: A 1471 ASP cc_start: 0.7907 (t0) cc_final: 0.7688 (t0) outliers start: 45 outliers final: 26 residues processed: 155 average time/residue: 0.0841 time to fit residues: 18.6101 Evaluate side-chains 134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 VAL Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1012 THR Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1092 VAL Chi-restraints excluded: chain A residue 1109 THR Chi-restraints excluded: chain A residue 1182 CYS Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1448 CYS Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 705 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.148727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105215 restraints weight = 16464.087| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.41 r_work: 0.3395 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9117 Z= 0.123 Angle : 0.549 9.009 12376 Z= 0.272 Chirality : 0.040 0.143 1442 Planarity : 0.003 0.036 1541 Dihedral : 4.975 49.656 1278 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.04 % Allowed : 21.68 % Favored : 76.28 % 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: 2.36 (0.26), residues: 1130 helix: 2.00 (0.19), residues: 763 sheet: -0.36 (0.70), residues: 56 loop : 1.04 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1482 TYR 0.010 0.001 TYR A 507 PHE 0.011 0.001 PHE A1445 TRP 0.019 0.001 TRP A1166 HIS 0.001 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9117) covalent geometry : angle 0.54902 (12376) hydrogen bonds : bond 0.04156 ( 567) hydrogen bonds : angle 3.99706 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8588 (mp) REVERT: A 405 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8202 (tp30) REVERT: A 539 SER cc_start: 0.9250 (m) cc_final: 0.9025 (m) REVERT: A 652 MET cc_start: 0.7006 (tmm) cc_final: 0.6744 (tmm) REVERT: A 718 LYS cc_start: 0.9495 (tttt) cc_final: 0.9087 (mmtp) REVERT: A 738 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7742 (pt0) REVERT: A 934 MET cc_start: 0.8695 (mtt) cc_final: 0.7371 (ppp) REVERT: A 1042 ASN cc_start: 0.8999 (m-40) cc_final: 0.8713 (t0) REVERT: A 1266 ASP cc_start: 0.9155 (m-30) cc_final: 0.8716 (t0) REVERT: A 1471 ASP cc_start: 0.7834 (t0) cc_final: 0.7612 (t0) outliers start: 20 outliers final: 15 residues processed: 145 average time/residue: 0.0911 time to fit residues: 18.6151 Evaluate side-chains 136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.0050 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105660 restraints weight = 16460.336| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.37 r_work: 0.3388 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9117 Z= 0.122 Angle : 0.552 8.116 12376 Z= 0.271 Chirality : 0.040 0.139 1442 Planarity : 0.003 0.035 1541 Dihedral : 4.769 45.597 1278 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.35 % Allowed : 22.49 % 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: 2.44 (0.25), residues: 1130 helix: 2.10 (0.19), residues: 763 sheet: -0.17 (0.70), residues: 56 loop : 0.92 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 719 TYR 0.009 0.001 TYR A1100 PHE 0.009 0.001 PHE A1057 TRP 0.018 0.001 TRP A1166 HIS 0.002 0.000 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9117) covalent geometry : angle 0.55231 (12376) hydrogen bonds : bond 0.03971 ( 567) hydrogen bonds : angle 3.90698 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 405 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8189 (tp30) REVERT: A 482 ASP cc_start: 0.8352 (p0) cc_final: 0.8140 (p0) REVERT: A 539 SER cc_start: 0.9266 (m) cc_final: 0.9038 (m) REVERT: A 595 ASP cc_start: 0.8727 (t0) cc_final: 0.8454 (t0) REVERT: A 798 LYS cc_start: 0.8252 (mmtp) cc_final: 0.7667 (mttm) REVERT: A 934 MET cc_start: 0.8703 (mtt) cc_final: 0.7332 (ppp) REVERT: A 1042 ASN cc_start: 0.8975 (m-40) cc_final: 0.8714 (t0) REVERT: A 1107 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8009 (mp0) REVERT: A 1183 MET cc_start: 0.8710 (tpp) cc_final: 