Starting phenix.real_space_refine on Thu Jun 12 03:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9b_39072/06_2025/8y9b_39072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9b_39072/06_2025/8y9b_39072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y9b_39072/06_2025/8y9b_39072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9b_39072/06_2025/8y9b_39072.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9b_39072/06_2025/8y9b_39072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9b_39072/06_2025/8y9b_39072.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.109 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 Zn 1 6.06 5 S 36 5.16 5 C 8528 2.51 5 N 2115 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13380 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 12910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1607, 12910 Classifications: {'peptide': 1607} Link IDs: {'PTRANS': 35, 'TRANS': 1571} Chain breaks: 4 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 469 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 63} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'ARG%COO:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5669 SG CYS B 698 42.702 76.196 133.701 1.00 30.81 S Time building chain proxies: 8.53, per 1000 atoms: 0.64 Number of scatterers: 13380 At special positions: 0 Unit cell: (111.961, 108.7, 178.268, 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) Zn 1 29.99 S 36 16.00 O 2700 8.00 N 2115 7.00 C 8528 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: 3.30 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B2401 " pdb="ZN ZN B2401 " - pdb=" SG CYS B 698 " pdb="ZN ZN B2401 " - pdb=" NE2 HIS B 757 " pdb="ZN ZN B2401 " - pdb=" ND1 HIS B 653 " 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 18 sheets defined 41.3% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 41 through 63 Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.653A pdb=" N ASN B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 137 through 157 Processing helix chain 'B' and resid 167 through 197 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.603A pdb=" N SER B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.964A pdb=" N LEU B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 281 removed outlier: 3.838A pdb=" N ILE B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 325 removed outlier: 3.818A pdb=" N LEU B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 removed outlier: 3.957A pdb=" N MET B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'B' and resid 355 through 359 Processing helix chain 'B' and resid 393 through 420 removed outlier: 3.759A pdb=" N SER B 413 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Proline residue: B 416 - end of helix removed outlier: 3.586A pdb=" N GLU B 420 " --> pdb=" O PRO B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 438 Processing helix chain 'B' and resid 443 through 453 removed outlier: 3.649A pdb=" N MET B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 removed outlier: 3.790A pdb=" N ASN B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 484 removed outlier: 3.743A pdb=" N TYR B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 502 No H-bonds generated for 'chain 'B' and resid 500 through 502' Processing helix chain 'B' and resid 504 through 508 removed outlier: 3.884A pdb=" N ILE B 508 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 519 Processing helix chain 'B' and resid 523 through 539 Processing helix chain 'B' and resid 558 through 569 Processing helix chain 'B' and resid 587 through 601 removed outlier: 4.161A pdb=" N THR B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 641 removed outlier: 3.531A pdb=" N SER B 641 " --> pdb=" O SER B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 683 Processing helix chain 'B' and resid 706 through 709 Processing helix chain 'B' and resid 710 through 727 removed outlier: 5.140A pdb=" N ASP B 721 " --> pdb=" O LEU B 717 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS B 722 " --> pdb=" O LYS B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 774 Processing helix chain 'B' and resid 793 through 808 Processing helix chain 'B' and resid 814 through 838 Processing helix chain 'B' and resid 849 through 876 removed outlier: 3.598A pdb=" N ASN B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 936 removed outlier: 3.580A pdb=" N GLU B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 930 " --> pdb=" O THR B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 971 Processing helix chain 'B' and resid 980 through 995 Processing helix chain 'B' and resid 