Starting phenix.real_space_refine on Sun Jan 19 08:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y9b_39072/01_2025/8y9b_39072.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y9b_39072/01_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_39072/01_2025/8y9b_39072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y9b_39072/01_2025/8y9b_39072.map" model { file = "/net/cci-nas-00/data/ceres_data/8y9b_39072/01_2025/8y9b_39072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y9b_39072/01_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-5571/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: 7.80, per 1000 atoms: 0.58 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: 3.03 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: 2.39 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: 8.44 Time building geometry restraints manager: 3.56 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: 3.740 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: 0.270 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- 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 13610 Z= 0.277 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 *********************** 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 : 1.622 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: 0.2699 time to fit residues: 72.2071 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 : 1.537 ------------------------------------------------------------------------------- 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 = 0.108781 restraints weight = 17253.527| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.83 r_work: 0.3015 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- 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 13610 Z= 0.318 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 *********************** 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 : 1.481 Fit side-chains REVERT: B 85 GLU cc_start: 0.7594 (mp0) cc_final: 0.6805 (mp0) REVERT: B 494 ILE cc_start: 0.8715 (mm) cc_final: 0.8477 (mm) REVERT: B 1517 LYS cc_start: 0.7575 (mtpt) cc_final: 0.7317 (ttmm) REVERT: B 1840 ASP cc_start: 0.8109 (t0) cc_final: 0.7737 (t0) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.2488 time to fit residues: 55.1891 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 : 1.550 ------------------------------------------------------------------------------- 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: 0.9990 chunk 93 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** B1839 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108288 restraints weight = 17361.436| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.81 r_work: 0.3019 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13610 Z= 0.283 Angle : 0.506 5.494 18403 Z= 0.278 Chirality : 0.045 0.146 2086 Planarity : 0.003 0.043 2377 Dihedral : 4.396 25.336 1781 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.32 % Allowed : 8.83 % Favored : 89.85 % 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: 1.83 (0.20), residues: 629 sheet: -0.24 (0.27), residues: 368 loop : -0.60 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 118 HIS 0.003 0.001 HIS B 35 PHE 0.015 0.001 PHE A 12 TYR 0.018 0.002 TYR B1645 ARG 0.003 0.000 ARG B1652 *********************** 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: 20 poor density : 143 time to evaluate : 1.524 Fit side-chains REVERT: B 32 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7832 (tt0) REVERT: B 85 GLU cc_start: 0.7580 (mp0) cc_final: 0.7037 (mp0) REVERT: B 494 ILE cc_start: 0.8685 (mm) cc_final: 0.8380 (mm) REVERT: B 1409 LEU cc_start: 0.6946 (tp) cc_final: 0.6740 (tp) REVERT: B 1517 LYS cc_start: 0.7593 (mtpt) cc_final: 0.7301 (ttmm) REVERT: B 1840 ASP cc_start: 0.8040 (t0) cc_final: 0.7636 (t0) outliers start: 20 outliers final: 15 residues processed: 155 average time/residue: 0.2425 time to fit residues: 58.5736 Evaluate side-chains 149 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 1.608 ------------------------------------------------------------------------------- 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 307 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: 0.7980 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 36 optimal weight: 0.0070 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 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 = 0.3517 r_free = 0.3517 target = 0.136923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.109272 restraints weight = 17288.256| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.79 r_work: 0.3031 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13610 Z= 0.222 Angle : 0.471 5.240 18403 Z= 0.259 Chirality : 0.044 0.142 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.251 23.243 1781 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.25 % Allowed : 10.68 % Favored : 88.07 % 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: 0.72 (0.21), residues: 1660 