Starting phenix.real_space_refine on Fri Jul 3 16:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5b_28864/07_2026/8f5b_28864.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 293 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 9121 2.51 5 N 2378 2.21 5 O 2572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14152 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1924, 13954 Classifications: {'peptide': 1924} Incomplete info: {'truncation_to_alanine': 350} Link IDs: {'PTRANS': 98, 'TRANS': 1825} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1440 Unresolved non-hydrogen angles: 1823 Unresolved non-hydrogen dihedrals: 1221 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 35, 'GLN:plan1': 21, 'TRP:plan': 9, 'ASN:plan1': 21, 'GLU:plan': 54, 'PHE:plan': 22, 'HIS:plan': 9, 'ASP:plan': 37, 'TYR:plan': 13} Unresolved non-hydrogen planarities: 998 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {' MG': 2, 'ANP': 2, 'NAG': 4} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.46, per 1000 atoms: 0.24 Number of scatterers: 14152 At special positions: 0 Unit cell: (80.7751, 94.4125, 217.149, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 73 16.00 P 6 15.00 Mg 2 11.99 O 2572 8.00 N 2378 7.00 C 9121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 519 " distance=2.03 Simple disulfide: pdb=" SG CYS A 641 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1455 " distance=2.03 Simple disulfide: pdb=" SG CYS A1488 " - pdb=" SG CYS A1502 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A2301 " - " ASN A 98 " " NAG A2302 " - " ASN A 504 " " NAG A2303 " - " ASN A1662 " " NAG A2306 " - " ASN A 444 " " NAG B 1 " - " ASN A 415 " Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 714.8 milliseconds 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 11 sheets defined 57.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 21 through 45 Proline residue: A 32 - end of helix removed outlier: 4.175A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.974A pdb=" N SER A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 114 Processing helix chain 'A' and resid 116 through 137 removed outlier: 4.278A pdb=" N GLN A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 290 Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 290 through 301 Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 342 through 349 removed outlier: 4.504A pdb=" N LYS A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 Processing helix chain 'A' and resid 384 through 396 Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'A' and resid 415 through 445 removed outlier: 3.969A pdb=" N LEU A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 433 " --> pdb=" O LYS A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 499 through 505 removed outlier: 3.831A pdb=" N PHE A 503 " --> pdb=" O TRP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 Processing helix chain 'A' and resid 530 through 544 removed outlier: 3.621A pdb=" N GLU A 544 " --> pdb=" O SER A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 607 Processing helix chain 'A' and resid 607 through 623 Processing helix chain 'A' and resid 645 through 649 removed outlier: 3.921A pdb=" N ILE A 649 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 663 Proline residue: A 656 - end of helix removed outlier: 3.780A pdb=" N TRP A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 680 Processing helix chain 'A' and resid 681 through 690 Processing helix chain 'A' and resid 692 through 723 Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.553A pdb=" N PHE A 755 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.591A pdb=" N GLY A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Proline residue: A 775 - end of helix Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 797 through 815 Processing helix chain 'A' and resid 835 through 861 removed outlier: 4.004A pdb=" N GLN A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 968 through 976 removed outlier: 3.627A pdb=" N LEU A 976 " --> pdb=" O THR A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 removed outlier: 3.663A pdb=" N SER A1004 " --> pdb=" O ALA A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1030 Processing helix chain 'A' and resid 1034 through 1050 Processing helix chain 'A' and resid 1063 through 1077 Processing helix chain 'A' and resid 1093 through 1107 removed outlier: 3.786A pdb=" N SER A1099 " --> pdb=" O TYR A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1127 Processing helix chain 'A' and resid 1143 through 1151 Processing helix chain 'A' and resid 1205 through 1216 Processing helix chain 'A' and resid 1241 through 1253 Processing helix chain 'A' and resid 1268 through 1281 removed outlier: 3.935A pdb=" N ILE A1272 " --> pdb=" O PRO A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1369 Processing helix chain 'A' and resid 1369 through 1392 removed outlier: 4.438A pdb=" N LEU A1379 " --> pdb=" O ALA A1375 " (cutoff:3.500A) Proline residue: A1380 - end of helix Processing helix chain 'A' and resid 1406 through 1410 removed outlier: 3.758A pdb=" N TYR A1410 " --> pdb=" O PRO A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1437 Processing helix chain 'A' and resid 1467 through 1477 