Starting phenix.real_space_refine on Sat Aug 23 22:03:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5b_28864/08_2025/8f5b_28864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5b_28864/08_2025/8f5b_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_28864/08_2025/8f5b_28864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5b_28864/08_2025/8f5b_28864.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f5b_28864/08_2025/8f5b_28864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5b_28864/08_2025/8f5b_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-2.0-5787/lib/python3.9/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: 9 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: 9 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: 2.96, per 1000 atoms: 0.21 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: 1.09 Conformation dependent library (CDL) restraints added in 601.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.41 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: 2.88 Time building geometry restraints manager: 1.41 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: 8161 24.81 - 49.62: 421 49.62 - 74.44: 70 74.44 - 99.25: 26 99.25 - 124.06: 16 Dihedral angle restraints: 8694 sinusoidal: 3131 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 8691 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 13.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 16.735 124.061 5074 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 aren 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 covalent geometry : bond 0.00415 (14472) covalent geometry : angle 0.71529 (19801) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.61619 ( 12) hydrogen bonds : bond 0.10194 ( 774) hydrogen bonds : angle 4.84039 ( 2289) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 1.67579 ( 12) link_NAG-ASN : bond 0.01266 ( 5) link_NAG-ASN : angle 3.48007 ( 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 : 0.543 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: 0.0819 time to fit residues: 21.5894 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 : 0.567 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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** 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 = 0.064740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053373 restraints weight = 105790.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.054564 restraints weight = 67604.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055372 restraints weight = 49604.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.055828 restraints weight = 40175.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056212 restraints weight = 35209.406| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0807 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= 0.134 Angle : 0.659 9.045 19840 Z= 0.315 Chirality : 0.043 0.222 2391 Planarity : 0.004 0.041 2494 Dihedral : 11.464 90.630 2288 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 1.19 % Allowed : 11.09 % Favored : 87.71 % 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 aren not related in a simple way. whole: 0.21 (0.20), residues: 1904 helix: 1.60 (0.16), residues: 1038 sheet: -0.68 (0.45), residues: 146 loop : -1.94 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2139 TYR 0.027 0.002 TYR A2016 PHE 0.020 0.001 PHE A1026 TRP 0.017 0.001 TRP A 31 HIS 0.007 0.001 HIS A1023 Details of bonding type rmsd covalent geometry : bond 0.00292 (14472) covalent geometry : angle 0.65284 (19801) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.42948 ( 12) hydrogen bonds : bond 0.03564 ( 774) hydrogen bonds : angle 4.41396 ( 2289) link_BETA1-4 : bond 0.00387 ( 4) link_BETA1-4 : angle 2.35192 ( 12) link_NAG-ASN : bond 0.00618 ( 5) link_NAG-ASN : angle 2.76796 ( 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 : 0.555 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 769 TYR cc_start: 0.9046 (t80) cc_final: 0.8838 (t80) REVERT: A 1026 PHE cc_start: 0.7810 (m-80) cc_final: 0.7535 (m-80) REVERT: A 1115 MET cc_start: 0.6005 (ppp) cc_final: 0.5777 (ppp) REVERT: A 1679 ASP cc_start: 0.8877 (m-30) cc_final: 0.8568 (m-30) REVERT: A 1690 MET cc_start: 0.8141 (mmt) cc_final: 0.7731 (mmt) REVERT: A 1733 MET cc_start: 0.8911 (tmm) cc_final: 0.8393 (tmm) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.0853 time to fit residues: 21.5720 Evaluate side-chains 139 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.485 ------------------------------------------------------------------------------- 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: 0.8980 chunk 123 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 165 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.064773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.053358 restraints weight = 105676.