Starting phenix.real_space_refine on Fri Jun 13 11:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f5b_28864/06_2025/8f5b_28864.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f5b_28864/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f5b_28864/06_2025/8f5b_28864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f5b_28864/06_2025/8f5b_28864.map" model { file = "/net/cci-nas-00/data/ceres_data/8f5b_28864/06_2025/8f5b_28864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f5b_28864/06_2025/8f5b_28864.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 21, 'ASP:plan': 37, 'TYR:plan': 13, 'ASN:plan1': 21, 'TRP:plan': 9, 'HIS:plan': 9, 'PHE:plan': 22, 'GLU:plan': 54, 'ARG:plan': 35} 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: 8.98, per 1000 atoms: 0.63 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: 3.99 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.99 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: 5.51 Time building geometry restraints manager: 4.65 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.640 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- 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 : 14.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (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 TRP 0.025 0.001 TRP A 31 HIS 0.006 0.001 HIS A 52 PHE 0.023 0.001 PHE A 655 TYR 0.026 0.001 TYR A1735 ARG 0.002 0.000 ARG A2139 Details of bonding type rmsd link_NAG-ASN : bond 0.01266 ( 5) link_NAG-ASN : angle 3.48007 ( 15) link_BETA1-4 : bond 0.00421 ( 4) link_BETA1-4 : angle 1.67579 ( 12) hydrogen bonds : bond 0.10194 ( 774) hydrogen bonds : angle 4.84039 ( 2289) SS BOND : bond 0.00187 ( 6) SS BOND : angle 0.61619 ( 12) covalent geometry : bond 0.00415 (14472) covalent geometry : angle 0.71529 (19801) *********************** 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 : 1.667 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: 0.2123 time to fit residues: 55.1507 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 : 1.582 ------------------------------------------------------------------------------- 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 162 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.0570 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 0.0370 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.065119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.053786 restraints weight = 104632.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.054959 restraints weight = 67022.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.055734 restraints weight = 49468.941| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0826 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= 0.126 Angle : 0.656 9.204 19840 Z= 0.313 Chirality : 0.043 0.225 2391 Planarity : 0.004 0.041 2494 Dihedral : 11.390 89.441 2288 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 1.19 % Allowed : 11.47 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (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 TRP 0.017 0.001 TRP A 31 HIS 0.007 0.001 HIS A1023 PHE 0.017 0.001 PHE A1728 TYR 0.028 0.001 TYR A2016 ARG 0.005 0.000 ARG A2139 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 5) link_NAG-ASN : angle 2.81187 ( 15) link_BETA1-4 : bond 0.00335 ( 4) link_BETA1-4 : angle 2.38181 ( 12) hydrogen bonds : bond 0.03546 ( 774) hydrogen bonds : angle 4.39008 ( 2289) SS BOND : bond 0.00196 ( 6) SS BOND : angle 0.43271 ( 12) covalent geometry : bond 0.00273 (14472) covalent geometry : angle 0.64927 (19801) *********************** 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 : 1.842 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 1026 PHE cc_start: 0.7780 (m-80) cc_final: 0.7488 (m-80) REVERT: A 1679 ASP cc_start: 0.8884 (m-30) cc_final: 0.8579 (m-30) REVERT: A 1690 MET cc_start: 0.8207 (mmt) cc_final: 0.7801 (mmt) REVERT: A 1733 MET cc_start: 0.8917 (tmm) cc_final: 0.8398 (tmm) outliers start: 16 outliers final: 12 residues processed: 150 average time/residue: 0.2047 time to fit residues: 51.8856 Evaluate side-chains 138 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 1 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 11 optimal weight: 0.0370 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 chunk 8 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1820 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.064857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.053465 restraints weight = 104934.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.054621 restraints weight = 67279.