Processing helix chain 'A' and resid 1530 through 1547 Proline residue: A1539 - end of helix Processing helix chain 'A' and resid 1573 through 1588 Processing helix chain 'A' and resid 1592 through 1600 Processing helix chain 'A' and resid 1601 through 1609 removed outlier: 3.700A pdb=" N HIS A1608 " --> pdb=" O ASP A1604 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A1609 " --> pdb=" O PHE A1605 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1639 Processing helix chain 'A' and resid 1668 through 1693 WARNING: missing atoms! Processing helix chain 'A' and resid 1694 through 1696 No H-bonds generated for 'chain 'A' and resid 1694 through 1696' Processing helix chain 'A' and resid 1697 through 1707 removed outlier: 4.076A pdb=" N LEU A1701 " --> pdb=" O PHE A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1715 Processing helix chain 'A' and resid 1719 through 1750 Processing helix chain 'A' and resid 1751 through 1756 Processing helix chain 'A' and resid 1759 through 1779 Proline residue: A1776 - end of helix Processing helix chain 'A' and resid 1780 through 1784 Processing helix chain 'A' and resid 1790 through 1817 Processing helix chain 'A' and resid 1822 through 1828 Processing helix chain 'A' and resid 1836 through 1862 Processing helix chain 'A' and resid 1875 through 1900 Processing helix chain 'A' and resid 1919 through 1931 Processing helix chain 'A' and resid 1977 through 1987 Processing helix chain 'A' and resid 2006 through 2012 Processing helix chain 'A' and resid 2028 through 2041 removed outlier: 3.970A pdb=" N GLY A2041 " --> pdb=" O ALA A2037 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2045 No H-bonds generated for 'chain 'A' and resid 2043 through 2045' Processing helix chain 'A' and resid 2046 through 2059 Processing helix chain 'A' and resid 2072 through 2085 Processing helix chain 'A' and resid 2102 through 2120 removed outlier: 3.826A pdb=" N ARG A2106 " --> pdb=" O ASP A2102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A2107 " --> pdb=" O PRO A2103 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A2108 " --> pdb=" O GLN A2104 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2137 removed outlier: 3.678A pdb=" N CYS A2133 " --> pdb=" O SER A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2161 Processing helix chain 'A' and resid 2186 through 2193 Processing helix chain 'A' and resid 2214 through 2226 removed outlier: 4.380A pdb=" N ILE A2218 " --> pdb=" O SER A2214 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2253 Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 399 removed outlier: 5.828A pdb=" N ILE A 398 " --> pdb=" O GLU A 526 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 550 through 552 removed outlier: 3.745A pdb=" N MET A 573 " --> pdb=" O GLN A1659 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 632 through 636 removed outlier: 3.562A pdb=" N VAL A1617 " --> pdb=" O TYR A 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 930 through 932 Processing sheet with id=AA5, first strand: chain 'A' and resid 1114 through 1116 removed outlier: 3.501A pdb=" N MET A1115 " --> pdb=" O THR A 959 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA A 960 " --> pdb=" O ALA A1131 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ILE A1133 " --> pdb=" O ALA A 960 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 962 " --> pdb=" O ILE A1133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1005 through 1006 Processing sheet with id=AA7, first strand: chain 'A' and resid 1155 through 1157 Processing sheet with id=AA8, first strand: chain 'A' and resid 1461 through 1462 Processing sheet with id=AA9, first strand: chain 'A' and resid 1961 through 1962 removed outlier: 3.590A pdb=" N VAL A1962 " --> pdb=" O LEU A1938 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A1938 " --> pdb=" O VAL A1962 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N GLU A1942 " --> pdb=" O ASP A1995 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP A1995 " --> pdb=" O GLU A1942 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A1944 " --> pdb=" O SER A1993 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A1993 " --> pdb=" O THR A1944 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 2091 through 2093 removed outlier: 9.042A pdb=" N ALA A2141 " --> pdb=" O CYS A1967 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLY A1969 " --> pdb=" O ALA A2141 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N MET A2143 " --> pdb=" O GLY A1969 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A1971 " --> pdb=" O MET A2143 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A2150 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A2144 " --> pdb=" O PHE A2148 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N PHE A2148 " --> pdb=" O VAL A2144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 2205 through 2210 removed outlier: 4.084A pdb=" N ILE A2166 " --> pdb=" O THR A2237 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A2237 " --> pdb=" O ILE A2166 " (cutoff:3.500A) 774 hydrogen bonds defined for protein. 