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.054539 restraints weight = 67444.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.055206 restraints weight = 49638.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.055887 restraints weight = 41232.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.056199 restraints weight = 35168.803| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1066 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= 0.123 Angle : 0.638 9.418 19840 Z= 0.302 Chirality : 0.043 0.204 2391 Planarity : 0.004 0.039 2494 Dihedral : 8.818 71.832 2288 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % Rotamer: Outliers : 1.71 % Allowed : 15.86 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.20), residues: 1904 helix: 1.66 (0.16), residues: 1039 sheet: -0.83 (0.44), residues: 148 loop : -1.94 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2139 TYR 0.022 0.001 TYR A1779 PHE 0.014 0.001 PHE A 734 TRP 0.013 0.001 TRP A 31 HIS 0.008 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00270 (14472) covalent geometry : angle 0.63079 (19801) SS BOND : bond 0.00149 ( 6) SS BOND : angle 0.40577 ( 12) hydrogen bonds : bond 0.03431 ( 774) hydrogen bonds : angle 4.27241 ( 2289) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 2.45101 ( 12) link_NAG-ASN : bond 0.00550 ( 5) link_NAG-ASN : angle 2.79109 ( 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 165 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.516 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 74 PHE cc_start: 0.9010 (t80) cc_final: 0.8768 (t80) REVERT: A 746 MET cc_start: 0.8796 (tpp) cc_final: 0.8542 (tpp) REVERT: A 769 TYR cc_start: 0.9052 (t80) cc_final: 0.8837 (t80) REVERT: A 840 MET cc_start: 0.8106 (mmp) cc_final: 0.7905 (mmp) REVERT: A 1115 MET cc_start: 0.6037 (ppp) cc_final: 0.5800 (ppp) REVERT: A 1679 ASP cc_start: 0.8906 (m-30) cc_final: 0.8705 (m-30) REVERT: A 1690 MET cc_start: 0.8150 (mmt) cc_final: 0.7687 (mmt) REVERT: A 1733 MET cc_start: 0.8941 (tmm) cc_final: 0.8399 (tmm) REVERT: A 1735 TYR cc_start: 0.7650 (t80) cc_final: 0.7319 (t80) REVERT: A 2101 MET cc_start: 0.7422 (ttt) cc_final: 0.7051 (tmm) REVERT: A 2169 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8039 (mpp) outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 0.0821 time to fit residues: 21.2894 Evaluate side-chains 144 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 1701 LEU 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 2169 MET 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: 0.3980 chunk 14 optimal weight: 50.0000 chunk 100 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 42 optimal weight: 0.0170 chunk 180 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.064443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.053032 restraints weight = 104824.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054205 restraints weight = 66915.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055046 restraints weight = 49246.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.055523 restraints weight = 39855.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.055945 restraints weight = 34702.180| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1229 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= 0.126 Angle : 0.634 10.323 19840 Z= 0.301 Chirality : 0.042 0.193 2391 Planarity : 0.004 0.038 2494 Dihedral : 7.613 71.726 2288 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.56 % Allowed : 18.84 % Favored : 79.60 % 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 aren not related in a simple way. whole: 0.29 (0.20), residues: 1904 helix: 1.70 (0.16), residues: 1039 sheet: -0.79 (0.45), residues: 142 loop : -1.94 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2139 TYR 0.019 