helix: 1.98 (0.20), residues: 629 sheet: -0.22 (0.27), residues: 369 loop : -0.53 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS B 35 PHE 0.019 0.001 PHE B1464 TYR 0.015 0.001 TYR B1645 ARG 0.002 0.000 ARG B1652 *********************** 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 163 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.646 Fit side-chains REVERT: B 32 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: B 85 GLU cc_start: 0.7512 (mp0) cc_final: 0.7020 (mp0) REVERT: B 494 ILE cc_start: 0.8676 (mm) cc_final: 0.8346 (mm) REVERT: B 592 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 1517 LYS cc_start: 0.7547 (mtpt) cc_final: 0.7242 (ttmm) REVERT: B 1840 ASP cc_start: 0.8033 (t0) cc_final: 0.7626 (t0) outliers start: 19 outliers final: 17 residues processed: 156 average time/residue: 0.2571 time to fit residues: 60.6474 Evaluate side-chains 158 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1429 ILE Chi-restraints excluded: chain B residue 1436 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 112 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 0.0270 chunk 161 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.136393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109462 restraints weight = 17393.407| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.82 r_work: 0.3011 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13610 Z= 0.268 Angle : 0.494 5.226 18403 Z= 0.272 Chirality : 0.045 0.150 2086 Planarity : 0.003 0.044 2377 Dihedral : 4.328 20.836 1781 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.65 % Allowed : 12.06 % 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: 0.65 (0.21), residues: 1660 helix: 1.96 (0.20), residues: 628 sheet: -0.25 (0.27), residues: 367 loop : -0.60 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 118 HIS 0.002 0.001 HIS B 99 PHE 0.014 0.001 PHE A 12 TYR 0.017 0.001 TYR B1645 ARG 0.002 0.000 ARG B1652 *********************** 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 166 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.671 Fit side-chains REVERT: B 32 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7929 (tt0) REVERT: B 85 GLU cc_start: 0.7570 (mp0) cc_final: 0.7340 (mt-10) REVERT: B 347 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: B 455 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8600 (ptm160) REVERT: B 494 ILE cc_start: 0.8699 (mm) cc_final: 0.8340 (mm) REVERT: B 592 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8090 (mm-30) REVERT: B 927 GLU cc_start: 0.8289 (pp20) cc_final: 0.7988 (pp20) REVERT: B 1442 HIS cc_start: 0.7349 (t-170) cc_final: 0.7073 (t70) REVERT: B 1517 LYS cc_start: 0.7571 (mtpt) cc_final: 0.7268 (ttmm) REVERT: B 1840 ASP cc_start: 0.8055 (t0) cc_final: 0.7768 (t0) outliers start: 25 outliers final: 19 residues processed: 159 average time/residue: 0.2519 time to fit residues: 60.7789 Evaluate side-chains 160 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 578 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1429 ILE Chi-restraints excluded: chain B residue 1436 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 110 optimal weight: 0.8980 chunk 158 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** 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 = 0.3528 r_free = 0.3528 target = 0.138021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111027 restraints weight = 17340.928| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.82 r_work: 0.3044 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13610 Z= 0.178 Angle : 0.449 6.419 18403 Z= 0.248 Chirality : 0.043 0.151 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.092 17.726 1781 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.65 % Allowed : 12.33 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.21), residues: 1660 helix: 2.16 (0.21), residues: 630 sheet: -0.18 (0.27), residues: 367 loop : -0.45 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 11 HIS 0.002 0.001 HIS B 35 PHE 0.022 0.001 PHE B1464 TYR 0.014 0.001 TYR B1645 ARG 0.002 0.000 ARG B1353 *********************** 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 166 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.649 Fit side-chains REVERT: B 32 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: B 181 ASP cc_start: 0.8445 (m-30) cc_final: 0.8168 (m-30) REVERT: B 347 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: B 366 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7961 (mtp) REVERT: B 455 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8508 (ptm160) REVERT: B 494 ILE cc_start: 0.8674 (mm) cc_final: 0.8372 (mm) REVERT: B 592 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8101 (mm-30) REVERT: B 927 GLU cc_start: 0.8314 (pp20) cc_final: 0.7987 (pp20) REVERT: B 1442 HIS cc_start: 0.7358 (t-170) cc_final: 0.7069 (t70) REVERT: B 1517 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7318 (ttmm) REVERT: B 1550 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.8011 (tt) REVERT: B 1840 ASP cc_start: 0.8039 (t0) cc_final: 0.7774 (t0) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 0.2456 time to fit residues: 58.5988 Evaluate side-chains 156 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 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 578 ILE 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 1429 ILE Chi-restraints excluded: chain B residue 1436 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 158 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 135 optimal weight: 0.1980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.135940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.108520 restraints weight = 17386.991| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.76 r_work: 0.3007 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13610 Z= 0.270 Angle : 0.494 6.394 18403 Z= 0.272 Chirality : 0.045 0.158 2086 Planarity : 0.003 0.043 2377 Dihedral : 4.269 17.292 1781 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.71 % Allowed : 12.20 % Favored : 86.09 % 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: 0.72 (0.21), residues: 1660 helix: 2.03 (0.20), residues: 628 sheet: -0.26 (0.27), residues: 367 loop : -0.54 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.002 0.001 HIS B 35 PHE 0.013 0.001 PHE B1638 TYR 0.017 0.001 TYR B1645 ARG 0.002 0.000 ARG B1353 *********************** 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 164 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.401 Fit side-chains REVERT: B 32 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: B 347 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: B 366 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: B 455 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8637 (ptm160) REVERT: B 494 ILE cc_start: 0.8690 (mm) cc_final: 0.8364 (mm) REVERT: B 592 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8093 (mm-30) REVERT: B 927 GLU cc_start: 0.8285 (pp20) cc_final: 0.7969 (pp20) REVERT: B 1442 HIS cc_start: 0.7387 (t-170) cc_final: 0.6935 (t70) REVERT: B 1517 LYS cc_start: 0.7687 (mtpt) cc_final: 0.7359 (ttmm) REVERT: B 1550 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7826 (tt) REVERT: B 1840 ASP cc_start: 0.8081 (t0) cc_final: 0.7782 (t0) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 0.2486 time to fit residues: 60.4736 Evaluate side-chains 159 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.526 ------------------------------------------------------------------------------- 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 270 ASP 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 578 ILE Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 1429 ILE 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 1590 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: 0.0050 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.139306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.111850 restraints weight = 17416.479| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.80 r_work: 0.3077 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13610 Z= 0.135 Angle : 0.432 7.758 18403 Z= 0.239 Chirality : 0.042 0.150 2086 Planarity : 0.003 0.041 2377 Dihedral : 3.938 16.459 1781 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.58 % Allowed : 12.66 % Favored : 85.76 % 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: 1.01 (0.21), residues: 1660 helix: 2.30 (0.21), residues: 632 sheet: -0.19 (0.27), residues: 368 loop : -0.38 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 11 HIS 0.002 0.001 HIS B 99 PHE 0.025 0.001 PHE B1464 TYR 0.014 0.001 TYR B1425 ARG 0.002 0.000 ARG B1353 *********************** 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 164 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.494 Fit side-chains revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: B 181 ASP cc_start: 0.8403 (m-30) cc_final: 0.8176 (m-30) REVERT: B 347 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: B 455 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8413 (ptm160) REVERT: B 494 ILE cc_start: 0.8593 (mm) cc_final: 0.8306 (mm) REVERT: B 592 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 927 GLU cc_start: 0.8263 (pp20) cc_final: 0.7919 (pp20) REVERT: B 1442 HIS cc_start: 0.7383 (t-170) cc_final: 0.6921 (t70) REVERT: B 1517 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7258 (ttmm) REVERT: B 1840 ASP cc_start: 0.7981 (t0) cc_final: 0.7721 (t0) outliers start: 24 outliers final: 15 residues processed: 156 average time/residue: 0.2504 time to fit residues: 59.2118 Evaluate side-chains 155 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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 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 1713 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 30 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 161 optimal weight: 0.3980 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3522 r_free = 0.3522 