2289 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: 2.98 Time building geometry restraints manager: 1.55 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: 4522 1.34 - 1.46: 3241 1.46 - 1.58: 6588 1.58 - 1.70: 7 1.70 - 1.82: 114 Bond restraints: 14472 Sorted by residual: bond pdb=" O3A ANP A2304 " pdb=" PB ANP A2304 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" O3A ANP A2305 " pdb=" PB ANP A2305 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" N3B ANP A2304 " pdb=" PG ANP A2304 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N3B ANP A2305 " pdb=" PG ANP A2305 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O5' ANP A2304 " pdb=" PA ANP A2304 " ideal model delta sigma weight residual 1.655 1.574 0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 14467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 19680 3.70 - 7.40: 110 7.40 - 11.10: 9 11.10 - 14.79: 0 14.79 - 18.49: 2 Bond angle restraints: 19801 Sorted by residual: angle pdb=" PB ANP A2304 " pdb=" N3B ANP A2304 " pdb=" PG ANP A2304 " ideal model delta sigma weight residual 126.95 108.46 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" PB ANP A2305 " pdb=" N3B ANP A2305 " pdb=" PG ANP A2305 " ideal model delta sigma weight residual 126.95 108.85 18.10 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C ASN A 444 " pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 110.09 101.94 8.15 1.67e+00 3.59e-01 2.38e+01 angle pdb=" C TYR A 97 " pdb=" CA TYR A 97 " pdb=" CB TYR A 97 " ideal model delta sigma weight residual 111.82 106.62 5.20 1.28e+00 6.10e-01 1.65e+01 angle pdb=" N ASN A 444 " pdb=" CA ASN A 444 " pdb=" CB ASN A 444 " ideal model delta sigma weight residual 110.49 116.24 -5.75 1.48e+00 4.57e-01 1.51e+01 ... (remaining 19796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 8146 24.81 - 49.62: 418 49.62 - 74.44: 68 74.44 - 99.25: 16 99.25 - 124.06: 8 Dihedral angle restraints: 8656 sinusoidal: 3093 harmonic: 5563 Sorted by residual: dihedral pdb=" CB CYS A 75 " pdb=" SG CYS A 75 " pdb=" SG CYS A 324 " pdb=" CB CYS A 324 " ideal model delta sinusoidal sigma weight residual -86.00 -8.32 -77.68 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CA ASN A 98 " pdb=" C ASN A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta harmonic sigma weight residual 180.00 150.64 29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CB CYS A 370 " pdb=" SG CYS A 370 " pdb=" SG CYS A 519 " pdb=" CB CYS A 519 " ideal model delta sinusoidal sigma weight residual 93.00 48.59 44.41 1 1.00e+01 1.00e-02 2.74e+01 ... (remaining 8653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2001 0.057 - 0.114: 355 0.114 - 0.170: 26 0.170 - 0.227: 3 0.227 - 0.284: 6 Chirality restraints: 2391 Sorted by residual: chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.87e+00 chirality pdb=" C3' ANP A2304 " pdb=" C2' ANP A2304 " pdb=" C4' ANP A2304 " pdb=" O3' ANP A2304 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2388 not shown) Planarity restraints: 2499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.007 2.00e-02 2.50e+03 3.28e-02 1.35e+01 pdb=" CG ASN A 444 " 0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 444 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASN A 444 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN A 444 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 444 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.021 2.00e-02 2.50e+03 1.96e-02 4.81e+00 pdb=" CG ASN A 98 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.015 2.00e-02 2.50e+03 pdb=" C1 NAG A2301 " -0.018 2.00e-02 2.50e+03 ... (remaining 2496 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 178 2.57 - 3.16: 12686 3.16 - 3.74: 23880 3.74 - 4.32: 28498 4.32 - 4.90: 46837 Nonbonded interactions: 112079 Sorted by model distance: nonbonded pdb=" O1G ANP A2305 " pdb="MG MG A2307 " model vdw 1.993 2.170 nonbonded pdb=" OE1 GLN A2019 " pdb="MG MG A2307 " model vdw 2.007 2.170 nonbonded pdb=" N3B ANP A2304 " pdb="MG MG A2308 " model vdw 2.017 2.250 nonbonded pdb=" OG1 THR A 970 " pdb="MG MG A2308 " model vdw 2.025 2.170 nonbonded pdb=" O2A ANP A2304 " pdb="MG MG A2308 " model vdw 2.033 2.170 ... (remaining 112074 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 0.152 14487 Z= 0.202 Angle : 0.722 18.492 19840 Z= 0.337 Chirality : 0.044 0.284 2391 Planarity : 0.004 0.041 2494 Dihedral : 15.756 124.061 5036 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.20), residues: 1904 helix: 1.70 (0.17), residues: 1021 sheet: -0.24 (0.48), residues: 139 loop : -1.98 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.026 0.001 TYR A1735 PHE 0.023 0.001 PHE A 655 TRP 0.025 0.001 TRP A 31 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (14472) covalent geometry : angle 0.71529 / 0.34 (19801) SS BOND : bond 0.00187 / 0.10 ( 6) SS BOND : angle 0.61619 / 0.35 ( 12) hydrogen bonds : bond 0.10194 / 6.80 ( 774) hydrogen bonds : angle 4.84039 / 3.64 ( 2289) link_BETA1-4 : bond 0.00421 / 0.21 ( 4) link_BETA1-4 : angle 1.67579 / 0.96 ( 12) link_NAG-ASN : bond 0.01266 / 0.66 ( 5) link_NAG-ASN : angle 3.48007 / 1.87 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.498 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1018 LEU cc_start: 0.8813 (tp) cc_final: 0.8547 (tp) REVERT: A 1115 MET cc_start: 0.6220 (ppp) cc_final: 0.5970 (ppp) REVERT: A 1679 ASP cc_start: 0.8855 (m-30) cc_final: 0.8591 (m-30) REVERT: A 1733 MET cc_start: 0.8877 (tmm) cc_final: 0.8367 (tmm) REVERT: A 1770 TYR cc_start: 0.9118 (t80) cc_final: 0.8764 (t80) outliers start: 1 outliers final: 1 residues processed: 157 average time/residue: 0.0894 time to fit residues: 23.2882 Evaluate side-chains 126 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1670 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0570 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1659 GLN A1727 ASN A1799 ASN A2238 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.064751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.053373 restraints weight = 105744.