Starting phenix.real_space_refine on Sat Oct 12 22:33:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9b_39072/10_2024/8y9b_39072.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9b_39072/10_2024/8y9b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9b_39072/10_2024/8y9b_39072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9b_39072/10_2024/8y9b_39072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9b_39072/10_2024/8y9b_39072.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y9b_39072/10_2024/8y9b_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-5477/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: 7.35, per 1000 atoms: 0.55 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 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: 2.08 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: 6.57 Time building geometry restraints manager: 3.51 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: 1.800 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: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.310 Find NCS groups from input model: 0.170 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.960 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.579 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: 0.2605 time to fit residues: 69.6247 Evaluate side-chains 133 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.621 Fit side-chains REVERT: B 32 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: B 85 GLU cc_start: 0.7119 (mp0) cc_final: 0.6310 (mp0) REVERT: B 494 ILE cc_start: 0.8669 (mm) cc_final: 0.8460 (mm) REVERT: B 1517 LYS cc_start: 0.7135 (mtpt) cc_final: 0.6852 (ttmm) REVERT: B 1840 ASP cc_start: 0.7507 (t0) cc_final: 0.7167 (t0) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.2422 time to fit residues: 54.2679 Evaluate side-chains 140 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 GLU 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 83 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13610 Z= 0.157 Angle : 0.441 5.413 18403 Z= 0.244 Chirality : 0.043 0.148 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.081 24.283 1781 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.86 % Allowed : 8.70 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.21), residues: 1660 helix: 2.11 (0.21), residues: 629 sheet: -0.13 (0.27), residues: 369 loop : -0.43 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 11 HIS 0.002 0.001 HIS B 35 PHE 0.014 0.001 PHE A 12 TYR 0.013 0.001 TYR B1645 ARG 0.002 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 169 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.535 Fit side-chains REVERT: B 85 GLU cc_start: 0.6923 (mp0) cc_final: 0.6456 (mp0) REVERT: B 181 ASP cc_start: 0.7966 (m-30) cc_final: 0.7552 (m-30) REVERT: B 494 ILE cc_start: 0.8590 (mm) cc_final: 0.8362 (mm) REVERT: B 592 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 1517 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6760 (ttmm) REVERT: B 1840 ASP cc_start: 0.7410 (t0) cc_final: 0.7071 (t0) outliers start: 13 outliers final: 8 residues processed: 163 average time/residue: 0.2444 time to fit residues: 60.3236 Evaluate side-chains 146 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 690 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.0070 chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.2060 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13610 Z= 0.240 Angle : 0.479 5.320 18403 Z= 0.263 Chirality : 0.044 0.143 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.206 22.190 1781 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.45 % Allowed : 10.28 % Favored : 88.27 % 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: 0.82 (0.21), residues: 1660 helix: 2.06 (0.20), residues: 630 sheet: -0.21 (0.27), residues: 369 loop : -0.44 (0.24), residues: 661 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 0.017 0.001 TYR B1645 ARG 0.003 0.000 ARG B1353 *********************** 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 165 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 143 time to evaluate : 1.416 Fit side-chains REVERT: B 85 GLU cc_start: 0.7031 (mp0) cc_final: 0.6567 (mp0) REVERT: B 494 ILE cc_start: 0.8605 (mm) cc_final: 0.8319 (mm) REVERT: B 1517 LYS cc_start: 0.7152 (mtpt) cc_final: 0.6833 (ttmm) REVERT: B 1840 ASP cc_start: 0.7424 (t0) cc_final: 0.7050 (t0) outliers start: 22 outliers final: 16 residues processed: 157 average time/residue: 0.2377 time to fit residues: 57.2336 Evaluate side-chains 157 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 307 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1425 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= 0.170 Angle : 0.440 6.413 18403 Z= 0.243 Chirality : 0.043 0.142 2086 Planarity : 0.003 0.042 2377 Dihedral : 4.015 19.840 1781 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.52 % Allowed : 11.34 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.21), residues: 1660 helix: 2.22 (0.20), residues: 632 sheet: -0.15 (0.27), residues: 367 loop : -0.38 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 11 HIS 0.002 0.001 HIS B 35 PHE 0.015 0.001 PHE A 12 TYR 0.013 0.001 TYR B1645 ARG 0.002 0.000 ARG B1353 *********************** 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 fitting. rotamer outliers: 23 poor density : 143 