1003 through 1016 Processing helix chain 'B' and resid 1370 through 1374 Processing helix chain 'B' and resid 1432 through 1439 removed outlier: 3.718A pdb=" N LEU B1436 " --> pdb=" O GLU B1432 " (cutoff:3.500A) Processing helix chain 'B' and resid 1439 through 1450 Processing helix chain 'B' and resid 1558 through 1573 removed outlier: 3.566A pdb=" N GLY B1573 " --> pdb=" O MET B1569 " (cutoff:3.500A) Processing helix chain 'B' and resid 1580 through 1587 Processing helix chain 'B' and resid 1650 through 1652 No H-bonds generated for 'chain 'B' and resid 1650 through 1652' Processing helix chain 'B' and resid 1679 through 1682 Processing helix chain 'B' and resid 1684 through 1688 Processing helix chain 'B' and resid 1773 through 1779 Processing helix chain 'B' and resid 1791 through 1799 Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 39 through 57 Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'B' and resid 237 through 239 removed outlier: 6.566A pdb=" N LEU B 98 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE B 130 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE B 100 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL B 101 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLN B 385 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N LYS B 374 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 605 through 609 removed outlier: 6.034A pdb=" N ILE B 578 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR B 649 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR B 580 " --> pdb=" O THR B 649 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE B 651 " --> pdb=" O TYR B 580 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 582 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N HIS B 653 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS B 698 " --> pdb=" O GLY B 652 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 735 " --> pdb=" O PHE B 780 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE B 780 " --> pdb=" O ILE B 735 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 617 through 622 Processing sheet with id=AA5, first strand: chain 'B' and resid 744 through 746 Processing sheet with id=AA6, first strand: chain 'B' and resid 882 through 892 removed outlier: 10.061A pdb=" N PHE B 886 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 11.402A pdb=" N ILE B 901 " --> pdb=" O PHE B 886 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP B 888 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 899 " --> pdb=" O ASP B 888 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 937 through 940 removed outlier: 4.873A pdb=" N VAL B 945 " --> pdb=" O ASP B 938 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1313 through 1317 removed outlier: 6.693A pdb=" N TYR B1314 " --> pdb=" O ASN B1335 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU B1337 " --> pdb=" O TYR B1314 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE B1316 " --> pdb=" O GLU B1337 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE B1334 " --> pdb=" O ASN B1390 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N SER B1392 " --> pdb=" O ILE B1334 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B1336 " --> pdb=" O SER B1392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1323 through 1326 removed outlier: 6.382A pdb=" N TYR B1323 " --> pdb=" O ILE B1345 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP B1347 " --> pdb=" O TYR B1323 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU B1325 " --> pdb=" O ASP B1347 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP B1344 " --> pdb=" O PHE B1401 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B1403 " --> pdb=" O TRP B1344 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B1412 " --> pdb=" O ILE B1408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1459 through 1465 Processing sheet with id=AB2, first strand: chain 'B' and resid 1514 through 1521 removed outlier: 5.265A pdb=" N ASP B1515 " --> pdb=" O TYR B1530 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N TYR B1530 " --> pdb=" O ASP B1515 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASN B1525 " --> pdb=" O LEU B1544 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU B1544 " --> pdb=" O ASN B1525 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B1554 " --> pdb=" O SER B1541 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B1543 " --> pdb=" O LEU B1552 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B1552 " --> pdb=" O THR B1543 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN B1545 " --> pdb=" O ILE B1550 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B1550 " --> pdb=" O GLN B1545 " (cutoff:3.500A) removed outlier: 15.843A pdb=" N THR B1549 " --> pdb=" O ASP B1607 " (cutoff:3.500A) removed outlier: 16.279A pdb=" N ASN B1609 " --> pdb=" O THR B1549 " (cutoff:3.500A) removed outlier: 12.225A pdb=" N LYS B1551 " --> pdb=" O ASN B1609 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N ILE B1611 " --> pdb=" O LYS B1551 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B1553 " --> pdb=" O ILE B1611 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N SER B1613 " --> pdb=" O ASN B1553 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B1555 " --> pdb=" O SER B1613 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N THR B1615 " --> pdb=" O VAL B1555 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B1557 " --> pdb=" O THR B1615 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N PHE B1610 " --> pdb=" O CYS B1625 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B1625 " --> pdb=" O PHE B1610 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN B1620 " --> pdb=" O ILE B1636 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B1636 " --> pdb=" O GLN B1620 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLU B1622 " --> pdb=" O TYR B1634 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR B1648 " --> pdb=" O ASN B1654 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN B1654 " --> pdb=" O TYR B1648 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N MET B1655 " --> pdb=" O VAL B1692 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1673 through 1677 removed outlier: 6.376A pdb=" N ILE B1674 " --> pdb=" O ASN B1703 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR B1705 " --> pdb=" O ILE B1674 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B1676 " --> pdb=" O THR B1705 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B1702 " --> pdb=" O ASN B1732 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1814 through 1818 Processing sheet with id=AB5, first strand: chain 'B' and resid 1834 through 1837 Processing sheet with id=AB6, first strand: chain 'B' and resid 1855 through 1859 removed outlier: 3.834A pdb=" N ALA B1873 " --> pdb=" O ASN B1867 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1877 through 1880 Processing sheet with id=AB8, first strand: chain 'B' and resid 1897 through 1901 Processing sheet with id=AB9, first strand: chain 'A' and resid 22 through 27 removed outlier: 6.921A pdb=" N PHE A 31 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N GLN A 63 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 33 " --> pdb=" O GLN A 63 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ARG A 65 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1860 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: 6.43 Time building geometry restraints manager: 3.94 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: 4359 1.34 - 1.46: 2405 1.46 - 1.57: 6781 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 13610 Sorted by residual: bond pdb=" CB VAL B1692 " pdb=" CG2 VAL B1692 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" CG GLU B 85 " pdb=" CD GLU B 85 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.29e+00 bond pdb=" CG1 ILE B1656 " pdb=" CD1 ILE B1656 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.28e-01 bond pdb=" CG1 ILE B1750 " pdb=" CD1 ILE B1750 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.48e-01 bond pdb=" CB VAL B1790 " pdb=" CG1 VAL B1790 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.71e-01 ... (remaining 13605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18097 1.73 - 3.47: 274 3.47 - 5.20: 27 5.20 - 6.94: 4 6.94 - 8.67: 1 Bond angle restraints: 18403 Sorted by residual: angle pdb=" N TYR B 453 " pdb=" CA TYR B 453 " pdb=" C TYR B 453 " ideal model delta sigma weight residual 111.33 115.86 -4.53 1.21e+00 6.83e-01 1.40e+01 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " ideal model delta sigma weight residual 110.16 115.11 -4.95 1.48e+00 4.57e-01 1.12e+01 angle pdb=" C ARG B 445 " pdb=" N PHE B 446 " pdb=" CA PHE B 446 " ideal model delta sigma weight residual 120.38 124.17 -3.79 1.37e+00 5.33e-01 7.66e+00 angle pdb=" N VAL B1348 " pdb=" CA VAL B1348 " pdb=" C VAL B1348 " ideal model delta sigma weight residual 111.88 109.07 2.81 1.06e+00 8.90e-01 7.04e+00 angle pdb=" C ASP B 120 " pdb=" N VAL B 121 " pdb=" CA VAL B 121 " ideal model delta sigma weight residual 121.35 117.20 4.15 1.58e+00 4.01e-01 6.89e+00 ... (remaining 18398 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7488 17.64 - 35.27: 598 35.27 - 52.91: 113 52.91 - 70.55: 18 70.55 - 88.18: 15 Dihedral angle restraints: 