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054548 restraints weight = 67635.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055345 restraints weight = 49778.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.055904 restraints weight = 40291.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.056288 restraints weight = 34952.443| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14487 Z= 0.136 Angle : 0.649 9.069 19840 Z= 0.313 Chirality : 0.042 0.216 2391 Planarity : 0.004 0.041 2494 Dihedral : 10.246 91.404 2250 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 1.19 % Allowed : 11.32 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1904 helix: 1.59 (0.16), residues: 1038 sheet: -0.68 (0.45), residues: 146 loop : -1.95 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2139 TYR 0.028 0.001 TYR A2016 PHE 0.022 0.001 PHE A1026 TRP 0.016 0.001 TRP A 31 HIS 0.006 0.001 HIS A1023 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (14472) covalent geometry : angle 0.64303 / 0.31 (19801) SS BOND : bond 0.00204 / 0.11 ( 6) SS BOND : angle 0.43368 / 0.27 ( 12) hydrogen bonds : bond 0.03623 / 2.37 ( 774) hydrogen bonds : angle 4.41851 / 3.34 ( 2289) link_BETA1-4 : bond 0.00286 / 0.14 ( 4) link_BETA1-4 : angle 1.80927 / 1.04 ( 12) link_NAG-ASN : bond 0.00499 / 0.26 ( 5) link_NAG-ASN : angle 2.77882 / 1.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.551 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 769 TYR cc_start: 0.9056 (t80) cc_final: 0.8834 (t80) REVERT: A 1026 PHE cc_start: 0.7847 (m-80) cc_final: 0.7571 (m-80) REVERT: A 1115 MET cc_start: 0.5981 (ppp) cc_final: 0.5758 (ppp) REVERT: A 1679 ASP cc_start: 0.8876 (m-30) cc_final: 0.8565 (m-30) REVERT: A 1690 MET cc_start: 0.8178 (mmt) cc_final: 0.7765 (mmt) REVERT: A 1733 MET cc_start: 0.8906 (tmm) cc_final: 0.8391 (tmm) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.0872 time to fit residues: 22.2019 Evaluate side-chains 137 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 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 = 0.3609 r_free = 0.3609 target = 0.065395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.054010 restraints weight = 105780.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055191 restraints weight = 67639.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056039 restraints weight = 49864.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056528 restraints weight = 40209.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056856 restraints weight = 34965.666| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14487 Z= 0.115 Angle : 0.633 9.620 19840 Z= 0.299 Chirality : 0.042 0.199 2391 Planarity : 0.004 0.039 2494 Dihedral : 8.495 72.035 2250 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 1.49 % Allowed : 15.26 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1904 helix: 1.68 (0.16), residues: 1039 sheet: -0.78 (0.44), residues: 148 loop : -1.94 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2139 TYR 0.021 0.001 TYR A1779 PHE 0.014 0.001 PHE A 734 TRP 0.012 0.001 TRP A 31 HIS 0.008 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (14472) covalent geometry : angle 0.62728 / 0.30 (19801) SS BOND : bond 0.00135 / 0.07 ( 6) SS BOND : angle 0.39443 / 0.24 ( 12) hydrogen bonds : bond 0.03387 / 2.22 ( 774) hydrogen bonds : angle 4.25348 / 3.22 ( 2289) link_BETA1-4 : bond 0.00391 / 0.19 ( 4) link_BETA1-4 : angle 1.74585 / 1.00 ( 12) link_NAG-ASN : bond 0.00572 / 0.30 ( 5) link_NAG-ASN : angle 2.75297 / 1.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.542 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 74 PHE cc_start: 0.9028 (t80) cc_final: 0.8761 (t80) REVERT: A 746 MET cc_start: 0.8775 (tpp) cc_final: 0.8548 (tpp) REVERT: A 769 TYR cc_start: 0.9020 (t80) cc_final: 0.8816 (t80) REVERT: A 1115 MET cc_start: 0.5996 (ppp) cc_final: 0.5782 (ppp) REVERT: A 1679 ASP cc_start: 0.8903 (m-30) cc_final: 0.8700 (m-30) REVERT: A 1690 MET cc_start: 0.8146 (mmt) cc_final: 0.7726 (mmt) REVERT: A 1733 MET cc_start: 0.8929 (tmm) cc_final: 0.8385 (tmm) REVERT: A 1735 TYR cc_start: 0.7605 (t80) cc_final: 0.7274 (t80) REVERT: A 2169 MET cc_start: 0.8775 (tpt) cc_final: 0.8030 (mpp) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 0.0894 time to fit residues: 23.0692 Evaluate side-chains 141 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 0.0040 chunk 14 optimal weight: 50.0000 chunk 100 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1426 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.053971 restraints weight = 104892.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055180 restraints weight = 67018.