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: B 347 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: B 366 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7498 (mtp) REVERT: B 455 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8155 (ptm160) REVERT: B 494 ILE cc_start: 0.8595 (mm) cc_final: 0.8299 (mm) REVERT: B 1517 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6814 (ttmm) REVERT: B 1840 ASP cc_start: 0.7409 (t0) cc_final: 0.7033 (t0) outliers start: 23 outliers final: 15 residues processed: 158 average time/residue: 0.2512 time to fit residues: 60.2993 Evaluate side-chains 155 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 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 878 LEU 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 1713 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 154 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13610 Z= 0.161 Angle : 0.441 10.108 18403 Z= 0.241 Chirality : 0.043 0.144 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.935 17.048 1781 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.32 % Allowed : 11.87 % 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: 1.07 (0.21), residues: 1660 helix: 2.31 (0.21), residues: 632 sheet: -0.10 (0.27), residues: 367 loop : -0.34 (0.24), residues: 661 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 0.023 0.001 PHE B1464 TYR 0.013 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 157 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: B 347 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 366 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: B 455 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8185 (ptm160) REVERT: B 494 ILE cc_start: 0.8651 (mm) cc_final: 0.8355 (mm) REVERT: B 927 GLU cc_start: 0.7654 (pp20) cc_final: 0.7389 (pp20) REVERT: B 1517 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6787 (ttmm) REVERT: B 1550 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7687 (mt) REVERT: B 1840 ASP cc_start: 0.7393 (t0) cc_final: 0.7019 (t0) outliers start: 20 outliers final: 14 residues processed: 151 average time/residue: 0.2421 time to fit residues: 55.8582 Evaluate side-chains 149 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 SER 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 690 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 98 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1581 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= 0.166 Angle : 0.441 9.061 18403 Z= 0.242 Chirality : 0.043 0.143 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.913 15.424 1781 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.45 % Allowed : 12.00 % Favored : 86.55 % 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: 1.08 (0.21), residues: 1660 helix: 2.32 (0.20), residues: 633 sheet: -0.10 (0.27), residues: 367 loop : -0.34 (0.24), residues: 660 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 0.013 0.001 PHE A 12 TYR 0.013 0.001 TYR B1645 ARG 0.001 0.000 ARG B1652 *********************** 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 fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: B 347 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: B 366 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7602 (mtp) REVERT: B 455 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8208 (ptm160) REVERT: B 494 ILE cc_start: 0.8610 (mm) cc_final: 0.8322 (mm) REVERT: B 927 GLU cc_start: 0.7655 (pp20) cc_final: 0.7386 (pp20) REVERT: B 1517 LYS cc_start: 0.7153 (mtpt) cc_final: 0.6792 (ttmm) REVERT: B 1550 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7651 (mt) REVERT: B 1840 ASP cc_start: 0.7395 (t0) cc_final: 0.7015 (t0) outliers start: 22 outliers final: 16 residues processed: 147 average time/residue: 0.2780 time to fit residues: 61.0044 Evaluate side-chains 151 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 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 878 LEU Chi-restraints excluded: chain B residue 926 THR 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 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 63 optimal weight: 0.4980 chunk 95 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.0270 chunk 101 optimal weight: 0.0040 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13610 Z= 0.116 Angle : 0.410 8.552 18403 Z= 0.226 Chirality : 0.042 0.137 2086 Planarity : 0.003 0.040 2377 Dihedral : 3.681 14.950 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 : 0.99 % Allowed : 12.66 % Favored : 86.35 % 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: 1.27 (0.21), residues: 1660 helix: 2.51 (0.21), residues: 633 sheet: -0.03 (0.27), residues: 374 loop : -0.25 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 11 HIS 0.002 0.000 HIS B 35 PHE 0.025 0.001 PHE B1464 TYR 0.012 0.001 TYR B1645 ARG 0.002 0.000 ARG A 16 *********************** 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 159 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: B 234 GLN cc_start: 0.7996 (mt0) cc_final: 0.7378 (mm-40) REVERT: B 366 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7511 (mtp) REVERT: B 455 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7967 (ptm160) REVERT: B 494 ILE cc_start: 0.8632 (mm) cc_final: 0.8358 (mm) REVERT: B 927 GLU cc_start: 0.7675 (pp20) cc_final: 0.7383 (pp20) REVERT: B 1449 TYR cc_start: 0.8445 (t80) cc_final: 