Starting phenix.real_space_refine on Fri May 16 02:48:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ty1_41710/05_2025/8ty1_41710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ty1_41710/05_2025/8ty1_41710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ty1_41710/05_2025/8ty1_41710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ty1_41710/05_2025/8ty1_41710.map" model { file = "/net/cci-nas-00/data/ceres_data/8ty1_41710/05_2025/8ty1_41710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ty1_41710/05_2025/8ty1_41710.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8618 2.51 5 N 2290 2.21 5 O 2535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13508 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1236, 10004 Classifications: {'peptide': 1236} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 59, 'TRANS': 1176} Chain breaks: 7 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1570 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1784 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 223} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.97, per 1000 atoms: 0.74 Number of scatterers: 13508 At special positions: 0 Unit cell: (81.164, 123.716, 178.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2535 8.00 N 2290 7.00 C 8618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 180 " distance=2.04 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 106 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 220 " distance=2.04 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG D 1 " - " ASN A 240 " " NAG E 1 " - " ASN A1810 " " NAG F 1 " - " ASN C 28 " Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 9.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 120 through 128 removed outlier: 4.426A pdb=" N GLU A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A 126 " --> pdb=" O GLU A 123 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 127 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 128 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.733A pdb=" N GLU A 195 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 538 through 546 removed outlier: 4.228A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 595 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 694 through 700 removed outlier: 4.156A pdb=" N ASN A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1755 removed outlier: 3.551A pdb=" N ASN A1753 " --> pdb=" O GLY A1750 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS A1755 " --> pdb=" O LEU A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 Processing helix chain 'A' and resid 1842 through 1847 removed outlier: 3.514A pdb=" N ASP A1846 " --> pdb=" O ASP A1842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1888 No H-bonds generated for 'chain 'A' and resid 1886 through 1888' Processing helix chain 'A' and resid 1891 through 1895 removed outlier: 3.618A pdb=" N VAL A1895 " --> pdb=" O THR A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1915 Processing helix chain 'A' and resid 2002 through 2007 Processing helix chain 'A' and resid 2047 through 2051 removed outlier: 4.084A pdb=" N LEU A2050 " --> pdb=" O ALA A2047 " (cutoff:3.500A) Processing helix chain 'A' and resid 2186 through 2190 Processing helix chain 'A' and resid 2204 through 2208 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.572A pdb=" N ALA B 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 184 through 191 removed outlier: 4.429A pdb=" N HIS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 removed outlier: 4.056A pdb=" N GLN C 75 " --> pdb=" O HIS C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.970A pdb=" N THR C 101 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 removed outlier: 4.108A pdb=" N THR C 155 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.596A pdb=" N TYR A 6 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 90 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.596A pdb=" N TYR A 6 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 removed outlier: 5.763A pdb=" N ILE A 77 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N CYS A 180 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA5, first strand: chain 'A' and resid 200 through 203 Processing sheet with id=AA6, first