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055982 restraints weight = 49058.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.056542 restraints weight = 39688.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.056762 restraints weight = 34423.431| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14487 Z= 0.109 Angle : 0.633 11.111 19840 Z= 0.297 Chirality : 0.042 0.200 2391 Planarity : 0.004 0.039 2494 Dihedral : 7.564 71.814 2250 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.27 % Allowed : 18.09 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1904 helix: 1.73 (0.16), residues: 1039 sheet: -0.82 (0.43), residues: 156 loop : -1.91 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2139 TYR 0.018 0.001 TYR A1779 PHE 0.013 0.001 PHE A1026 TRP 0.013 0.001 TRP A 605 HIS 0.012 0.001 HIS A1016 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (14472) covalent geometry : angle 0.62737 / 0.30 (19801) SS BOND : bond 0.00125 / 0.07 ( 6) SS BOND : angle 0.38046 / 0.25 ( 12) hydrogen bonds : bond 0.03263 / 2.14 ( 774) hydrogen bonds : angle 4.17281 / 3.15 ( 2289) link_BETA1-4 : bond 0.00374 / 0.19 ( 4) link_BETA1-4 : angle 1.67049 / 0.96 ( 12) link_NAG-ASN : bond 0.00517 / 0.28 ( 5) link_NAG-ASN : angle 2.72042 / 1.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.587 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 74 PHE cc_start: 0.9038 (t80) cc_final: 0.8754 (t80) REVERT: A 659 MET cc_start: 0.8511 (mtt) cc_final: 0.8014 (mtm) REVERT: A 746 MET cc_start: 0.8810 (tpp) cc_final: 0.8493 (tpp) REVERT: A 769 TYR cc_start: 0.9031 (t80) cc_final: 0.8811 (t80) REVERT: A 1026 PHE cc_start: 0.7929 (m-80) cc_final: 0.7702 (m-80) REVERT: A 1115 MET cc_start: 0.5967 (ppp) cc_final: 0.5745 (ppp) REVERT: A 1679 ASP cc_start: 0.8889 (m-30) cc_final: 0.8676 (m-30) REVERT: A 1690 MET cc_start: 0.8107 (mmt) cc_final: 0.7603 (mmt) REVERT: A 1731 ASP cc_start: 0.8467 (p0) cc_final: 0.8244 (p0) REVERT: A 1733 MET cc_start: 0.8949 (tmm) cc_final: 0.8399 (tmm) REVERT: A 1735 TYR cc_start: 0.7523 (t80) cc_final: 0.7068 (t80) REVERT: A 2169 MET cc_start: 0.8821 (tpt) cc_final: 0.8089 (mpp) outliers start: 17 outliers final: 14 residues processed: 146 average time/residue: 0.0880 time to fit residues: 21.7445 Evaluate side-chains 144 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 0.0470 chunk 141 optimal weight: 0.7980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 HIS ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 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 = 0.3622 r_free = 0.3622 target = 0.065979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.054582 restraints weight = 105758.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.055809 restraints weight = 67585.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056510 restraints weight = 49440.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.057193 restraints weight = 40817.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.057519 restraints weight = 34686.141| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14487 Z= 0.105 Angle : 0.632 11.885 19840 Z= 0.293 Chirality : 0.042 0.237 2391 Planarity : 0.004 0.038 2494 Dihedral : 7.076 71.130 2250 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.94 % Allowed : 19.06 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1904 helix: 1.76 (0.16), residues: 1038 sheet: -0.80 (0.43), residues: 156 loop : -1.92 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.018 0.001 TYR A1779 PHE 0.012 0.001 PHE A 734 TRP 0.014 0.001 TRP A 605 HIS 0.009 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (14472) covalent geometry : angle 0.62665 / 0.29 (19801) SS BOND : bond 0.00106 / 0.06 ( 6) SS BOND : angle 0.35150 / 0.22 ( 12) hydrogen bonds : bond 0.03117 / 2.04 ( 774) hydrogen bonds : angle 4.09084 / 3.09 ( 2289) link_BETA1-4 : bond 0.00376 / 0.19 ( 4) link_BETA1-4 : angle 1.63653 / 0.94 ( 12) link_NAG-ASN : bond 0.00506 / 0.27 ( 5) link_NAG-ASN : angle 2.70915 / 1.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.689 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8781 (tpp) cc_final: 0.8457 (tpp) REVERT: A 769 TYR cc_start: 0.9016 (t80) cc_final: 0.8800 (t80) REVERT: A 1026 PHE cc_start: 0.7680 (m-80) cc_final: 0.7451 (m-80) REVERT: A 1115 MET cc_start: 0.6007 (ppp) cc_final: 0.5776 (ppp) REVERT: A 1679 ASP cc_start: 0.8876 (m-30) cc_final: 0.8653 (m-30) REVERT: A 1690 MET cc_start: 0.8103 (mmt) cc_final: 0.7616 (mmt) REVERT: A 1731 ASP cc_start: 0.8472 (p0) cc_final: 0.8211 (p0) REVERT: A 1733 MET cc_start: 0.8954 (tmm) cc_final: 0.8407 (tmm) REVERT: A 1735 TYR cc_start: 0.7550 (t80) cc_final: 0.7132 (t80) REVERT: A 2130 MET cc_start: 0.8472 (pmm) cc_final: 0.7686 (ptp) REVERT: A 2169 MET cc_start: 0.8843 (tpt) cc_final: 0.8171 (mpp) outliers start: 26 outliers final: 15 residues processed: 156 average time/residue: 0.0879 time to fit residues: 23.3059 Evaluate side-chains 149 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 120 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 79 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN A 635 GLN ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054184 restraints weight = 105393.