0.8154 (t80) REVERT: B 1517 LYS cc_start: 0.7114 (mtpt) cc_final: 0.6748 (ttmm) REVERT: B 1840 ASP cc_start: 0.7308 (t0) cc_final: 0.6943 (t0) outliers start: 15 outliers final: 10 residues processed: 154 average time/residue: 0.2715 time to fit residues: 64.0569 Evaluate side-chains 145 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 878 LEU 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 1713 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.5980 chunk 139 optimal weight: 0.0980 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 0.0470 chunk 134 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13610 Z= 0.130 Angle : 0.425 8.386 18403 Z= 0.233 Chirality : 0.042 0.147 2086 Planarity : 0.003 0.041 2377 Dihedral : 3.679 14.654 1781 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 0.99 % Allowed : 13.12 % 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: 1.34 (0.21), residues: 1660 helix: 2.55 (0.21), residues: 633 sheet: 0.08 (0.27), residues: 371 loop : -0.24 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 11 HIS 0.001 0.000 HIS B 35 PHE 0.013 0.001 PHE A 12 TYR 0.013 0.001 TYR B1425 ARG 0.002 0.000 ARG A 16 *********************** 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 147 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.449 Fit side-chains REVERT: B 234 GLN cc_start: 0.8038 (mt0) cc_final: 0.7422 (mm-40) REVERT: B 347 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: B 366 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7546 (mtp) REVERT: B 489 MET cc_start: 0.8165 (mmt) cc_final: 0.7958 (mmt) REVERT: B 494 ILE cc_start: 0.8614 (mm) cc_final: 0.8368 (mm) REVERT: B 927 GLU cc_start: 0.7680 (pp20) cc_final: 0.7388 (pp20) REVERT: B 1449 TYR cc_start: 0.8449 (t80) cc_final: 0.7985 (t80) REVERT: B 1517 LYS cc_start: 0.7116 (mtpt) cc_final: 0.6756 (ttmm) REVERT: B 1840 ASP cc_start: 0.7309 (t0) cc_final: 0.6935 (t0) outliers start: 15 outliers final: 11 residues processed: 143 average time/residue: 0.2566 time to fit residues: 56.2650 Evaluate side-chains 144 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 562 LEU Chi-restraints excluded: chain B residue 567 SER 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 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 157 optimal weight: 7.9990 chunk 96 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 104 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- 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** B1589 ASN B1689 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13610 Z= 0.124 Angle : 0.424 8.136 18403 Z= 0.233 Chirality : 0.042 0.137 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.636 14.617 1781 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 0.99 % Allowed : 13.25 % 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: 1.39 (0.21), residues: 1660 helix: 2.58 (0.20), residues: 633 sheet: 0.13 (0.27), residues: 370 loop : -0.21 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 11 HIS 0.011 0.001 HIS B1442 PHE 0.026 0.001 PHE B1464 TYR 0.011 0.001 TYR B1645 ARG 0.004 0.000 ARG B1353 ********************** 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 152 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.480 Fit side-chains REVERT: B 234 GLN cc_start: 0.8000 (mt0) cc_final: 0.7394 (mm-40) REVERT: B 347 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: B 366 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7469 (mtp) REVERT: B 455 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8028 (ptm160) REVERT: B 489 MET cc_start: 0.8161 (mmt) cc_final: 0.7954 (mmt) REVERT: B 494 ILE cc_start: 0.8608 (mm) cc_final: 0.8399 (mm) REVERT: B 927 GLU cc_start: 0.7660 (pp20) cc_final: 0.7377 (pp20) REVERT: B 1449 TYR cc_start: 0.8415 (t80) cc_final: 0.7980 (t80) REVERT: B 1517 LYS cc_start: 0.7110 (mtpt) cc_final: 0.6762 (ttmm) REVERT: B 1840 ASP cc_start: 0.7326 (t0) cc_final: 0.6950 (t0) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.2762 time to fit residues: 60.7594 Evaluate side-chains 144 residues out of total 1531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 948 VAL 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 1713 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 135 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 115 optimal weight: 0.0870 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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** B1689 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117615 restraints weight = 17098.583| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.48 r_work: 0.3126 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13610 Z= 0.129 Angle : 0.427 8.092 18403 Z= 0.234 Chirality : 0.042 0.141 2086 Planarity : 0.003 0.042 2377 Dihedral : 3.630 14.581 1781 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.65 % Favored : 97.29 % Rotamer: Outliers : 1.05 % Allowed : 13.51 % 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: 1.40 (0.21), residues: 1660 helix: 2.60 (0.20), residues: 633 sheet: 0.14 (0.27), residues: 370 loop : -0.21 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 11 HIS 0.011 0.001 HIS B1442 PHE 0.015 0.001 PHE A 55 TYR 0.012 0.001 TYR B1645 ARG 0.006 0.000 ARG B1353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2966.87 seconds wall clock time: 55 minutes 1.90 seconds (3301.90 seconds total)