strand: chain 'A' and resid 246 through 248 removed outlier: 5.617A pdb=" N LEU A 246 " --> pdb=" O ARG A 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 429 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 477 removed outlier: 3.905A pdb=" N TYR A 476 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 534 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.901A pdb=" N ILE A 574 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 658 through 659 removed outlier: 3.700A pdb=" N PHE A 658 " --> pdb=" O GLU A 665 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 665 " --> pdb=" O PHE A 658 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1695 through 1697 Processing sheet with id=AB3, first strand: chain 'A' and resid 1701 through 1707 Processing sheet with id=AB4, first strand: chain 'A' and resid 1763 through 1765 removed outlier: 6.421A pdb=" N ILE A1763 " --> pdb=" O LEU A1856 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS A1858 " --> pdb=" O ILE A1763 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A1765 " --> pdb=" O CYS A1858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1917 through 1921 Processing sheet with id=AB6, first strand: chain 'A' and resid 1933 through 1935 removed outlier: 3.629A pdb=" N TYR A2017 " --> pdb=" O MET A1934 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A2016 " --> pdb=" O GLY A1994 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1975 through 1976 Processing sheet with id=AB8, first strand: chain 'A' and resid 1963 through 1965 Processing sheet with id=AB9, first strand: chain 'A' and resid 2062 through 2064 removed outlier: 6.953A pdb=" N CYS A2169 " --> pdb=" O ILE A2081 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ILE A2081 " --> pdb=" O CYS A2169 " (cutoff:3.500A) removed outlier: 13.348A pdb=" N ILE A2071 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N THR A2154 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N VAL A2073 " --> pdb=" O HIS A2152 " (cutoff:3.500A) removed outlier: 11.960A pdb=" N HIS A2152 " --> pdb=" O VAL A2073 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N LEU A2075 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 11.952A pdb=" N ARG A2150 " --> pdb=" O LEU A2075 " (cutoff:3.500A) removed outlier: 9.660A pdb=" N ALA A2077 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR A2148 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2089 through 2091 Processing sheet with id=AC2, first strand: chain 'A' and resid 2191 through 2192 removed outlier: 3.948A pdb=" N THR A2272 " --> pdb=" O SER A2264 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2293 through 2296 removed outlier: 4.969A pdb=" N VAL A2240 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N CYS A2326 " --> pdb=" O VAL A2240 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id=AC5, first strand: chain 'B' and resid 5 through 7 removed outlier: 12.177A pdb=" N CYS B 23 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N THR B 75 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N ALA B 25 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 11.974A pdb=" N THR B 73 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.512A pdb=" N GLN B 27 " --> pdb=" O ASP B 71 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP B 71 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.547A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.547A pdb=" N LEU B 11 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLN B 91 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 99 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 116 through 120 Processing sheet with id=AC9, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.371A pdb=" N TRP B 150 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLU C 10 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 109 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER C 43 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 44 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG C 60 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP C 46 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 58 " --> pdb=" O TRP C 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.387A pdb=" N GLU C 10 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS C 106 " --> pdb=" O TRP C 127 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TRP C 127 " --> pdb=" O CYS C 106 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ARG C 108 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 125 " --> pdb=" O ARG C 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.033A pdb=" N SER C 144 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C 200 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 144 through 148 removed outlier: 4.033A pdb=" N SER C 144 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR C 200 " --> pdb=" O ASP C 168 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 174 through 177 340 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 3.80 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: 4283 1.34 - 1.46: 3586 1.46 - 1.59: 5896 1.59 - 1.71: 1 1.71 - 1.83: 103 Bond restraints: 13869 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.70e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.453 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 13864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18287 2.33 - 4.65: 440 4.65 - 6.98: 59 6.98 - 9.30: 22 9.30 - 11.63: 8 Bond angle restraints: 18816 Sorted by residual: angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.12e+01 angle pdb=" C ASN A1805 " pdb=" CA ASN A1805 " pdb=" CB ASN A1805 " ideal model delta sigma weight residual 116.54 110.18 6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C HIS A2315 " pdb=" N GLN A2316 " pdb=" CA GLN A2316 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" N GLN A2316 " pdb=" CA GLN A2316 " pdb=" CB GLN A2316 " ideal model delta sigma weight residual 110.49 118.97 -8.48 1.69e+00 3.50e-01 2.52e+01 angle pdb=" C VAL A2314 " pdb=" N HIS A2315 " pdb=" CA HIS A2315 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 7469 23.52 - 47.03: 713 47.03 - 70.55: 105 70.55 - 94.06: 42 94.06 - 117.58: 18 Dihedral angle restraints: 8347 sinusoidal: 3473 harmonic: 4874 Sorted by residual: dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.96 -61.96 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 220 " pdb=" CB CYS C 220 " ideal model delta sinusoidal sigma weight residual 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CA CYS A 180 " pdb=" C CYS A 180 " pdb=" N ARG A 181 " pdb=" CA ARG A 181 " ideal model delta harmonic sigma weight residual -180.00 -148.81 -31.19 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1598 0.055 - 0.110: 384 0.110 - 0.164: 81 0.164 - 0.219: 5 0.219 - 0.274: 3 Chirality restraints: 2071 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2068 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 208 " 0.119 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO C 209 " -0.299 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 127 " -0.018 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP C 127 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 127 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 127 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 127 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP C 127 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.025 2.00e-02 2.50e+03 2.40e-02 1.45e+01 pdb=" CG TRP A 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.006 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 222 2.58 - 3.16: 11640 3.16 - 3.74: 21330 3.74 - 4.32: 29351 4.32 - 4.90: 47611 Nonbonded interactions: 110154 Sorted by model distance: nonbonded pdb=" OE2 GLU A 111 " pdb=" OH TYR A 115 " model vdw 2.005 3.040 nonbonded pdb=" O ALA A1877 " pdb=" ND2 ASN A1922 " model vdw 2.124 3.120 nonbonded pdb=" OE1 GLN A 135 " pdb=" OH TYR A 137 " model vdw 2.136 3.040 nonbonded pdb=" OG SER A 628 " pdb=" O LYS A 707 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU A 389 " pdb=" NH2 ARG A 439 " model vdw 2.139 3.120 ... (remaining 110149 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 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.570 Find NCS groups from input model: 0.160 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 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 : 0.005 0.119 13892 Z= 0.232 Angle : 0.899 11.625 18874 Z= 0.454 Chirality : 0.050 0.274 2071 Planarity : 0.006 0.173 2379 Dihedral : 