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055400 restraints weight = 67478.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.056257 restraints weight = 49535.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.056757 restraints weight = 39776.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.057133 restraints weight = 34458.557| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14487 Z= 0.117 Angle : 0.648 13.552 19840 Z= 0.301 Chirality : 0.041 0.261 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.866 70.421 2250 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.86 % Allowed : 20.10 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.20), residues: 1904 helix: 1.76 (0.16), residues: 1037 sheet: -0.95 (0.42), residues: 158 loop : -1.91 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.018 0.001 TYR A1779 PHE 0.019 0.001 PHE A 802 TRP 0.012 0.001 TRP A 925 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (14472) covalent geometry : angle 0.64255 / 0.30 (19801) SS BOND : bond 0.00119 / 0.07 ( 6) SS BOND : angle 0.36844 / 0.25 ( 12) hydrogen bonds : bond 0.03176 / 2.09 ( 774) hydrogen bonds : angle 4.11232 / 3.10 ( 2289) link_BETA1-4 : bond 0.00379 / 0.19 ( 4) link_BETA1-4 : angle 1.59343 / 0.91 ( 12) link_NAG-ASN : bond 0.00441 / 0.23 ( 5) link_NAG-ASN : angle 2.74386 / 1.54 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.567 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 61 MET cc_start: 0.9052 (tpp) cc_final: 0.8852 (tpp) REVERT: A 293 MET cc_start: 0.9166 (pmm) cc_final: 0.8869 (pmm) REVERT: A 573 MET cc_start: 0.7171 (ptm) cc_final: 0.6894 (ptm) REVERT: A 746 MET cc_start: 0.8822 (tpp) cc_final: 0.8442 (tpp) REVERT: A 769 TYR cc_start: 0.9038 (t80) cc_final: 0.8797 (t80) REVERT: A 1115 MET cc_start: 0.6025 (ppp) cc_final: 0.5741 (ppp) REVERT: A 1386 LEU cc_start: 0.9015 (mm) cc_final: 0.8693 (mt) REVERT: A 1679 ASP cc_start: 0.8867 (m-30) cc_final: 0.8638 (m-30) REVERT: A 1690 MET cc_start: 0.8043 (mmt) cc_final: 0.7542 (mmt) REVERT: A 1733 MET cc_start: 0.8973 (tmm) cc_final: 0.8456 (tmm) REVERT: A 1735 TYR cc_start: 0.7655 (t80) cc_final: 0.7274 (t80) REVERT: A 2130 MET cc_start: 0.8587 (pmm) cc_final: 0.7710 (ptp) REVERT: A 2169 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8144 (mpp) outliers start: 25 outliers final: 22 residues processed: 152 average time/residue: 0.0879 time to fit residues: 22.6419 Evaluate side-chains 154 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2190 GLN Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 161 optimal weight: 0.1980 chunk 154 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.066109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.054729 restraints weight = 104522.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.055960 restraints weight = 66824.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.056817 restraints weight = 48951.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.057423 restraints weight = 39317.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.057770 restraints weight = 33734.385| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14487 Z= 0.108 Angle : 0.655 13.329 19840 Z= 0.302 Chirality : 0.041 0.307 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.731 70.310 2250 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.86 % Allowed : 20.63 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1904 helix: 1.78 (0.16), residues: 1038 sheet: -0.78 (0.43), residues: 156 loop : -1.89 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.017 0.001 TYR A1779 PHE 0.026 0.001 PHE A 655 TRP 0.014 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (14472) covalent geometry : angle 0.65018 / 0.30 (19801) SS BOND : bond 0.00093 / 0.05 ( 6) SS BOND : angle 0.33518 / 0.21 ( 12) hydrogen bonds : bond 0.03162 / 2.08 ( 774) hydrogen bonds : angle 4.05372 / 3.05 ( 2289) link_BETA1-4 : bond 0.00371 / 0.19 ( 4) link_BETA1-4 : angle 1.56997 / 0.90 ( 12) link_NAG-ASN : bond 0.00459 / 0.25 ( 5) link_NAG-ASN : angle 2.71221 / 1.52 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.456 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 293 MET cc_start: 0.9167 (pmm) cc_final: 0.8856 (pmm) REVERT: A 659 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8194 (mtm) REVERT: A 746 MET cc_start: 0.8780 (tpp) cc_final: 0.8400 (tpp) REVERT: A 769 TYR cc_start: 0.9000 (t80) cc_final: 0.8784 (t80) REVERT: A 1115 MET cc_start: 0.6028 (ppp) cc_final: 0.5768 (ppp) REVERT: A 1386 LEU cc_start: 0.9001 (mm) cc_final: 0.8672 (mt) REVERT: A 1609 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8979 (mm) REVERT: A 1679 ASP cc_start: 0.8855 (m-30) cc_final: 0.8621 (m-30) REVERT: A 1690 MET cc_start: 0.8018 (mmt) cc_final: 0.7546 (mmt) REVERT: A 1733 MET cc_start: 0.8947 (tmm) cc_final: 0.8411 (tmm) REVERT: A 1735 TYR cc_start: 0.7480 (t80) cc_final: 0.7121 (t80) REVERT: A 2130 MET cc_start: 0.8575 (pmm) cc_final: 0.7692 (ptm) REVERT: A 2169 MET cc_start: 0.8823 (tpt) cc_final: 0.8130 (mpp) outliers start: 25 outliers final: 18 residues processed: 154 average time/residue: 0.0838 time to fit residues: 21.9548 Evaluate side-chains 154 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2190 GLN Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 0.0070 chunk 115 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 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 = 0.3619 r_free = 0.3619 target = 0.065553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054190 restraints weight = 104265.