0.001 TYR A1779 PHE 0.013 0.001 PHE A 734 TRP 0.012 0.001 TRP A 605 HIS 0.009 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00277 (14472) covalent geometry : angle 0.62780 (19801) SS BOND : bond 0.00161 ( 6) SS BOND : angle 0.42007 ( 12) hydrogen bonds : bond 0.03359 ( 774) hydrogen bonds : angle 4.23849 ( 2289) link_BETA1-4 : bond 0.00356 ( 4) link_BETA1-4 : angle 2.24915 ( 12) link_NAG-ASN : bond 0.00487 ( 5) link_NAG-ASN : angle 2.79176 ( 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 158 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.386 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8800 (tpp) cc_final: 0.8489 (tpp) REVERT: A 769 TYR cc_start: 0.9051 (t80) cc_final: 0.8807 (t80) REVERT: A 1026 PHE cc_start: 0.8054 (m-80) cc_final: 0.7823 (m-80) REVERT: A 1115 MET cc_start: 0.6058 (ppp) cc_final: 0.5768 (ppp) REVERT: A 1679 ASP cc_start: 0.8897 (m-30) cc_final: 0.8682 (m-30) REVERT: A 1690 MET cc_start: 0.8090 (mmt) cc_final: 0.7604 (mmt) REVERT: A 1731 ASP cc_start: 0.8490 (p0) cc_final: 0.8257 (p0) REVERT: A 1733 MET cc_start: 0.8948 (tmm) cc_final: 0.8392 (tmm) REVERT: A 1735 TYR cc_start: 0.7662 (t80) cc_final: 0.7400 (t80) REVERT: A 2169 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8146 (mpp) outliers start: 21 outliers final: 15 residues processed: 148 average time/residue: 0.0749 time to fit residues: 19.0229 Evaluate side-chains 146 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 1691 SER 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 2085 LEU Chi-restraints excluded: chain A residue 2169 MET 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: 5.9990 chunk 87 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3603 r_free = 0.3603 target = 0.064873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.053471 restraints weight = 106048.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.054660 restraints weight = 67713.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.055441 restraints weight = 49725.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.056038 restraints weight = 40324.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.056339 restraints weight = 34806.309| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1332 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= 0.113 Angle : 0.640 11.707 19840 Z= 0.299 Chirality : 0.042 0.236 2391 Planarity : 0.004 0.038 2494 Dihedral : 7.171 71.079 2288 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.86 % Allowed : 20.18 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.20), residues: 1904 helix: 1.71 (0.16), residues: 1039 sheet: -1.00 (0.43), residues: 158 loop : -1.91 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.019 0.001 TYR A1779 PHE 0.013 0.001 PHE A 734 TRP 0.012 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00248 (14472) covalent geometry : angle 0.63445 (19801) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.38620 ( 12) hydrogen bonds : bond 0.03249 ( 774) hydrogen bonds : angle 4.17764 ( 2289) link_BETA1-4 : bond 0.00398 ( 4) link_BETA1-4 : angle 2.02356 ( 12) link_NAG-ASN : bond 0.00492 ( 5) link_NAG-ASN : angle 2.76967 ( 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 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.348 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8826 (tpp) cc_final: 0.8467 (tpp) REVERT: A 769 TYR cc_start: 0.9026 (t80) cc_final: 0.8798 (t80) REVERT: A 1026 PHE cc_start: 0.7784 (m-80) cc_final: 0.7546 (m-80) REVERT: A 1115 MET cc_start: 0.6052 (ppp) cc_final: 0.5758 (ppp) REVERT: A 1679 ASP cc_start: 0.8876 (m-30) cc_final: 0.8654 (m-30) REVERT: A 1690 MET cc_start: 0.8000 (mmt) cc_final: 0.7391 (mmt) REVERT: A 1700 TYR cc_start: 0.8133 (t80) cc_final: 0.7925 (t80) REVERT: A 1731 ASP cc_start: 0.8505 (p0) cc_final: 0.8235 (p0) REVERT: A 1733 MET cc_start: 0.8984 (tmm) cc_final: 0.8448 (tmm) REVERT: A 1735 TYR cc_start: 0.7673 (t80) cc_final: 0.7261 (t80) REVERT: A 2169 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8178 (mpp) outliers start: 25 outliers final: 16 residues processed: 150 average time/residue: 0.0710 time to fit residues: 17.8991 Evaluate side-chains 148 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL 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 1459 THR Chi-restraints excluded: chain A residue 1670 GLU 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 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 2218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 120 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3587 r_free = 0.3587 target = 0.064143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.052770 restraints weight = 106679.