19.173 117.576 5186 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.53 % Favored : 88.99 % Rotamer: Outliers : 0.68 % Allowed : 27.90 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.57 (0.20), residues: 1653 helix: -1.71 (0.52), residues: 74 sheet: -1.19 (0.22), residues: 491 loop : -2.05 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.004 TRP C 127 HIS 0.009 0.002 HIS A2005 PHE 0.033 0.002 PHE A1785 TYR 0.025 0.002 TYR B 88 ARG 0.010 0.001 ARG B 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 3) link_NAG-ASN : angle 5.34067 ( 9) link_BETA1-4 : bond 0.00558 ( 6) link_BETA1-4 : angle 2.89423 ( 18) link_ALPHA1-3 : bond 0.00426 ( 3) link_ALPHA1-3 : angle 1.71437 ( 9) hydrogen bonds : bond 0.15833 ( 315) hydrogen bonds : angle 8.58911 ( 822) SS BOND : bond 0.00367 ( 11) SS BOND : angle 1.16668 ( 22) covalent geometry : bond 0.00527 (13869) covalent geometry : angle 0.88656 (18816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 MET cc_start: 0.7284 (ppp) cc_final: 0.6583 (ttt) REVERT: A 625 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7894 (mp) REVERT: A 666 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6903 (t0) REVERT: A 683 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6127 (mm-30) REVERT: A 1711 MET cc_start: 0.3602 (mpp) cc_final: 0.3044 (mpp) REVERT: A 1794 ASP cc_start: 0.5830 (t0) cc_final: 0.4916 (p0) REVERT: A 1797 GLU cc_start: 0.4601 (tp30) cc_final: 0.4215 (tp30) REVERT: A 2180 MET cc_start: 0.7767 (tpt) cc_final: 0.7433 (tpt) REVERT: A 2313 TRP cc_start: 0.4492 (p90) cc_final: 0.4154 (p90) REVERT: C 42 TYR cc_start: 0.4728 (p90) cc_final: 0.4482 (p90) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.2493 time to fit residues: 61.7731 Evaluate side-chains 154 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2231 GLN C 1 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.194473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.153125 restraints weight = 24081.298| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.39 r_work: 0.4200 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13892 Z= 0.163 Angle : 0.752 10.368 18874 Z= 0.374 Chirality : 0.048 0.251 2071 Planarity : 0.006 0.109 2379 Dihedral : 12.968 115.053 2078 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.95 % Favored : 90.62 % Rotamer: Outliers : 4.23 % Allowed : 25.24 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.52 (0.20), residues: 1653 helix: -1.41 (0.56), residues: 75 sheet: -1.28 (0.22), residues: 478 loop : -1.97 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 127 HIS 0.006 0.001 HIS A2005 PHE 0.023 0.002 PHE A1785 TYR 0.020 0.002 TYR B 92 ARG 0.005 0.001 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 3) link_NAG-ASN : angle 5.16181 ( 9) link_BETA1-4 : bond 0.00923 ( 6) link_BETA1-4 : angle 2.95240 ( 18) link_ALPHA1-3 : bond 0.01130 ( 3) link_ALPHA1-3 : angle 2.42702 ( 9) hydrogen bonds : bond 0.04042 ( 315) hydrogen bonds : angle 7.27141 ( 822) SS BOND : bond 0.00304 ( 11) SS BOND : angle 1.02113 ( 22) covalent geometry : bond 0.00369 (13869) covalent geometry : angle 0.73623 (18816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 152 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8401 (tmm) cc_final: 0.8024 (tmm) REVERT: A 279 VAL cc_start: 0.2885 (OUTLIER) cc_final: 0.2655 (t) REVERT: A 292 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.5790 (mp) REVERT: A 313 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7663 (mp) REVERT: A 324 HIS cc_start: 0.5803 (m-70) cc_final: 0.5420 (m-70) REVERT: A 1711 MET cc_start: 0.3040 (mpp) cc_final: 0.2651 (mpp) REVERT: A 1794 ASP cc_start: 0.5842 (t0) cc_final: 0.5012 (p0) REVERT: A 2167 MET cc_start: 0.5969 (mmt) cc_final: 0.5584 (mmt) REVERT: A 2180 MET cc_start: 0.7821 (tpt) cc_final: 0.7521 (tpt) REVERT: A 2238 MET cc_start: 0.4548 (mmm) cc_final: 0.4270 (mmm) REVERT: A 2324 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6812 (mt) REVERT: C 1 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7017 (pt0) REVERT: C 57 TRP cc_start: 0.8267 (OUTLIER) cc_final: 0.7662 (t60) outliers start: 62 outliers final: 29 residues processed: 199 average time/residue: 0.2344 time to fit residues: 70.8591 Evaluate side-chains 172 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 