target = 0.138424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.118674 restraints weight = 17112.490| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.04 r_work: 0.3102 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13610 Z= 0.166 Angle : 0.450 10.138 18403 Z= 0.246 Chirality : 0.043 0.167 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.931 16.125 1781 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.45 % Allowed : 12.72 % Favored : 85.83 % 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: 1.03 (0.21), residues: 1660 helix: 2.33 (0.21), residues: 632 sheet: -0.14 (0.27), residues: 365 loop : -0.40 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 118 HIS 0.002 0.001 HIS B 99 PHE 0.013 0.001 PHE A 12 TYR 0.013 0.001 TYR B1645 ARG 0.001 0.000 ARG B1353 *********************** 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 161 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: B 181 ASP cc_start: 0.8201 (m-30) cc_final: 0.7987 (m-30) REVERT: B 347 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: B 455 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8487 (ptm160) REVERT: B 494 ILE cc_start: 0.8711 (mm) cc_final: 0.8505 (mm) REVERT: B 1449 TYR cc_start: 0.8541 (t80) cc_final: 0.8242 (t80) REVERT: B 1517 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7445 (ttmm) REVERT: B 1840 ASP cc_start: 0.7837 (t0) cc_final: 0.7619 (t0) outliers start: 22 outliers final: 16 residues processed: 155 average time/residue: 0.2458 time to fit residues: 57.8060 Evaluate side-chains 150 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 1516 VAL Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1532 LEU 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: 3.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 83 optimal weight: 0.0770 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1442 HIS ** 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 = 0.3510 r_free = 0.3510 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115714 restraints weight = 17248.508| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.23 r_work: 0.3107 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13610 Z= 0.204 Angle : 0.474 9.468 18403 Z= 0.259 Chirality : 0.043 0.149 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.021 16.156 1781 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.38 % Allowed : 13.18 % Favored : 85.43 % 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: 2.25 (0.21), residues: 632 sheet: -0.19 (0.27), residues: 365 loop : -0.43 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 118 HIS 0.012 0.001 HIS B1442 PHE 0.025 0.001 PHE B1464 TYR 0.014 0.001 TYR B1425 ARG 0.002 0.000 ARG B 165 ********************** 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 153 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: B 32 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: B 181 ASP cc_start: 0.8193 (m-30) cc_final: 0.7954 (m-30) REVERT: B 347 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: B 455 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8514 (ptm160) REVERT: B 494 ILE cc_start: 0.8686 (mm) cc_final: 0.8455 (mm) REVERT: B 1449 TYR cc_start: 0.8594 (t80) cc_final: 0.8267 (t80) REVERT: B 1517 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7322 (ttmm) REVERT: B 1840 ASP cc_start: 0.7780 (t0) cc_final: 0.7537 (t0) outliers start: 21 outliers final: 16 residues processed: 148 average time/residue: 0.2389 time to fit residues: 54.7564 Evaluate side-chains 150 residues out of total 1531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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 1516 VAL Chi-restraints excluded: chain B residue 1518 VAL Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1532 LEU 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: 0.0870 chunk 102 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 131 optimal weight: 0.0020 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.9168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1442 HIS ** 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 = 0.3513 r_free = 0.3513 target = 0.137696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116696 restraints weight = 17262.371| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.12 r_work: 0.3096 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13610 Z= 0.192 Angle : 0.464 9.102 18403 Z= 0.254 Chirality : 0.043 0.148 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.994 16.311 1781 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.52 % Allowed : 13.18 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.21), residues: 1660 helix: 2.27 (0.20), residues: 632 sheet: -0.17 (0.27), residues: 364 loop : -0.44 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 11 HIS 0.013 0.001 HIS B1442 PHE 0.015 0.001 PHE A 55 TYR 0.014 0.001 TYR B1645 ARG 0.002 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7006.43 seconds wall clock time: 125 minutes 30.95 seconds (7530.95 seconds total)