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053945 restraints weight = 67772.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.054763 restraints weight = 49635.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.055216 restraints weight = 40221.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.055690 restraints weight = 35305.252| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1449 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= 0.131 Angle : 0.645 11.596 19840 Z= 0.305 Chirality : 0.042 0.223 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.945 70.457 2288 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.38 % Allowed : 20.18 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.20), residues: 1904 helix: 1.71 (0.16), residues: 1039 sheet: -1.15 (0.42), residues: 158 loop : -1.90 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2139 TYR 0.019 0.001 TYR A1779 PHE 0.013 0.001 PHE A 734 TRP 0.013 0.001 TRP A 605 HIS 0.011 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00289 (14472) covalent geometry : angle 0.63948 (19801) SS BOND : bond 0.00153 ( 6) SS BOND : angle 0.41631 ( 12) hydrogen bonds : bond 0.03293 ( 774) hydrogen bonds : angle 4.18143 ( 2289) link_BETA1-4 : bond 0.00372 ( 4) link_BETA1-4 : angle 1.78962 ( 12) link_NAG-ASN : bond 0.00448 ( 5) link_NAG-ASN : angle 2.83400 ( 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 167 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.462 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 61 MET cc_start: 0.9022 (tpp) cc_final: 0.8790 (tpp) REVERT: A 573 MET cc_start: 0.7283 (ptm) cc_final: 0.6998 (ptm) REVERT: A 769 TYR cc_start: 0.9062 (t80) cc_final: 0.8823 (t80) REVERT: A 1007 MET cc_start: 0.8674 (tpp) cc_final: 0.8444 (tpp) REVERT: A 1026 PHE cc_start: 0.7828 (m-80) cc_final: 0.7610 (m-80) REVERT: A 1115 MET cc_start: 0.6091 (ppp) cc_final: 0.5773 (ppp) REVERT: A 1386 LEU cc_start: 0.9087 (mm) cc_final: 0.8751 (mt) REVERT: A 1679 ASP cc_start: 0.8877 (m-30) cc_final: 0.8651 (m-30) REVERT: A 1690 MET cc_start: 0.8005 (mmt) cc_final: 0.7393 (mmt) REVERT: A 1700 TYR cc_start: 0.8091 (t80) cc_final: 0.7465 (t80) REVERT: A 1733 MET cc_start: 0.8980 (tmm) cc_final: 0.8447 (tmm) REVERT: A 1735 TYR cc_start: 0.7664 (t80) cc_final: 0.7312 (t80) REVERT: A 2169 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8170 (mpp) outliers start: 32 outliers final: 25 residues processed: 154 average time/residue: 0.0775 time to fit residues: 20.0092 Evaluate side-chains 157 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 659 MET 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 733 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 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 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: 5.9990 chunk 107 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 161 optimal weight: 0.0770 chunk 154 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3593 r_free = 0.3593 target = 0.064350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.052966 restraints weight = 105136.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.054162 restraints weight = 66835.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.054927 restraints weight = 49058.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055538 restraints weight = 39890.