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.055464 restraints weight = 49666.443| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1045 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= 0.119 Angle : 0.637 9.663 19840 Z= 0.301 Chirality : 0.042 0.219 2391 Planarity : 0.004 0.039 2494 Dihedral : 8.953 71.989 2288 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 1.64 % Allowed : 15.56 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1904 helix: 1.68 (0.16), residues: 1039 sheet: -0.72 (0.44), residues: 148 loop : -1.94 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 31 HIS 0.008 0.001 HIS A 52 PHE 0.014 0.001 PHE A 734 TYR 0.021 0.001 TYR A1779 ARG 0.002 0.000 ARG A 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00563 ( 5) link_NAG-ASN : angle 2.76590 ( 15) link_BETA1-4 : bond 0.00376 ( 4) link_BETA1-4 : angle 2.43092 ( 12) hydrogen bonds : bond 0.03380 ( 774) hydrogen bonds : angle 4.25801 ( 2289) SS BOND : bond 0.00154 ( 6) SS BOND : angle 0.37247 ( 12) covalent geometry : bond 0.00257 (14472) covalent geometry : angle 0.63048 (19801) *********************** 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 162 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.693 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 74 PHE cc_start: 0.9037 (t80) cc_final: 0.8787 (t80) REVERT: A 659 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: A 746 MET cc_start: 0.8772 (tpp) cc_final: 0.8394 (tpp) REVERT: A 769 TYR cc_start: 0.9062 (t80) cc_final: 0.8852 (t80) REVERT: A 1026 PHE cc_start: 0.7736 (m-80) cc_final: 0.7436 (m-80) REVERT: A 1690 MET cc_start: 0.8152 (mmt) cc_final: 0.7707 (mmt) REVERT: A 1733 MET cc_start: 0.8949 (tmm) cc_final: 0.8408 (tmm) REVERT: A 1735 TYR cc_start: 0.7644 (t80) cc_final: 0.7302 (t80) REVERT: A 2169 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8056 (mpp) outliers start: 22 outliers final: 14 residues processed: 150 average time/residue: 0.2096 time to fit residues: 52.9356 Evaluate side-chains 145 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 163 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 108 optimal weight: 0.0070 chunk 182 optimal weight: 0.9990 chunk 65 optimal weight: 0.0040 chunk 161 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN A 635 GLN ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.064511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.053163 restraints weight = 104287.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054314 restraints weight = 66807.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.055128 restraints weight = 49325.542| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1207 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= 0.132 Angle : 0.637 9.814 19840 Z= 0.302 Chirality : 0.042 0.199 2391 Planarity : 0.004 0.038 2494 Dihedral : 7.623 71.901 2288 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.71 % Allowed : 18.54 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1904 helix: 1.70 (0.16), residues: 1039 sheet: -0.77 (0.44), residues: 148 loop : -1.95 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 925 HIS 0.009 0.001 HIS A 52 PHE 0.014 0.001 PHE A 734 TYR 0.019 0.001 TYR A1779 ARG 0.003 0.000 ARG A2139 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 5) link_NAG-ASN : angle 2.79924 ( 15) link_BETA1-4 : bond 0.00373 ( 4) link_BETA1-4 : angle 2.24570 ( 12) hydrogen bonds : bond 0.03335 ( 774) hydrogen bonds : angle 4.23916 ( 2289) SS BOND : bond 0.00168 ( 6) SS BOND : angle 0.42868 ( 12) covalent geometry : bond 0.00288 (14472) covalent geometry : angle 0.63061 (19801) *********************** 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 160 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 1.678 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8785 (tpp) cc_final: 0.8350 (tpp) REVERT: A 769 TYR cc_start: 0.9072 (t80) cc_final: 0.8841 (t80) REVERT: A 1690 MET cc_start: 0.8120 (mmt) cc_final: 0.7627 (mmt) REVERT: A 1731 ASP cc_start: 0.8532 (p0) cc_final: 0.8301 (p0) REVERT: A 1733 MET cc_start: 0.8961 (tmm) cc_final: 0.8409 (tmm) REVERT: A 1735 TYR cc_start: 0.7686 (t80) cc_final: 0.7430 (t80) REVERT: A 2130 MET cc_start: 0.7046 (ptp) cc_final: 0.6773 (ptp) REVERT: A 2169 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8155 (mpp) outliers start: 23 outliers final: 15 residues processed: 149 average time/residue: 0.2021 time to fit residues: 50.8304 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 : 1.661 ------------------------------------------------------------------------------- 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 54 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 118 optimal weight: 0.0040 chunk 156 optimal weight: 8.