8232 sinusoidal: 3295 harmonic: 4937 Sorted by residual: dihedral pdb=" CA ASP B1534 " pdb=" C ASP B1534 " pdb=" N ASP B1535 " pdb=" CA ASP B1535 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " pdb=" CG ASP B 109 " pdb=" OD1 ASP B 109 " ideal model delta sinusoidal sigma weight residual -30.00 -88.47 58.47 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA THR B 935 " pdb=" C THR B 935 " pdb=" N ILE B 936 " pdb=" CA ILE B 936 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 8229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1279 0.035 - 0.070: 561 0.070 - 0.105: 155 0.105 - 0.140: 83 0.140 - 0.175: 8 Chirality restraints: 2086 Sorted by residual: chirality pdb=" CG LEU B1488 " pdb=" CB LEU B1488 " pdb=" CD1 LEU B1488 " pdb=" CD2 LEU B1488 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ILE B1656 " pdb=" N ILE B1656 " pdb=" C ILE B1656 " pdb=" CB ILE B1656 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA TYR B 407 " pdb=" N TYR B 407 " pdb=" C TYR B 407 " pdb=" CB TYR B 407 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 2083 not shown) Planarity restraints: 2377 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1847 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO B1848 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B1848 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B1848 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 255 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C TYR B 255 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR B 255 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU B 256 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 92 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO B 93 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.022 5.00e-02 4.00e+02 ... (remaining 2374 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 125 2.64 - 3.21: 11971 3.21 - 3.77: 19300 3.77 - 4.34: 27738 4.34 - 4.90: 47154 Nonbonded interactions: 106288 Sorted by model distance: nonbonded pdb=" OD1 ASP B 546 " pdb="ZN ZN B2401 " model vdw 2.077 2.230 nonbonded pdb=" OH TYR B1508 " pdb=" O ASP B1546 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU B 32 " pdb=" ND2 ASN B 36 " model vdw 2.261 3.120 nonbonded pdb=" NE2 GLN B1457 " pdb=" O ASN B1459 " model vdw 2.277 3.120 nonbonded pdb=" OD2 ASP B1349 " pdb=" NZ LYS B1364 " model vdw 2.282 3.120 ... (remaining 106283 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: 3.270 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 39.470 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.041 13613 Z= 0.178 Angle : 0.542 8.674 18403 Z= 0.303 Chirality : 0.046 0.175 2086 Planarity : 0.003 0.043 2377 Dihedral : 13.743 88.181 5042 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.21), residues: 1660 helix: 1.58 (0.21), residues: 623 sheet: -0.04 (0.27), residues: 365 loop : -0.62 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 118 HIS 0.003 0.001 HIS B 35 PHE 0.020 0.002 PHE B1484 TYR 0.020 0.002 TYR B1645 ARG 0.005 0.001 ARG B 262 Details of bonding type rmsd hydrogen bonds : bond 0.13544 ( 656) hydrogen bonds : angle 5.81298 ( 1860) metal coordination : bond 0.00448 ( 3) covalent geometry : bond 0.00428 (13610) covalent geometry : angle 0.54183 (18403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.421 Fit side-chains REVERT: B 494 ILE cc_start: 0.8841 (mm) cc_final: 0.8601 (mm) REVERT: B 1517 LYS cc_start: 0.7162 (mtpt) cc_final: 0.6882 (ttmm) REVERT: B 1840 ASP cc_start: 0.7577 (t0) cc_final: 0.7284 (t0) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2454 time to fit residues: 65.8766 Evaluate side-chains 133 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 150 optimal weight: 6.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN B 763 ASN ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.135963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.108779 restraints weight = 17253.544| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.84 r_work: 0.3024 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13613 Z= 0.199 Angle : 0.537 6.406 18403 Z= 0.294 Chirality : 0.046 0.149 2086 Planarity : 0.004 0.044 2377 Dihedral : 4.461 26.421 1781 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.79 % Allowed : 7.05 % Favored : 92.