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055848 restraints weight = 34246.279| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14487 Z= 0.120 Angle : 0.658 12.967 19840 Z= 0.306 Chirality : 0.042 0.277 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.838 70.208 2288 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.31 % Allowed : 20.92 % Favored : 76.77 % 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 aren not related in a simple way. whole: 0.31 (0.20), residues: 1904 helix: 1.75 (0.16), residues: 1039 sheet: -1.14 (0.42), residues: 158 loop : -1.89 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.019 0.001 TYR A1779 PHE 0.025 0.001 PHE A 655 TRP 0.012 0.001 TRP A 605 HIS 0.011 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00265 (14472) covalent geometry : angle 0.65241 (19801) SS BOND : bond 0.00128 ( 6) SS BOND : angle 0.39119 ( 12) hydrogen bonds : bond 0.03285 ( 774) hydrogen bonds : angle 4.14564 ( 2289) link_BETA1-4 : bond 0.00370 ( 4) link_BETA1-4 : angle 1.73748 ( 12) link_NAG-ASN : bond 0.00427 ( 5) link_NAG-ASN : angle 2.81739 ( 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 168 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.357 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 293 MET cc_start: 0.9183 (pmm) cc_final: 0.8905 (pmm) REVERT: A 659 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8235 (mtm) REVERT: A 746 MET cc_start: 0.8835 (tpp) cc_final: 0.8420 (tpp) REVERT: A 769 TYR cc_start: 0.9043 (t80) cc_final: 0.8807 (t80) REVERT: A 1007 MET cc_start: 0.8684 (tpp) cc_final: 0.8426 (tpp) REVERT: A 1115 MET cc_start: 0.6086 (ppp) cc_final: 0.5744 (ppp) REVERT: A 1386 LEU cc_start: 0.9094 (mm) cc_final: 0.8752 (mt) REVERT: A 1679 ASP cc_start: 0.8870 (m-30) cc_final: 0.8644 (m-30) REVERT: A 1690 MET cc_start: 0.8007 (mmt) cc_final: 0.7446 (mmt) REVERT: A 1700 TYR cc_start: 0.8089 (t80) cc_final: 0.7500 (t80) REVERT: A 1733 MET cc_start: 0.8989 (tmm) cc_final: 0.8453 (tmm) REVERT: A 1735 TYR cc_start: 0.7597 (t80) cc_final: 0.7279 (t80) REVERT: A 2169 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8170 (mpp) outliers start: 31 outliers final: 26 residues processed: 155 average time/residue: 0.0724 time to fit residues: 18.8677 Evaluate side-chains 158 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 130 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL 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 733 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 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 2085 LEU Chi-restraints excluded: chain A residue 2144 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 0.0970 chunk 14 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 115 optimal weight: 0.0070 chunk 143 optimal weight: 0.0060 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 overall best weight: 0.2612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A2190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.065548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.054178 restraints weight = 104215.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055393 restraints weight = 66389.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056242 restraints weight = 48751.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.056754 restraints weight = 39260.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.057182 restraints weight = 34053.504| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1612 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= 0.111 Angle : 0.673 13.840 19840 Z= 0.310 Chirality : 0.042 0.301 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.694 70.148 2288 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.79 % Allowed : 22.19 % Favored : 76.02 % 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 aren not related in a simple way. whole: 0.32 (0.20), residues: 1904 helix: 1.73 (0.16), residues: 1037 sheet: -0.98 (0.42), residues: 158 loop : -1.89 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.016 0.001 TYR A1779 PHE 0.020 0.001 PHE A 655 TRP 0.015 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00234 (14472) covalent geometry : angle 0.66816 (19801) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.37122 ( 12) hydrogen bonds : bond 0.03215 ( 774) hydrogen bonds : angle 4.07516 ( 2289) link_BETA1-4 : bond 0.00382 ( 4) link_BETA1-4 : angle 1.68394 ( 12) link_NAG-ASN : bond 0.00479 ( 5) link_NAG-ASN : angle 2.75354 ( 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 170 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.556 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.8939 (tpp) cc_final: 0.8702 (tpp) REVERT: A 293 MET cc_start: 0.9175 (pmm) cc_final: 0.8882 (pmm) REVERT: A 659 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8365 (mtm) REVERT: A 746 MET cc_start: 0.8786 (tpp) cc_final: 0.8383 (tpp) REVERT: A 769 TYR cc_start: 0.9024 (t80) cc_final: 0.8782 (t80) REVERT: A 1007 MET cc_start: 0.8703 (tpp) cc_final: 0.8477 (tpp) REVERT: A 1115 MET cc_start: 0.5965 (ppp) cc_final: 0.5682 (ppp) REVERT: A 1386 LEU cc_start: 0.9056 (mm) cc_final: 0.8713 (mt) REVERT: A 1679 ASP cc_start: 0.8837 (m-30) cc_final: 0.8609 (m-30) REVERT: A 1690 MET cc_start: 0.7969 (mmt) cc_final: 0.7376 (mmt) REVERT: A 1700 TYR cc_start: 0.8109 (t80) cc_final: 0.7576 (t80) REVERT: A 1733 MET cc_start: 0.8977 (tmm) cc_final: 0.8425 (tmm) REVERT: A 2169 MET cc_start: 0.8840 (tpt) cc_final: 0.8164 (mpp) outliers start: 24 outliers final: 19 residues processed: 161 average time/residue: 0.0737 time to fit residues: 20.2082 Evaluate side-chains 156 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 1998 VAL Chi-restraints excluded: chain A residue 2085 LEU 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: 2.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 46 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.0060 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3617 r_free = 0.3617 target = 0.065658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054316 restraints weight = 105262.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.055534 restraints weight = 67026.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.056384 restraints weight = 49177.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.056884 restraints weight = 39565.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.057318 restraints weight = 34378.349| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14487 Z= 0.112 Angle : 0.686 13.940 19840 Z= 0.316 Chirality : 0.042 0.310 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.549 69.725 2288 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.64 % Allowed : 23.16 % Favored : 75.20 % 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 aren not related in a simple way. whole: 0.33 (0.20), residues: 1904 helix: 1.72 (0.16), residues: 1035 sheet: -0.91 (0.42), residues: 158 loop : -1.85 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.044 0.001 TYR A1735 PHE 0.024 0.001 PHE A 802 TRP 0.015 0.001 TRP A 605 HIS 0.011 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00245 (14472) covalent geometry : angle 0.68128 (19801) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.34132 ( 12) hydrogen bonds : bond 0.03195 ( 774) hydrogen bonds : angle 4.16087 ( 2289) link_BETA1-4 : bond 0.00412 ( 4) link_BETA1-4 : angle 1.65327 ( 12) link_NAG-ASN : bond 0.00430 ( 5) link_NAG-ASN : angle 2.76940 ( 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 161 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.381 Fit side-chains REVERT: A 293 MET cc_start: 0.9132 (pmm) cc_final: 0.8811 (pmm) REVERT: A 659 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8359 (mtm) REVERT: A 746 MET cc_start: 0.8816 (tpp) cc_final: 0.8384 (tpp) REVERT: A 769 TYR cc_start: 0.9026 (t80) cc_final: 0.8772 (t80) REVERT: A 1115 MET cc_start: 0.6067 (ppp) cc_final: 0.5793 (ppp) REVERT: A 1386 LEU cc_start: 0.9046 (mm) cc_final: 0.8730 (mt) REVERT: A 1679 ASP cc_start: 0.8838 (m-30) cc_final: 0.8597 (m-30) REVERT: A 1690 MET cc_start: 0.8360 (mmt) cc_final: 0.7963 (mmt) REVERT: A 1700 TYR cc_start: 0.8103 (t80) cc_final: 0.7507 (t80) REVERT: A 1733 MET cc_start: 0.8928 (tmm) cc_final: 0.8429 (tmm) REVERT: A 2153 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 2169 MET cc_start: 0.8861 (tpt) cc_final: 0.8169 (mpp) outliers start: 22 outliers final: 18 residues processed: 153 average time/residue: 0.0791 time to fit residues: 20.6276 Evaluate side-chains 156 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 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 1998 VAL Chi-restraints excluded: chain A residue 2085 LEU Chi-restraints excluded: chain A residue 2144 VAL Chi-restraints excluded: chain A residue 2153 THR 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: 7.9990 chunk 55 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3607 r_free = 0.3607 target = 0.065264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.053966 restraints weight = 105096.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.055164 restraints weight = 67261.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.056048 restraints weight = 49366.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.056549 restraints weight = 39723.