1 GLN Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 98 optimal weight: 0.2980 chunk 39 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1957 HIS ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2087 GLN ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.193811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.152652 restraints weight = 24216.136| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 4.07 r_work: 0.4201 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6198 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13892 Z= 0.196 Angle : 0.755 9.820 18874 Z= 0.377 Chirality : 0.049 0.247 2071 Planarity : 0.005 0.084 2379 Dihedral : 11.844 114.559 2069 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.98 % Favored : 89.59 % Rotamer: Outliers : 5.32 % Allowed : 25.17 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.61 (0.20), residues: 1653 helix: -1.46 (0.56), residues: 75 sheet: -1.36 (0.22), residues: 479 loop : -2.02 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 127 HIS 0.009 0.001 HIS A2005 PHE 0.028 0.002 PHE A1785 TYR 0.021 0.002 TYR A 159 ARG 0.004 0.000 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 3) link_NAG-ASN : angle 5.24913 ( 9) link_BETA1-4 : bond 0.00834 ( 6) link_BETA1-4 : angle 2.91951 ( 18) link_ALPHA1-3 : bond 0.01189 ( 3) link_ALPHA1-3 : angle 2.31311 ( 9) hydrogen bonds : bond 0.03879 ( 315) hydrogen bonds : angle 7.24539 ( 822) SS BOND : bond 0.00403 ( 11) SS BOND : angle 1.15991 ( 22) covalent geometry : bond 0.00449 (13869) covalent geometry : angle 0.73930 (18816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 144 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8399 (tmm) cc_final: 0.8115 (tmm) REVERT: A 279 VAL cc_start: 0.2624 (OUTLIER) cc_final: 0.2394 (t) REVERT: A 292 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.5939 (mp) REVERT: A 324 HIS cc_start: 0.5883 (m-70) cc_final: 0.5453 (m-70) REVERT: A 407 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.4983 (t80) REVERT: A 666 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6936 (t0) REVERT: A 1794 ASP cc_start: 0.5816 (t0) cc_final: 0.5023 (p0) REVERT: A 2010 MET cc_start: 0.8046 (tpp) cc_final: 0.7838 (mpp) REVERT: A 2167 MET cc_start: 0.5934 (mmt) cc_final: 0.5532 (mmt) REVERT: A 2180 MET cc_start: 0.7621 (tpt) cc_final: 0.7125 (tpt) REVERT: A 2238 MET cc_start: 0.4982 (mmm) cc_final: 0.4774 (tpp) REVERT: A 2324 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6815 (mt) REVERT: B 110 ARG cc_start: 0.4874 (OUTLIER) cc_final: 0.3414 (ptp-170) REVERT: C 57 TRP cc_start: 0.8260 (OUTLIER) cc_final: 0.7576 (t60) outliers start: 78 outliers final: 48 residues processed: 205 average time/residue: 0.2341 time to fit residues: 72.1893 Evaluate side-chains 189 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 134 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 97 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1867 HIS ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** 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 = 0.4948 r_free = 0.4948 target = 0.193491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.152865 restraints weight = 24140.559| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 4.23 r_work: 0.4187 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13892 Z= 0.192 Angle : 0.758 10.769 18874 Z= 0.378 Chirality : 0.049 0.254 2071 Planarity : 0.005 0.074 2379 Dihedral : 10.652 114.017 2069 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.41 % Favored : 89.17 % Rotamer: Outliers : 6.48 % Allowed : 24.35 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.67 (0.20), residues: 1653 helix: -1.70 (0.52), residues: 88 sheet: -1.32 (0.22), residues: 472 loop : -2.08 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 209 HIS 0.011 0.001 HIS A2005 PHE 0.029 0.002 PHE A1785 TYR 0.023 0.002 TYR A 159 ARG 0.004 0.001 ARG A2033 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 3) link_NAG-ASN : angle 5.70095 ( 9) link_BETA1-4 : bond 0.00842 ( 6) link_BETA1-4 : angle 2.77067 ( 18) link_ALPHA1-3 : bond 0.01164 ( 3) link_ALPHA1-3 : angle 2.37554 ( 9) hydrogen bonds : bond 0.03619 ( 315) hydrogen bonds : angle 7.36080 ( 822) SS BOND : bond 0.00344 ( 11) SS BOND : angle 1.15174 ( 22) covalent geometry : bond 0.00438 (13869) covalent geometry : angle 0.74132 (18816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 144 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.4978 (m-80) REVERT: A 124 LYS cc_start: 0.6591 (tptp) cc_final: 0.6164 (tppt) REVERT: A 261 MET cc_start: 0.8395 (tmm) cc_final: 0.8171 (tmm) REVERT: A 279 VAL cc_start: 0.2704 (OUTLIER) cc_final: 0.2468 (t) REVERT: A 287 LEU cc_start: 0.4124 (OUTLIER) cc_final: 0.3825 (mt) REVERT: A 292 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.5928 (mp) REVERT: A 302 MET cc_start: 0.4730 (tpt) cc_final: 0.4223 (mmt) REVERT: A 324 HIS cc_start: 0.5818 (m-70) cc_final: 0.5311 (m-70) REVERT: A 407 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.5148 (t80) REVERT: A 645 GLN cc_start: 0.4891 (OUTLIER) cc_final: 0.4299 (mp10) REVERT: A 666 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7073 (t0) REVERT: A 1711 MET cc_start: 0.3233 (mpp) cc_final: 0.2828 (mpp) REVERT: A 1794 ASP cc_start: 0.5822 (t0) cc_final: 0.5079 (p0) REVERT: A 1958 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.4685 (m-80) REVERT: A 2010 MET cc_start: 0.8070 (tpp) cc_final: 0.7215 (mpp) REVERT: A 2033 ARG cc_start: 0.7111 (ptt90) cc_final: 0.6475 (ptp-110) REVERT: A 2167 MET cc_start: 0.6006 (mmt) cc_final: 0.5594 (mmt) REVERT: A 2180 MET cc_start: 0.7795 (tpt) cc_final: 0.7404 (tpt) REVERT: A 2238 MET cc_start: 0.5353 (mmm) cc_final: 0.4915 (tpp) REVERT: A 2321 MET cc_start: 0.6275 (mmm) cc_final: 0.6064 (mmm) REVERT: A 2324 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6936 (mt) REVERT: B 138 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8779 (pp) REVERT: B 141 PHE cc_start: 0.3900 (p90) cc_final: 0.3145 (p90) REVERT: C 57 TRP cc_start: 0.8300 (OUTLIER) cc_final: 0.7632 (t60) outliers start: 95 outliers final: 56 residues processed: 224 average time/residue: 0.2320 time to fit residues: 78.4513 Evaluate side-chains 202 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 135 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1958 PHE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 78 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 ASN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 ASN ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2091 GLN ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.195295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.154043 restraints weight = 24272.589| |-----------------------------------------------------------------------------| r_work (start): 0.4450 rms_B_bonded: 4.14 r_work: 0.4222 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13892 Z= 0.144 Angle : 0.724 10.849 18874 Z= 0.356 Chirality : 0.047 0.247 2071 Planarity : 0.005 0.074 2379 Dihedral : 9.892 112.977 2069 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.32 % Favored : 90.26 % Rotamer: Outliers : 5.53 % Allowed : 25.85 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.56 (0.20), residues: 1653 helix: -1.68 (0.52), residues: 88 sheet: -1.28 (0.22), residues: 480 loop : -1.99 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 209 HIS 0.006 0.001 HIS C 37 PHE 0.022 0.001 PHE A1785 TYR 0.025 0.002 TYR A 159 ARG 0.003 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 3) link_NAG-ASN : angle 5.86402 ( 9) link_BETA1-4 : bond 0.00823 ( 6) link_BETA1-4 : angle 2.71578 ( 18) link_ALPHA1-3 : bond 0.01145 ( 3) link_ALPHA1-3 : angle 2.32717 ( 9) hydrogen bonds : bond 0.03240 ( 315) hydrogen bonds : angle 7.11025 ( 822) SS BOND : bond 0.00307 ( 11) SS BOND : angle 0.88549 ( 22) covalent geometry : bond 0.00329 (13869) covalent geometry : angle 0.70613 (18816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 143 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8309 (tmm) cc_final: 0.8105 (tmm) REVERT: A 279 VAL cc_start: 0.2730 (OUTLIER) cc_final: 0.2495 (t) REVERT: A 292 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.5947 (mp) REVERT: A 302 MET cc_start: 0.4675 (tpt) cc_final: 0.4379 (tpp) REVERT: A 324 HIS cc_start: 0.5756 (m-70) cc_final: 0.5381 (m90) REVERT: A 407 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.5158 (t80) REVERT: A 665 GLU cc_start: 0.8623 (mp0) cc_final: 0.8295 (mp0) REVERT: A 1794 ASP cc_start: 0.5815 (t0) cc_final: 0.5082 (p0) REVERT: A 2033 ARG cc_start: 