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.20), residues: 1660 helix: 1.77 (0.21), residues: 629 sheet: -0.15 (0.27), residues: 365 loop : -0.59 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 118 HIS 0.003 0.001 HIS B 99 PHE 0.022 0.002 PHE A 12 TYR 0.020 0.002 TYR B1645 ARG 0.003 0.000 ARG B1652 Details of bonding type rmsd hydrogen bonds : bond 0.05496 ( 656) hydrogen bonds : angle 4.86626 ( 1860) metal coordination : bond 0.00547 ( 3) covalent geometry : bond 0.00491 (13610) covalent geometry : angle 0.53737 (18403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 2.078 Fit side-chains REVERT: B 85 GLU cc_start: 0.7602 (mp0) cc_final: 0.6812 (mp0) REVERT: B 494 ILE cc_start: 0.8712 (mm) cc_final: 0.8474 (mm) REVERT: B 1517 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7327 (ttmm) REVERT: B 1840 ASP cc_start: 0.8108 (t0) cc_final: 0.7739 (t0) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.3260 time to fit residues: 73.0386 Evaluate side-chains 139 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1374 THR Chi-restraints excluded: chain B residue 1429 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 234 GLN ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109466 restraints weight = 17335.049| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.82 r_work: 0.3032 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13613 Z= 0.152 Angle : 0.482 5.296 18403 Z= 0.265 Chirality : 0.044 0.142 2086 Planarity : 0.003 0.043 2377 Dihedral : 4.285 24.979 1781 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.19 % Allowed : 8.70 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1660 helix: 1.93 (0.20), residues: 628 sheet: -0.21 (0.27), residues: 369 loop : -0.53 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.001 HIS B 35 PHE 0.015 0.001 PHE A 12 TYR 0.016 0.001 TYR B1645 ARG 0.003 0.000 ARG B1652 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 656) hydrogen bonds : angle 4.66221 ( 1860) metal coordination : bond 0.00409 ( 3) covalent geometry : bond 0.00369 (13610) covalent geometry : angle 0.48180 (18403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.478 Fit side-chains REVERT: B 32 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: B 85 GLU cc_start: 0.7558 (mp0) cc_final: 0.7018 (mp0) REVERT: B 494 ILE cc_start: 0.8689 (mm) cc_final: 0.8407 (mm) REVERT: B 1409 LEU cc_start: 0.6898 (tp) cc_final: 0.6672 (tp) REVERT: B 1517 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7269 (ttmm) REVERT: B 1840 ASP cc_start: 0.8039 (t0) cc_final: 0.7647 (t0) outliers start: 18 outliers final: 14 residues processed: 155 average time/residue: 0.2340 time to fit residues: 55.9459 Evaluate side-chains 152 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1374 THR Chi-restraints excluded: chain B residue 1429 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 135 optimal weight: 0.0060 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.0030 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1850 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114927 restraints weight = 17185.732| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.75 r_work: 0.3110 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13613 Z= 0.084 Angle : 0.409 5.399 18403 Z= 0.227 Chirality : 0.042 0.143 2086 Planarity : 0.003 0.040 2377 Dihedral : 3.832 20.813 1781 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.99 % Allowed : 10.68 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.21), residues: 1660 helix: 2.30 (0.21), residues: 632 sheet: -0.06 (0.27), residues: 369 loop : -0.31 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 11 HIS 0.001 0.000 HIS B 334 PHE 0.021 0.001 PHE B1464 TYR 0.012 0.001 TYR B1645 ARG 0.002 0.000 ARG B1652 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 656) hydrogen bonds : angle 4.30885 ( 1860) metal coordination : bond 0.00140 ( 3) covalent geometry : bond 0.00173 (13610) covalent geometry : angle 0.40930 (18403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 181 ASP cc_start: 0.8373 (m-30) cc_final: 0.8086 (m-30) REVERT: B 494 ILE cc_start: 0.8675 (mm) cc_final: 0.8374 (mm) REVERT: B 592 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8000 (mm-30) REVERT: B 927 GLU cc_start: 0.8231 (pp20) cc_final: 0.7940 (pp20) REVERT: B 1517 LYS cc_start: 0.7516 (mtpt) cc_final: 0.7191 (ttmm) REVERT: B 1550 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7829 (mp) REVERT: B 1840 ASP cc_start: 0.8010 (t0) cc_final: 0.7661 (t0) outliers start: 15 outliers final: 10 residues processed: 165 average time/residue: 0.2915 time to fit residues: 74.3753 Evaluate side-chains 147 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 1436 LEU Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 70 optimal weight: 0.0770 chunk 161 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 694 ASN ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1839 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110424 restraints weight = 