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.065170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.053753 restraints weight = 105120.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.054951 restraints weight = 67138.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055741 restraints weight = 49436.439| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1328 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= 0.110 Angle : 0.642 11.742 19840 Z= 0.299 Chirality : 0.042 0.218 2391 Planarity : 0.004 0.038 2494 Dihedral : 7.155 71.242 2288 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.71 % Allowed : 19.96 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1904 helix: 1.71 (0.16), residues: 1039 sheet: -0.72 (0.44), residues: 148 loop : -1.96 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 PHE 0.013 0.001 PHE A 734 TYR 0.018 0.001 TYR A1779 ARG 0.002 0.000 ARG A2139 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 5) link_NAG-ASN : angle 2.75432 ( 15) link_BETA1-4 : bond 0.00384 ( 4) link_BETA1-4 : angle 2.01452 ( 12) hydrogen bonds : bond 0.03234 ( 774) hydrogen bonds : angle 4.16104 ( 2289) SS BOND : bond 0.00120 ( 6) SS BOND : angle 0.38279 ( 12) covalent geometry : bond 0.00240 (14472) covalent geometry : angle 0.63664 (19801) *********************** 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 161 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 1.741 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 746 MET cc_start: 0.8805 (tpp) cc_final: 0.8354 (tpp) REVERT: A 769 TYR cc_start: 0.9027 (t80) cc_final: 0.8817 (t80) REVERT: A 1018 LEU cc_start: 0.8710 (tp) cc_final: 0.8263 (tp) REVERT: A 1690 MET cc_start: 0.8080 (mmt) cc_final: 0.7551 (mmt) REVERT: A 1700 TYR cc_start: 0.8144 (t80) cc_final: 0.7922 (t80) REVERT: A 1731 ASP cc_start: 0.8531 (p0) cc_final: 0.8268 (p0) REVERT: A 1733 MET cc_start: 0.8964 (tmm) cc_final: 0.8420 (tmm) REVERT: A 1735 TYR cc_start: 0.7666 (t80) cc_final: 0.7231 (t80) REVERT: A 2143 MET cc_start: 0.8800 (ptm) cc_final: 0.8595 (ttt) REVERT: A 2169 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8156 (mpp) outliers start: 23 outliers final: 14 residues processed: 149 average time/residue: 0.2044 time to fit residues: 51.3318 Evaluate side-chains 146 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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 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 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 122 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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** A1426 GLN A2190 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.064602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.053239 restraints weight = 105775.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.054421 restraints weight = 67499.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.055264 restraints weight = 49482.859| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14487 Z= 0.130 Angle : 0.643 11.881 19840 Z= 0.304 Chirality : 0.042 0.244 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.956 70.621 2288 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.31 % Allowed : 20.18 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1904 helix: 1.71 (0.16), residues: 1039 sheet: -1.01 (0.42), residues: 158 loop : -1.91 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 PHE 0.012 0.001 PHE A 734 TYR 0.018 0.001 TYR A1779 ARG 0.002 0.000 ARG A2139 Details of bonding type rmsd link_NAG-ASN : bond 0.00442 ( 5) link_NAG-ASN : angle 2.81509 ( 15) link_BETA1-4 : bond 0.00366 ( 4) link_BETA1-4 : angle 1.83380 ( 12) hydrogen bonds : bond 0.03270 ( 774) hydrogen bonds : angle 4.17926 ( 2289) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.40518 ( 12) covalent geometry : bond 0.00288 (14472) covalent geometry : angle 0.63767 (19801) *********************** 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 166 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 2.551 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 61 MET cc_start: 0.9005 (tpp) cc_final: 0.8797 (tpp) REVERT: A 573 MET cc_start: 0.7263 (ptm) cc_final: 0.6992 (ptm) REVERT: A 769 TYR cc_start: 0.9052 (t80) cc_final: 0.8843 (t80) REVERT: A 1386 LEU cc_start: 0.9064 (mm) cc_final: 0.8729 (mt) REVERT: A 1609 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9080 (mm) REVERT: A 1679 ASP cc_start: 0.8911 (m-30) cc_final: 0.8699 (m-30) REVERT: A 1690 MET cc_start: 0.8024 (mmt) cc_final: 0.7459 (mmt) REVERT: A 1700 