0.7008 (ptt90) cc_final: 0.6484 (ptp-110) REVERT: A 2167 MET cc_start: 0.6156 (mmt) cc_final: 0.5766 (mmt) REVERT: A 2180 MET cc_start: 0.7726 (tpt) cc_final: 0.7376 (tpt) REVERT: A 2324 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6795 (mt) REVERT: B 138 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8752 (pp) REVERT: B 141 PHE cc_start: 0.4065 (p90) cc_final: 0.3370 (p90) REVERT: C 57 TRP cc_start: 0.8176 (OUTLIER) cc_final: 0.7570 (t60) outliers start: 81 outliers final: 56 residues processed: 208 average time/residue: 0.2329 time to fit residues: 73.4247 Evaluate side-chains 195 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 133 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1852 ILE Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 142 TYR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 118 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 35 optimal weight: 0.0070 chunk 128 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.196360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.153253 restraints weight = 24268.879| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 4.11 r_work: 0.4216 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6158 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13892 Z= 0.137 Angle : 0.710 10.652 18874 Z= 0.348 Chirality : 0.047 0.279 2071 Planarity : 0.005 0.077 2379 Dihedral : 9.193 110.338 2069 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.50 % Favored : 90.08 % Rotamer: Outliers : 6.00 % Allowed : 25.51 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.48 (0.20), residues: 1653 helix: -1.65 (0.53), residues: 88 sheet: -1.19 (0.23), residues: 479 loop : -1.95 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 209 HIS 0.005 0.001 HIS C 37 PHE 0.021 0.001 PHE A1785 TYR 0.034 0.002 TYR A 159 ARG 0.002 0.000 ARG C 82 Details of bonding type rmsd link_NAG-ASN : bond 0.00733 ( 3) link_NAG-ASN : angle 5.71740 ( 9) link_BETA1-4 : bond 0.00765 ( 6) link_BETA1-4 : angle 2.67735 ( 18) link_ALPHA1-3 : bond 0.01192 ( 3) link_ALPHA1-3 : angle 2.31611 ( 9) hydrogen bonds : bond 0.03137 ( 315) hydrogen bonds : angle 6.95707 ( 822) SS BOND : bond 0.00367 ( 11) SS BOND : angle 1.31228 ( 22) covalent geometry : bond 0.00312 (13869) covalent geometry : angle 0.69169 (18816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 146 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TRP cc_start: 0.6546 (t-100) cc_final: 0.5453 (t60) REVERT: A 261 MET cc_start: 0.8280 (tmm) cc_final: 0.8045 (tmm) REVERT: A 275 HIS cc_start: 0.3792 (OUTLIER) cc_final: 0.3015 (t-170) REVERT: A 279 VAL cc_start: 0.2708 (OUTLIER) cc_final: 0.2428 (t) REVERT: A 287 LEU cc_start: 0.4200 (OUTLIER) cc_final: 0.3839 (mt) REVERT: A 292 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.5994 (mp) REVERT: A 302 MET cc_start: 0.4604 (tpt) cc_final: 0.4385 (tpp) REVERT: A 324 HIS cc_start: 0.5715 (m-70) cc_final: 0.5362 (m90) REVERT: A 407 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5219 (t80) REVERT: A 665 GLU cc_start: 0.8184 (mp0) cc_final: 0.7819 (mp0) REVERT: A 1794 ASP cc_start: 0.5852 (t0) cc_final: 0.5096 (p0) REVERT: A 2167 MET cc_start: 0.6231 (mmt) cc_final: 0.5852 (mmt) REVERT: A 2180 MET cc_start: 0.7744 (tpt) cc_final: 0.7442 (tpt) REVERT: A 2238 MET cc_start: 0.4726 (mmm) cc_final: 0.3721 (mmm) REVERT: A 2321 MET cc_start: 0.6344 (mmm) cc_final: 0.5814 (mpp) REVERT: A 2324 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6784 (mt) REVERT: B 138 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8802 (pp) REVERT: B 141 PHE cc_start: 0.3855 (p90) cc_final: 0.3330 (p90) REVERT: C 57 TRP cc_start: 0.8204 (OUTLIER) cc_final: 0.7600 (t60) REVERT: C 108 ARG cc_start: 0.3749 (OUTLIER) cc_final: 0.3508 (ptt180) outliers start: 88 outliers final: 63 residues processed: 219 average time/residue: 0.2338 time to fit residues: 77.2690 Evaluate side-chains 209 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 137 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 156 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A1745 GLN A1778 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.191151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.149261 restraints weight = 23862.409| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 