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055404 restraints weight = 66923.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.056255 restraints weight = 49213.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.056787 restraints weight = 39735.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.057123 restraints weight = 34362.800| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14487 Z= 0.113 Angle : 0.668 13.444 19840 Z= 0.306 Chirality : 0.042 0.334 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.627 69.971 2250 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.79 % Allowed : 21.30 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1904 helix: 1.76 (0.16), residues: 1039 sheet: -0.87 (0.42), residues: 158 loop : -1.86 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.018 0.001 TYR A1779 PHE 0.022 0.001 PHE A 802 TRP 0.013 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (14472) covalent geometry : angle 0.66353 / 0.31 (19801) SS BOND : bond 0.00103 / 0.06 ( 6) SS BOND : angle 0.32921 / 0.21 ( 12) hydrogen bonds : bond 0.03150 / 2.07 ( 774) hydrogen bonds : angle 4.09650 / 3.08 ( 2289) link_BETA1-4 : bond 0.00380 / 0.19 ( 4) link_BETA1-4 : angle 1.56786 / 0.90 ( 12) link_NAG-ASN : bond 0.00420 / 0.22 ( 5) link_NAG-ASN : angle 2.73390 / 1.53 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.548 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.8897 (tpp) cc_final: 0.8655 (tpp) REVERT: A 293 MET cc_start: 0.9134 (pmm) cc_final: 0.8798 (pmm) REVERT: A 659 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8285 (mtm) REVERT: A 746 MET cc_start: 0.8816 (tpp) cc_final: 0.8414 (tpp) REVERT: A 769 TYR cc_start: 0.9010 (t80) cc_final: 0.8770 (t80) REVERT: A 1115 MET cc_start: 0.6062 (ppp) cc_final: 0.5781 (ppp) REVERT: A 1386 LEU cc_start: 0.9026 (mm) cc_final: 0.8709 (mt) REVERT: A 1609 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 1690 MET cc_start: 0.8011 (mmt) cc_final: 0.7603 (mmt) REVERT: A 1733 MET cc_start: 0.8968 (tmm) cc_final: 0.8469 (tmm) REVERT: A 1735 TYR cc_start: 0.7527 (t80) cc_final: 0.7194 (t80) REVERT: A 2130 MET cc_start: 0.8554 (pmm) cc_final: 0.7658 (ptm) REVERT: A 2169 MET cc_start: 0.8852 (tpt) cc_final: 0.8148 (mpp) outliers start: 24 outliers final: 19 residues processed: 150 average time/residue: 0.0852 time to fit residues: 21.6742 Evaluate side-chains 155 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 22 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 108 optimal weight: 0.5980 chunk 165 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 0.0040 chunk 46 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 0.0570 overall best weight: 1.1312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.065266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053919 restraints weight = 104889.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.055123 restraints weight = 67204.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.055975 restraints weight = 49319.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056565 restraints weight = 39854.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.056877 restraints weight = 34225.899| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14487 Z= 0.117 Angle : 0.667 13.395 19840 Z= 0.307 Chirality : 0.042 0.321 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.507 70.097 2250 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.94 % Allowed : 21.15 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1904 helix: 1.76 (0.16), residues: 1038 sheet: -0.91 (0.42), residues: 158 loop : -1.85 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.018 0.001 TYR A1779 PHE 0.022 0.001 PHE A 802 TRP 0.013 0.001 TRP A 605 HIS 0.011 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (14472) covalent geometry : angle 0.66230 / 0.31 (19801) SS BOND : bond 0.00106 / 0.06 ( 6) SS BOND : angle 0.33224 / 0.21 ( 12) hydrogen bonds : bond 0.03186 / 2.09 ( 774) hydrogen bonds : angle 4.10429 / 3.08 ( 2289) link_BETA1-4 : bond 0.00386 / 0.19 ( 4) link_BETA1-4 : angle 1.53781 / 0.88 ( 12) link_NAG-ASN : bond 0.00393 / 0.20 ( 5) link_NAG-ASN : angle 2.79000 / 1.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.443 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 61 MET cc_start: 0.8935 (tpp) cc_final: 0.8716 (tpp) REVERT: A 293 MET cc_start: 0.9100 (pmm) cc_final: 0.8759 (pmm) REVERT: A 659 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8378 (mtm) REVERT: A 708 MET cc_start: 0.8061 (tmm) cc_final: 0.7717 (tmm) REVERT: A 746 MET cc_start: 0.8788 (tpp) cc_final: 0.8385 (tpp) REVERT: A 769 TYR cc_start: 0.9001 (t80) cc_final: 0.8748 (t80) REVERT: A 1115 MET cc_start: 0.6059 (ppp) cc_final: 0.5731 (ppp) REVERT: A 1386 LEU cc_start: 0.9022 (mm) cc_final: 0.8698 (mt) REVERT: A 1733 MET cc_start: 0.8983 (tmm) cc_final: 0.8453 (tmm) REVERT: A 1735 TYR cc_start: 0.7556 (t80) cc_final: 0.7260 (t80) REVERT: A 2130 MET cc_start: 0.8623 (pmm) cc_final: 0.7787 (ptm) REVERT: A 2153 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8882 (p) REVERT: A 2169 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8158 (mpp) outliers start: 26 outliers final: 22 residues processed: 158 average time/residue: 0.0851 time to fit residues: 22.6389 Evaluate side-chains 162 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1991 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2190 GLN Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 0.0670 chunk 166 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.065478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054101 restraints weight = 104089.