17285.413| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.88 r_work: 0.3031 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13613 Z= 0.148 Angle : 0.477 10.377 18403 Z= 0.260 Chirality : 0.044 0.147 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.088 18.507 1781 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.38 % Allowed : 11.67 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.21), residues: 1660 helix: 2.17 (0.21), residues: 633 sheet: -0.12 (0.27), residues: 369 loop : -0.40 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.003 0.001 HIS B 35 PHE 0.019 0.001 PHE A 55 TYR 0.016 0.001 TYR B1645 ARG 0.002 0.000 ARG B1652 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 656) hydrogen bonds : angle 4.49099 ( 1860) metal coordination : bond 0.00379 ( 3) covalent geometry : bond 0.00359 (13610) covalent geometry : angle 0.47715 (18403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.559 Fit side-chains REVERT: B 32 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7948 (tt0) REVERT: B 347 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: B 455 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8628 (ptm160) REVERT: B 494 ILE cc_start: 0.8692 (mm) cc_final: 0.8345 (mm) REVERT: B 927 GLU cc_start: 0.8293 (pp20) cc_final: 0.8002 (pp20) REVERT: B 1517 LYS cc_start: 0.7542 (mtpt) cc_final: 0.7253 (ttmm) REVERT: B 1840 ASP cc_start: 0.8071 (t0) cc_final: 0.7667 (t0) outliers start: 21 outliers final: 15 residues processed: 153 average time/residue: 0.3422 time to fit residues: 80.4905 Evaluate side-chains 153 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1488 LEU Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 0.0770 chunk 158 optimal weight: 0.0570 chunk 107 optimal weight: 6.9990 chunk 42 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 966 GLN ** B1444 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 = 0.3569 r_free = 0.3569 target = 0.141713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.115804 restraints weight = 17288.364| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.73 r_work: 0.3104 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13613 Z= 0.084 Angle : 0.418 8.913 18403 Z= 0.229 Chirality : 0.042 0.136 2086 Planarity : 0.003 0.039 2377 Dihedral : 3.761 15.761 1781 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.12 % Allowed : 12.06 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1660 helix: 2.44 (0.21), residues: 633 sheet: -0.10 (0.27), residues: 370 loop : -0.25 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 11 HIS 0.001 0.000 HIS B 35 PHE 0.023 0.001 PHE B1464 TYR 0.012 0.001 TYR B1645 ARG 0.009 0.000 ARG B1353 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 656) hydrogen bonds : angle 4.23311 ( 1860) metal coordination : bond 0.00133 ( 3) covalent geometry : bond 0.00177 (13610) covalent geometry : angle 0.41840 (18403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.693 Fit side-chains REVERT: B 234 GLN cc_start: 0.8335 (mt0) cc_final: 0.7693 (mm-40) REVERT: B 366 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7603 (mtp) REVERT: B 455 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (ptm160) REVERT: B 494 ILE cc_start: 0.8667 (mm) cc_final: 0.8358 (mm) REVERT: B 592 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 927 GLU cc_start: 0.8290 (pp20) cc_final: 0.7969 (pp20) REVERT: B 1442 HIS cc_start: 0.7309 (t-170) cc_final: 0.7092 (t70) REVERT: B 1517 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7178 (ttmm) REVERT: B 1550 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7773 (mp) REVERT: B 1840 ASP cc_start: 0.7986 (t0) cc_final: 0.7605 (t0) outliers start: 17 outliers final: 8 residues processed: 153 average time/residue: 0.4105 time to fit residues: 97.5901 Evaluate side-chains 145 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 158 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 162 optimal weight: 0.0770 chunk 141 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1689 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111727 restraints weight = 17355.327| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.76 r_work: 0.3049 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13613 Z= 0.124 Angle : 0.460 8.737 18403 Z= 0.249 Chirality : 0.043 0.146 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.923 15.221 1781 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Rotamer: Outliers : 1.32 % Allowed : 11.93 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.21), residues: 1660 helix: 2.35 (0.21), residues: 633 sheet: -0.12 (0.27), residues: 370 loop : -0.31 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 