TYR cc_start: 0.8157 (t80) cc_final: 0.7553 (t80) REVERT: A 1733 MET cc_start: 0.8988 (tmm) cc_final: 0.8457 (tmm) REVERT: A 1735 TYR cc_start: 0.7662 (t80) cc_final: 0.7302 (t80) REVERT: A 2169 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8174 (mpp) outliers start: 31 outliers final: 22 residues processed: 155 average time/residue: 0.2485 time to fit residues: 67.2704 Evaluate side-chains 154 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 2.447 ------------------------------------------------------------------------------- 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 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 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 175 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 176 optimal weight: 0.0010 chunk 5 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 overall best weight: 3.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2155 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 = 0.3555 r_free = 0.3555 target = 0.062695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.051356 restraints weight = 108196.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052499 restraints weight = 68844.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.053280 restraints weight = 50524.304| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14487 Z= 0.202 Angle : 0.704 12.835 19840 Z= 0.339 Chirality : 0.043 0.270 2391 Planarity : 0.004 0.037 2494 Dihedral : 6.975 71.007 2288 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.38 % Allowed : 21.00 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1904 helix: 1.54 (0.16), residues: 1035 sheet: -1.07 (0.43), residues: 148 loop : -2.01 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 31 HIS 0.012 0.002 HIS A 52 PHE 0.023 0.002 PHE A 655 TYR 0.022 0.002 TYR A1779 ARG 0.003 0.000 ARG A 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 5) link_NAG-ASN : angle 3.01943 ( 15) link_BETA1-4 : bond 0.00405 ( 4) link_BETA1-4 : angle 1.70042 ( 12) hydrogen bonds : bond 0.03714 ( 774) hydrogen bonds : angle 4.42278 ( 2289) SS BOND : bond 0.00218 ( 6) SS BOND : angle 0.53759 ( 12) covalent geometry : bond 0.00434 (14472) covalent geometry : angle 0.69789 (19801) *********************** 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 169 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 3.017 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 66 MET cc_start: 0.8481 (mmp) cc_final: 0.8098 (mmt) REVERT: A 293 MET cc_start: 0.9165 (pmm) cc_final: 0.8903 (pmm) REVERT: A 746 MET cc_start: 0.8813 (tpp) cc_final: 0.8403 (tpp) REVERT: A 769 TYR cc_start: 0.9115 (t80) cc_final: 0.8897 (t80) REVERT: A 1386 LEU cc_start: 0.9150 (mm) cc_final: 0.8830 (mt) REVERT: A 1679 ASP cc_start: 0.8939 (m-30) cc_final: 0.8719 (m-30) REVERT: A 1690 MET cc_start: 0.7977 (mmt) cc_final: 0.7522 (mmt) REVERT: A 1733 MET cc_start: 0.9012 (tmm) cc_final: 0.8497 (tmm) REVERT: A 2169 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8191 (mpp) outliers start: 32 outliers final: 25 residues processed: 155 average time/residue: 0.2881 time to fit residues: 76.1511 Evaluate side-chains 159 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1687 ILE Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1693 VAL 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 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 126 optimal weight: 0.0030 chunk 119 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 110 optimal weight: 0.0870 chunk 161 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 10 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 overall best weight: 1.5170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 612 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.063524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.052263 restraints weight = 105960.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053467 restraints weight = 67105.