0.8395 (tpp) REVERT: A 1266 ASP cc_start: 0.9167 (m-30) cc_final: 0.8734 (t0) REVERT: A 1471 ASP cc_start: 0.7843 (t0) cc_final: 0.7617 (t0) outliers start: 23 outliers final: 18 residues processed: 145 average time/residue: 0.0790 time to fit residues: 16.7943 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1448 CYS Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1344 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.147181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.104049 restraints weight = 16370.040| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.34 r_work: 0.3378 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9117 Z= 0.183 Angle : 0.603 10.418 12376 Z= 0.294 Chirality : 0.041 0.152 1442 Planarity : 0.004 0.037 1541 Dihedral : 4.592 41.433 1275 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 23.42 % Favored : 74.34 % 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: 2.33 (0.25), residues: 1130 helix: 1.98 (0.19), residues: 767 sheet: -0.22 (0.70), residues: 56 loop : 0.97 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 719 TYR 0.022 0.002 TYR A1148 PHE 0.029 0.002 PHE A 992 TRP 0.024 0.001 TRP A 962 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 9117) covalent geometry : angle 0.60317 (12376) hydrogen bonds : bond 0.04368 ( 567) hydrogen bonds : angle 4.02691 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 MET cc_start: 0.9153 (tpp) cc_final: 0.8520 (tmm) REVERT: A 359 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8694 (mp) REVERT: A 405 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8250 (tp30) REVERT: A 539 SER cc_start: 0.9258 (m) cc_final: 0.9026 (m) REVERT: A 715 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8447 (pp30) REVERT: A 738 GLN cc_start: 0.8312 (mm-40) cc_final: 0.7645 (pt0) REVERT: A 798 LYS cc_start: 0.8211 (mmtp) cc_final: 0.7568 (mttm) REVERT: A 1042 ASN cc_start: 0.8984 (m-40) cc_final: 0.8742 (t0) REVERT: A 1266 ASP cc_start: 0.9182 (m-30) cc_final: 0.8755 (t0) REVERT: A 1471 ASP cc_start: 0.7912 (t0) cc_final: 0.7689 (t0) outliers start: 22 outliers final: 18 residues processed: 139 average time/residue: 0.0803 time to fit residues: 16.3952 Evaluate side-chains 140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1083 VAL Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1448 CYS Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 0.0270 chunk 9 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.150371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107616 restraints weight = 16435.518| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.39 r_work: 0.3445 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9117 Z= 0.111 Angle : 0.564 10.808 12376 Z= 0.273 Chirality : 0.039 0.148 1442 Planarity : 0.003 0.037 1541 Dihedral : 4.386 41.793 1275 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.84 % Allowed : 23.93 % Favored : 74.23 % 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: 2.55 (0.26), residues: 1130 helix: 2.21 (0.19), residues: 761 sheet: -0.17 (0.70), residues: 56 loop : 0.89 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 578 TYR 0.014 0.001 TYR A 933 PHE 0.027 0.001 PHE A 992 TRP 0.026 0.001 TRP A 962 HIS 0.001 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9117) covalent geometry : angle 0.56364 (12376) hydrogen bonds : bond 0.03750 ( 567) hydrogen bonds : angle 3.84776 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8194 (tp30) REVERT: A 482 ASP cc_start: 0.8349 (p0) cc_final: 0.8107 (p0) REVERT: A 539 SER cc_start: 0.9259 (m) cc_final: 0.9036 (m) REVERT: A 587 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 595 ASP cc_start: 0.8768 (t0) cc_final: 0.8550 (t0) REVERT: A 704 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8901 (mt-10) REVERT: A 715 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8499 (pp30) REVERT: A 718 LYS cc_start: 0.9520 (tttt) cc_final: 0.8998 (mtpp) REVERT: A 738 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7495 (pt0) REVERT: A 1042 ASN cc_start: 0.8939 (m-40) cc_final: 0.8729 (t0) REVERT: A 1183 MET cc_start: 0.8669 (tpp) cc_final: 0.8434 (tpp) REVERT: A 1266 ASP cc_start: 0.9181 (m-30) cc_final: 0.8753 (t0) REVERT: A 1471 ASP cc_start: 0.7810 (t0) cc_final: 0.7577 (t0) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.0767 time to fit residues: 16.0930 Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 8 optimal weight: 0.0570 chunk 108 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.150518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.107933 restraints weight = 16394.738| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.34 r_work: 0.3440 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9117 Z= 0.116 Angle : 0.582 16.629 12376 Z= 0.277 Chirality : 0.039 0.148 1442 Planarity : 0.003 0.041 1541 Dihedral : 4.253 40.410 1275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.53 % Allowed : 24.03 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.52 (0.26), residues: 1130 helix: 2.19 (0.19), residues: 764 sheet: -0.15 (0.71), residues: 56 loop : 0.84 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 719 TYR 0.009 0.001 TYR A1100 PHE 0.028 0.001 PHE A 992 TRP 0.029 0.001 TRP A 962 HIS 0.001 0.000 HIS A1333 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9117) covalent geometry : angle 0.58179 (12376) hydrogen bonds : bond 0.03745 ( 567) hydrogen bonds : angle 3.84876 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8176 (tp30) REVERT: A 482 ASP cc_start: 0.8323 (p0) cc_final: 0.8080 (p0) REVERT: A 539 SER cc_start: 0.9266 (m) cc_final: 0.9039 (m) REVERT: A 587 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 704 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8925 (mt-10) REVERT: A 715 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8518 (pp30) REVERT: A 718 LYS cc_start: 0.9520 (tttt) cc_final: 0.8997 (mtpp) REVERT: A 738 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7488 (pt0) REVERT: A 1042 ASN cc_start: 0.8902 (m-40) cc_final: 0.8673 (t0) REVERT: A 1183 MET cc_start: 0.8671 (tpp) cc_final: 0.8413 (tpp) REVERT: A 1266 ASP cc_start: 0.9190 (m-30) cc_final: 0.8749 (t0) REVERT: A 1471 ASP cc_start: 0.7802 (t0) cc_final: 0.7569 (t0) REVERT: A 1482 ARG cc_start: 0.9132 (mtp85) cc_final: 0.8859 (ttm110) REVERT: A 1492 MET cc_start: 0.8267 (mmm) cc_final: 0.8024 (mmm) outliers start: 15 outliers final: 14 residues processed: 133 average time/residue: 0.0784 time to fit residues: 15.4824 Evaluate side-chains 137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 538 SER Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1236 TYR Chi-restraints excluded: chain A residue 1265 VAL Chi-restraints excluded: chain A residue 1304 THR Chi-restraints excluded: chain A residue 1333 HIS Chi-restraints excluded: chain A residue 1352 THR Chi-restraints excluded: chain A residue 1449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 26 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107624 restraints weight = 16252.095| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.35 r_work: 0.3446 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9117 Z= 0.115 Angle : 0.585 16.353 12376 Z= 0.278 Chirality : 0.040 0.146 1442 Planarity : 0.003 0.041 1541 Dihedral : 4.127 40.023 1275 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.64 % Allowed : 24.34 % Favored : 74.03 % 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: 2.54 (0.26), residues: 1130 helix: 2.19 (0.19), residues: 767 sheet: -0.12 (0.71), residues: 56 loop : 0.89 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 578 TYR 0.024 0.001 TYR A1148 PHE 0.028 0.001 PHE A 992 TRP 0.033 0.001 TRP A 962 HIS 0.001 0.000 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9117) covalent geometry : angle 0.58461 (12376) hydrogen bonds : bond 0.03686 ( 567) hydrogen bonds : angle 3.81979 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3026.07 seconds wall clock time: 52 minutes 21.30 seconds (3141.30 seconds total)