520 HIS 0.002 0.001 HIS B 35 PHE 0.015 0.001 PHE A 12 TYR 0.014 0.001 TYR B1645 ARG 0.004 0.000 ARG B1353 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 656) hydrogen bonds : angle 4.34442 ( 1860) metal coordination : bond 0.00292 ( 3) covalent geometry : bond 0.00294 (13610) covalent geometry : angle 0.45958 (18403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 2.716 Fit side-chains REVERT: B 32 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: B 347 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: B 366 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7807 (mtp) REVERT: B 455 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8586 (ptm160) REVERT: B 494 ILE cc_start: 0.8690 (mm) cc_final: 0.8386 (mm) REVERT: B 592 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 927 GLU cc_start: 0.8228 (pp20) cc_final: 0.7929 (pp20) REVERT: B 1442 HIS cc_start: 0.7314 (t-170) cc_final: 0.7063 (t70) REVERT: B 1517 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7234 (ttmm) REVERT: B 1550 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7832 (tt) REVERT: B 1840 ASP cc_start: 0.8044 (t0) cc_final: 0.7629 (t0) outliers start: 20 outliers final: 13 residues processed: 147 average time/residue: 0.4385 time to fit residues: 99.2679 Evaluate side-chains 152 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1488 LEU Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113079 restraints weight = 17501.735| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.71 r_work: 0.3065 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13613 Z= 0.110 Angle : 0.444 8.848 18403 Z= 0.242 Chirality : 0.043 0.141 2086 Planarity : 0.003 0.041 2377 Dihedral : 3.866 15.356 1781 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 1.32 % Allowed : 12.06 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.21), residues: 1660 helix: 2.39 (0.20), residues: 633 sheet: -0.12 (0.27), residues: 370 loop : -0.30 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 11 HIS 0.002 0.001 HIS B 35 PHE 0.024 0.001 PHE B1464 TYR 0.013 0.001 TYR B1645 ARG 0.001 0.000 ARG B1652 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 656) hydrogen bonds : angle 4.30208 ( 1860) metal coordination : bond 0.00248 ( 3) covalent geometry : bond 0.00253 (13610) covalent geometry : angle 0.44390 (18403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 2.956 Fit side-chains REVERT: B 32 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: B 347 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: B 366 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7802 (mtp) REVERT: B 455 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8527 (ptm160) REVERT: B 494 ILE cc_start: 0.8687 (mm) cc_final: 0.8421 (mm) REVERT: B 592 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8067 (mm-30) REVERT: B 927 GLU cc_start: 0.8240 (pp20) cc_final: 0.7935 (pp20) REVERT: B 1442 HIS cc_start: 0.7300 (t-170) cc_final: 0.7051 (t70) REVERT: B 1517 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7227 (ttmm) REVERT: B 1550 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7849 (tt) REVERT: B 1840 ASP cc_start: 0.8007 (t0) cc_final: 0.7583 (t0) outliers start: 20 outliers final: 12 residues processed: 149 average time/residue: 0.3032 time to fit residues: 70.9009 Evaluate side-chains 149 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1488 LEU Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 41 optimal weight: 0.0370 chunk 161 optimal weight: 0.0980 chunk 164 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114096 restraints weight = 17128.085| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.69 r_work: 0.3087 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13613 Z= 0.093 Angle : 0.430 9.195 18403 Z= 0.234 Chirality : 0.042 0.138 2086 Planarity : 0.003 0.041 2377 Dihedral : 3.739 15.103 1781 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 1.12 % Allowed : 12.59 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1660 helix: 2.50 (0.20), residues: 633 sheet: -0.03 (0.27), residues: 374 loop : -0.26 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 11 HIS 0.001 0.000 HIS B 35 PHE 0.014 0.001 PHE A 12 TYR 0.014 0.001 TYR B1425 ARG 0.005 0.000 ARG B1353 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 656) hydrogen bonds : angle 4.20055 ( 1860) metal coordination : bond 0.00180 ( 3) covalent geometry : bond 0.00203 (13610) covalent geometry : angle 0.43043 (18403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.468 Fit side-chains REVERT: B 32 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: B 234 GLN cc_start: 0.8428 (mt0) cc_final: 0.7824 (mm-40) REVERT: B 366 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7745 (mtp) REVERT: B 455 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8487 (ptm160) REVERT: B 494 ILE cc_start: 0.8670 (mm) cc_final: 0.8414 (mm) REVERT: B 592 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 927 GLU cc_start: 0.8212 (pp20) cc_final: 0.7913 (pp20) REVERT: B 1442 HIS cc_start: 0.7310 (t-170) cc_final: 0.7066 (t70) REVERT: B 1449 TYR cc_start: 0.8617 (t80) cc_final: 0.8314 (t80) REVERT: B 1517 LYS cc_start: 0.7518 (mtpt) cc_final: 0.7201 (ttmm) REVERT: B 1550 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7831 (tt) REVERT: B 1840 ASP cc_start: 0.8015 (t0) cc_final: 0.7604 (t0) outliers start: 17 outliers final: 11 residues processed: 145 average time/residue: 0.2917 time to fit residues: 65.9407 Evaluate side-chains 145 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1488 LEU Chi-restraints excluded: chain B residue 1516 VAL Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 69 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1689 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113057 restraints weight = 17279.204| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.70 r_work: 0.3071 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13613 Z= 0.104 Angle : 0.441 9.283 18403 Z= 0.240 Chirality : 0.043 0.142 2086 Planarity : 0.003 0.041 2377 Dihedral : 3.788 15.073 1781 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 1.05 % Allowed : 12.99 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1660 helix: 2.46 (0.20), residues: 633 sheet: -0.02 (0.27), residues: 375 loop : -0.28 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 520 HIS 0.002 0.001 HIS B 35 PHE 0.026 0.001 PHE B1464 TYR 0.013 0.001 TYR B1645 ARG 0.006 0.000 ARG B1353 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 656) hydrogen bonds : angle 4.23274 ( 1860) metal coordination : bond 0.00212 ( 3) covalent geometry : bond 0.00238 (13610) covalent geometry : angle 0.44106 (18403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.451 Fit side-chains revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: B 347 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 366 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7811 (mtp) REVERT: B 455 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8546 (ptm160) REVERT: B 494 ILE cc_start: 0.8686 (mm) cc_final: 0.8423 (mm) REVERT: B 592 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 927 GLU cc_start: 0.8227 (pp20) cc_final: 0.7927 (pp20) REVERT: B 1442 HIS cc_start: 0.7308 (t-170) cc_final: 0.7055 (t70) REVERT: B 1449 TYR cc_start: 0.8626 (t80) cc_final: 0.8321 (t80) REVERT: B 1517 LYS cc_start: 0.7537 (mtpt) cc_final: 0.7228 (ttmm) REVERT: B 1550 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7862 (tt) REVERT: B 1840 ASP cc_start: 0.8006 (t0) cc_final: 0.7579 (t0) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.2445 time to fit residues: 53.5948 Evaluate side-chains 148 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 347 GLU Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 455 ARG Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1488 LEU Chi-restraints excluded: chain B residue 1516 VAL Chi-restraints excluded: chain B residue 1532 LEU Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 128 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 102 optimal weight: 0.0570 chunk 39 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 0.0040 chunk 148 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1689 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115975 restraints weight = 17337.322| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.73 r_work: 0.3116 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13613 Z= 0.085 Angle : 0.423 9.262 18403 Z= 0.231 Chirality : 0.042 0.140 2086 Planarity : 0.003 0.040 2377 Dihedral : 3.639 14.842 1781 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % Rotamer: Outliers : 1.05 % Allowed : 13.05 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1660 helix: 2.58 (0.20), residues: 633 sheet: 0.12 (0.27), residues: 371 loop : -0.24 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 11 HIS 0.002 0.000 HIS B 35 PHE 0.016 0.001 PHE A 55 TYR 0.011 0.001 TYR B1645 ARG 0.005 0.000 ARG B1353 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 656) hydrogen bonds : angle 4.11724 ( 1860) metal coordination : bond 0.00121 ( 3) covalent geometry : bond 0.00180 (13610) covalent geometry : angle 0.42302 (18403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8436.92 seconds wall clock time: 153 minutes 43.56 seconds (9223.56 seconds total)