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.054225 restraints weight = 48994.114| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14487 Z= 0.133 Angle : 0.687 13.429 19840 Z= 0.321 Chirality : 0.043 0.292 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.869 70.609 2288 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.23 % Allowed : 22.11 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1904 helix: 1.63 (0.16), residues: 1037 sheet: -1.07 (0.42), residues: 148 loop : -1.96 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 925 HIS 0.012 0.001 HIS A 52 PHE 0.020 0.001 PHE A 655 TYR 0.019 0.001 TYR A1779 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 5) link_NAG-ASN : angle 2.92681 ( 15) link_BETA1-4 : bond 0.00352 ( 4) link_BETA1-4 : angle 1.69683 ( 12) hydrogen bonds : bond 0.03477 ( 774) hydrogen bonds : angle 4.29728 ( 2289) SS BOND : bond 0.00157 ( 6) SS BOND : angle 0.49426 ( 12) covalent geometry : bond 0.00293 (14472) covalent geometry : angle 0.68175 (19801) *********************** 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 167 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 2.766 Fit side-chains TARDY: cannot create tardy model for: "GLU A1670 " (corrupted residue). Skipping it. REVERT: A 61 MET cc_start: 0.8952 (tpp) cc_final: 0.8667 (tpp) REVERT: A 293 MET cc_start: 0.9164 (pmm) cc_final: 0.8878 (pmm) REVERT: A 659 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8337 (mtm) REVERT: A 769 TYR cc_start: 0.9095 (t80) cc_final: 0.8842 (t80) REVERT: A 1007 MET cc_start: 0.8799 (tpp) cc_final: 0.8483 (tpp) REVERT: A 1386 LEU cc_start: 0.9138 (mm) cc_final: 0.8817 (mt) REVERT: A 1679 ASP cc_start: 0.8921 (m-30) cc_final: 0.8706 (m-30) REVERT: A 1690 MET cc_start: 0.8211 (mmt) cc_final: 0.7619 (mmt) REVERT: A 1700 TYR cc_start: 0.8139 (t80) cc_final: 0.7924 (t80) REVERT: A 1733 MET cc_start: 0.8993 (tmm) cc_final: 0.8490 (tmm) REVERT: A 1735 TYR cc_start: 0.7795 (t80) cc_final: 0.7225 (t80) REVERT: A 2169 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8173 (mpp) outliers start: 30 outliers final: 25 residues processed: 155 average time/residue: 0.2952 time to fit residues: 78.2777 Evaluate side-chains 161 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 1373 PHE Chi-restraints excluded: chain A residue 1379 LEU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain A residue 1609 LEU Chi-restraints excluded: chain A residue 1670 GLU Chi-restraints excluded: chain A residue 1691 SER Chi-restraints excluded: chain A residue 1693 VAL 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 2218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 109 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 72 optimal weight: 7.9990 chunk 79 optimal weight: 0.0020 chunk 157 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 131 optimal weight: 1.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 617 GLN ** A 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1052 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.065490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.054185 restraints weight = 104540.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.055380 restraints weight = 66513.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.056050 restraints weight = 48877.327| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14487 Z= 0.110 Angle : 0.681 13.737 19840 Z= 0.314 Chirality : 0.042 0.319 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.611 69.999 2288 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.56 % Allowed : 22.86 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1904 helix: 1.73 (0.16), residues: 1037 sheet: -1.06 (0.42), residues: 158 loop : -1.90 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 PHE 0.019 0.001 PHE A 655 TYR 0.016 0.001 TYR A1779 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 5) link_NAG-ASN : angle 2.81949 ( 15) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 1.67636 ( 12) hydrogen bonds : bond 0.03223 ( 774) hydrogen bonds : angle 4.08178 ( 2289) SS BOND : bond 0.00100 ( 6) SS BOND : angle 0.41826 ( 12) covalent geometry : bond 0.00236 (14472) covalent geometry : angle 0.67631 (19801) *********************** 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 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 66 MET cc_start: 0.8509 (mmp) cc_final: 0.8122 (mmt) REVERT: A 293 MET cc_start: 0.9108 (pmm) cc_final: 0.8803 (pmm) REVERT: A 659 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: A 746 MET cc_start: 0.8689 (tpp) cc_final: 0.8339 (tpp) REVERT: A 769 TYR cc_start: 0.8981 (t80) cc_final: 0.8759 (t80) REVERT: A 1007 MET cc_start: 0.8762 (tpp) cc_final: 0.8342 (tpp) REVERT: A 1386 LEU cc_start: 0.9080 (mm) cc_final: 0.8666 (mt) REVERT: A 1690 MET cc_start: 0.8318 (mmt) cc_final: 0.7837 (mmt) REVERT: A 1700 TYR cc_start: 0.8195 (t80) cc_final: 0.7809 (t80) REVERT: A 1733 MET cc_start: 0.8979 (tmm) cc_final: 0.8437 (tmm) REVERT: A 2169 MET cc_start: 0.8873 (tpt) cc_final: 0.8156 (mpp) outliers start: 21 outliers final: 19 residues processed: 154 average time/residue: 0.2202 time to fit residues: 57.1140 Evaluate side-chains 155 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 708 MET Chi-restraints excluded: chain A residue 712 ILE 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 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 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 2190 GLN Chi-restraints excluded: chain A residue 2218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.065293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.053992 restraints weight = 105223.