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055312 restraints weight = 66839.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.056163 restraints weight = 49258.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.056773 restraints weight = 39788.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057114 restraints weight = 34123.069| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14487 Z= 0.110 Angle : 0.684 14.028 19840 Z= 0.312 Chirality : 0.042 0.337 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.461 70.278 2250 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.71 % Allowed : 21.59 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.20), residues: 1904 helix: 1.73 (0.16), residues: 1039 sheet: -0.84 (0.42), residues: 158 loop : -1.86 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.018 0.001 TYR A1779 PHE 0.025 0.001 PHE A 802 TRP 0.014 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (14472) covalent geometry : angle 0.67906 / 0.31 (19801) SS BOND : bond 0.00091 / 0.05 ( 6) SS BOND : angle 0.33165 / 0.20 ( 12) hydrogen bonds : bond 0.03152 / 2.07 ( 774) hydrogen bonds : angle 4.12469 / 3.09 ( 2289) link_BETA1-4 : bond 0.00390 / 0.20 ( 4) link_BETA1-4 : angle 1.52837 / 0.88 ( 12) link_NAG-ASN : bond 0.00423 / 0.23 ( 5) link_NAG-ASN : angle 2.74617 / 1.55 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3808 Ramachandran restraints generated. 1904 Oldfield, 0 Emsley, 1904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.581 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 293 MET cc_start: 0.9100 (pmm) cc_final: 0.8734 (pmm) REVERT: A 659 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8368 (mtm) REVERT: A 746 MET cc_start: 0.8779 (tpp) cc_final: 0.8381 (tpp) REVERT: A 769 TYR cc_start: 0.8980 (t80) cc_final: 0.8742 (t80) REVERT: A 1115 MET cc_start: 0.6080 (ppp) cc_final: 0.5797 (ppp) REVERT: A 1386 LEU cc_start: 0.8984 (mm) cc_final: 0.8664 (mt) REVERT: A 1679 ASP cc_start: 0.8911 (m-30) cc_final: 0.8700 (m-30) REVERT: A 1733 MET cc_start: 0.8983 (tmm) cc_final: 0.8510 (tmm) REVERT: A 2130 MET cc_start: 0.8621 (pmm) cc_final: 0.7791 (ptm) REVERT: A 2153 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8879 (p) REVERT: A 2169 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8149 (mpp) outliers start: 23 outliers final: 19 residues processed: 156 average time/residue: 0.0757 time to fit residues: 20.2010 Evaluate side-chains 162 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1851 SER Chi-restraints excluded: chain A residue 1883 VAL Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 1998 VAL Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2153 THR Chi-restraints excluded: chain A residue 2169 MET Chi-restraints excluded: chain A residue 2190 GLN Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 186 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 155 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 612 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 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 = 0.3621 r_free = 0.3621 target = 0.065841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.054551 restraints weight = 104978.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.055774 restraints weight = 67018.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.056469 restraints weight = 49036.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.057151 restraints weight = 40545.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.057631 restraints weight = 34533.618| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14487 Z= 0.113 Angle : 0.688 13.841 19840 Z= 0.314 Chirality : 0.042 0.332 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.406 70.094 2250 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.71 % Allowed : 21.67 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1904 helix: 1.70 (0.16), residues: 1039 sheet: -0.63 (0.43), residues: 153 loop : -1.86 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.022 0.001 TYR A1735 PHE 0.024 0.001 PHE A 802 TRP 0.013 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14472) covalent geometry : angle 0.68318 / 0.31 (19801) SS BOND : bond 0.00095 / 0.05 ( 6) SS BOND : angle 0.32832 / 0.20 ( 12) hydrogen bonds : bond 0.03153 / 2.06 ( 774) hydrogen bonds : angle 4.12431 / 3.09 ( 2289) link_BETA1-4 : bond 0.00403 / 0.20 ( 4) link_BETA1-4 : angle 1.52994 / 0.89 ( 12) link_NAG-ASN : bond 0.00401 / 0.21 ( 5) link_NAG-ASN : angle 2.76067 / 1.58 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2243.39 seconds wall clock time: 39 minutes 47.76 seconds (2387.76 seconds total)