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.057041 restraints weight = 34377.204| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 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 0.033 14487 Z= 0.118 Angle : 0.684 13.637 19840 Z= 0.316 Chirality : 0.042 0.325 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.358 69.726 2285 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.64 % Allowed : 23.16 % Favored : 75.20 % 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 aren not related in a simple way. whole: 0.37 (0.20), residues: 1904 helix: 1.73 (0.16), residues: 1037 sheet: -0.86 (0.43), residues: 158 loop : -1.81 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.036 0.001 TYR A1735 PHE 0.023 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 covalent geometry : bond 0.00261 (14472) covalent geometry : angle 0.67947 (19801) SS BOND : bond 0.00107 ( 6) SS BOND : angle 0.34013 ( 12) hydrogen bonds : bond 0.03246 ( 774) hydrogen bonds : angle 4.17921 ( 2289) link_BETA1-4 : bond 0.00378 ( 4) link_BETA1-4 : angle 1.61917 ( 12) link_NAG-ASN : bond 0.00381 ( 5) link_NAG-ASN : angle 2.79520 ( 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 160 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.322 Fit side-chains REVERT: A 66 MET cc_start: 0.8550 (mmp) cc_final: 0.8203 (mmt) REVERT: A 293 MET cc_start: 0.9102 (pmm) cc_final: 0.8777 (pmm) REVERT: A 659 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8342 (mtm) REVERT: A 769 TYR cc_start: 0.9014 (t80) cc_final: 0.8749 (t80) REVERT: A 1115 MET cc_start: 0.6050 (ppp) cc_final: 0.5713 (ppp) REVERT: A 1386 LEU cc_start: 0.9066 (mm) cc_final: 0.8744 (mt) REVERT: A 1679 ASP cc_start: 0.8841 (m-30) cc_final: 0.8598 (m-30) REVERT: A 1690 MET cc_start: 0.8336 (mmt) cc_final: 0.7882 (mmt) REVERT: A 1700 TYR cc_start: 0.8121 (t80) cc_final: 0.7584 (t80) REVERT: A 1733 MET cc_start: 0.8963 (tmm) cc_final: 0.8483 (tmm) REVERT: A 2153 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 2169 MET cc_start: 0.8830 (tpt) cc_final: 0.8170 (mpp) outliers start: 22 outliers final: 20 residues processed: 152 average time/residue: 0.0729 time to fit residues: 18.7200 Evaluate side-chains 159 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 1373 PHE Chi-restraints excluded: chain A residue 1378 VAL 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 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 2144 VAL Chi-restraints excluded: chain A residue 2153 THR 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: 0.7980 chunk 33 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 13 optimal weight: 40.0000 chunk 135 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3614 r_free = 0.3614 target = 0.065538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054250 restraints weight = 105360.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055461 restraints weight = 67227.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.056304 restraints weight = 49334.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056805 restraints weight = 39797.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.057298 restraints weight = 34463.904| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1807 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= 0.112 Angle : 0.686 13.869 19840 Z= 0.315 Chirality : 0.042 0.334 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.304 69.772 2285 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.64 % Allowed : 23.23 % Favored : 75.13 % 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 aren not related in a simple way. whole: 0.36 (0.20), residues: 1904 helix: 1.72 (0.16), residues: 1036 sheet: -0.83 (0.43), residues: 158 loop : -1.81 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A2139 TYR 0.036 0.001 TYR A1735 PHE 0.023 0.001 PHE A 802 TRP 0.015 0.001 TRP A 605 HIS 0.011 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00247 (14472) covalent geometry : angle 0.68087 (19801) SS BOND : bond 0.00095 ( 6) SS BOND : angle 0.35278 ( 12) hydrogen bonds : bond 0.03202 ( 774) hydrogen bonds : angle 4.16575 ( 2289) link_BETA1-4 : bond 0.00391 ( 4) link_BETA1-4 : angle 1.60635 ( 12) link_NAG-ASN : bond 0.00393 ( 5) link_NAG-ASN : angle 2.76294 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.80 seconds wall clock time: 34 minutes 22.76 seconds (2062.76 seconds total)