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.055189 restraints weight = 66967.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.055979 restraints weight = 49082.564| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14487 Z= 0.115 Angle : 0.692 13.929 19840 Z= 0.317 Chirality : 0.042 0.330 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.427 69.742 2285 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.49 % Allowed : 23.23 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 1904 helix: 1.71 (0.16), residues: 1038 sheet: -0.96 (0.42), residues: 158 loop : -1.87 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 PHE 0.024 0.001 PHE A 802 TYR 0.017 0.001 TYR A1779 ARG 0.003 0.000 ARG A1248 Details of bonding type rmsd link_NAG-ASN : bond 0.00425 ( 5) link_NAG-ASN : angle 2.85665 ( 15) link_BETA1-4 : bond 0.00370 ( 4) link_BETA1-4 : angle 1.64937 ( 12) hydrogen bonds : bond 0.03234 ( 774) hydrogen bonds : angle 4.11144 ( 2289) SS BOND : bond 0.00101 ( 6) SS BOND : angle 0.36426 ( 12) covalent geometry : bond 0.00253 (14472) covalent geometry : angle 0.68744 (19801) ********************** 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 156 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.464 Fit side-chains REVERT: A 66 MET cc_start: 0.8497 (mmp) cc_final: 0.8060 (mmt) REVERT: A 293 MET cc_start: 0.9108 (pmm) cc_final: 0.8799 (pmm) REVERT: A 659 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8280 (mtm) REVERT: A 746 MET cc_start: 0.8788 (tpp) cc_final: 0.8416 (tpp) REVERT: A 769 TYR cc_start: 0.8988 (t80) cc_final: 0.8754 (t80) REVERT: A 1007 MET cc_start: 0.8698 (tpp) cc_final: 0.8330 (tpp) REVERT: A 1386 LEU cc_start: 0.9005 (mm) cc_final: 0.8693 (mt) REVERT: A 1690 MET cc_start: 0.8322 (mmt) cc_final: 0.7842 (mmt) REVERT: A 1700 TYR cc_start: 0.8183 (t80) cc_final: 0.7789 (t80) REVERT: A 1733 MET cc_start: 0.8996 (tmm) cc_final: 0.8498 (tmm) REVERT: A 2153 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8853 (p) REVERT: A 2169 MET cc_start: 0.8869 (tpt) cc_final: 0.8160 (mpp) outliers start: 20 outliers final: 17 residues processed: 148 average time/residue: 0.2059 time to fit residues: 51.1620 Evaluate side-chains 155 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.703 ------------------------------------------------------------------------------- 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 1701 LEU Chi-restraints excluded: chain A residue 1768 LEU Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1805 ASN Chi-restraints excluded: chain A residue 1960 VAL Chi-restraints excluded: chain A residue 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 8 optimal weight: 0.8980 chunk 29 optimal weight: 0.0470 chunk 163 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 165 optimal weight: 0.0870 chunk 108 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 150 optimal weight: 6.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.065854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.054493 restraints weight = 106820.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.055712 restraints weight = 68379.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.056568 restraints weight = 49985.711| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14487 Z= 0.110 Angle : 0.688 13.857 19840 Z= 0.314 Chirality : 0.042 0.328 2391 Planarity : 0.004 0.038 2494 Dihedral : 6.289 69.605 2285 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.41 % Allowed : 23.68 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1904 helix: 1.72 (0.16), residues: 1037 sheet: -0.84 (0.42), residues: 158 loop : -1.84 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 605 HIS 0.010 0.001 HIS A 52 PHE 0.023 0.001 PHE A 802 TYR 0.016 0.001 TYR A1779 ARG 0.002 0.000 ARG A1248 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 2.79401 ( 15) link_BETA1-4 : bond 0.00427 ( 4) link_BETA1-4 : angle 1.60902 ( 12) hydrogen bonds : bond 0.03183 ( 774) hydrogen bonds : angle 4.06819 ( 2289) SS BOND : bond 0.00083 ( 6) SS BOND : angle 0.35810 ( 12) covalent geometry : bond 0.00240 (14472) covalent geometry : angle 0.68289 (19801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4585.78 seconds wall clock time: 83 minutes 11.97 seconds (4991.97 seconds total)