4.20 r_work: 0.4137 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13892 Z= 0.243 Angle : 0.804 11.080 18874 Z= 0.402 Chirality : 0.050 0.249 2071 Planarity : 0.006 0.082 2379 Dihedral : 9.178 107.223 2069 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.25 % Favored : 88.32 % Rotamer: Outliers : 6.41 % Allowed : 26.33 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.77 (0.20), residues: 1653 helix: -1.93 (0.48), residues: 97 sheet: -1.32 (0.23), residues: 481 loop : -2.18 (0.18), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 209 HIS 0.011 0.002 HIS A2005 PHE 0.037 0.002 PHE A1785 TYR 0.054 0.002 TYR A 159 ARG 0.007 0.001 ARG C 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00845 ( 3) link_NAG-ASN : angle 5.65652 ( 9) link_BETA1-4 : bond 0.00713 ( 6) link_BETA1-4 : angle 2.78577 ( 18) link_ALPHA1-3 : bond 0.01117 ( 3) link_ALPHA1-3 : angle 2.45442 ( 9) hydrogen bonds : bond 0.03996 ( 315) hydrogen bonds : angle 7.40819 ( 822) SS BOND : bond 0.00565 ( 11) SS BOND : angle 1.18012 ( 22) covalent geometry : bond 0.00562 (13869) covalent geometry : angle 0.78808 (18816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 143 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5387 (OUTLIER) cc_final: 0.4943 (m-80) REVERT: A 209 TRP cc_start: 0.6697 (t-100) cc_final: 0.6432 (t-100) REVERT: A 261 MET cc_start: 0.8445 (tmm) cc_final: 0.8135 (tmm) REVERT: A 275 HIS cc_start: 0.3876 (OUTLIER) cc_final: 0.3069 (t-170) REVERT: A 287 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.3982 (mt) REVERT: A 292 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.5970 (mp) REVERT: A 324 HIS cc_start: 0.5847 (m-70) cc_final: 0.5308 (m-70) REVERT: A 407 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.5467 (t80) REVERT: A 539 MET cc_start: 0.4720 (OUTLIER) cc_final: 0.3480 (tmm) REVERT: A 665 GLU cc_start: 0.8313 (mp0) cc_final: 0.8054 (mp0) REVERT: A 666 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7170 (t0) REVERT: A 1794 ASP cc_start: 0.5835 (t0) cc_final: 0.5081 (p0) REVERT: A 2033 ARG cc_start: 0.7372 (ptt90) cc_final: 0.6749 (ptp-110) REVERT: A 2167 MET cc_start: 0.6276 (mmt) cc_final: 0.5849 (mmt) REVERT: A 2180 MET cc_start: 0.7766 (tpt) cc_final: 0.7399 (tpt) REVERT: A 2219 TRP cc_start: 0.5098 (t60) cc_final: 0.4080 (p-90) REVERT: A 2324 LEU cc_start: 0.7093 (mt) cc_final: 0.6880 (mt) REVERT: B 138 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8780 (pp) REVERT: C 1 GLN cc_start: 0.7858 (pp30) cc_final: 0.7550 (pm20) REVERT: C 57 TRP cc_start: 0.8312 (OUTLIER) cc_final: 0.7703 (t60) outliers start: 94 outliers final: 68 residues processed: 217 average time/residue: 0.2451 time to fit residues: 78.9313 Evaluate side-chains 210 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 133 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1958 PHE Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 228 ASN Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 164 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 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 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** C 45 HIS ** 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 = 0.4965 r_free = 0.4965 target = 0.195014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.153733 restraints weight = 23870.853| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 3.95 r_work: 0.4188 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13892 Z= 0.155 Angle : 0.743 10.592 18874 Z= 0.368 Chirality : 0.048 0.254 2071 Planarity : 0.005 0.078 2379 Dihedral : 8.811 105.260 2069 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.32 % Favored : 90.32 % Rotamer: Outliers : 5.80 % Allowed : 27.15 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.66 (0.20), residues: 1653 helix: -1.98 (0.49), residues: 94 sheet: -1.27 (0.23), residues: 472 loop : -2.07 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 209 HIS 0.005 0.001 HIS C 37 PHE 0.024 0.002 PHE A1785 TYR 0.042 0.002 TYR A 159 ARG 0.003 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00722 ( 3) link_NAG-ASN : angle 5.32991 ( 9) link_BETA1-4 : bond 0.00759 ( 6) link_BETA1-4 : angle 2.78846 ( 18) link_ALPHA1-3 : bond 0.01149 ( 3) link_ALPHA1-3 : angle 2.30047 ( 9) hydrogen bonds : bond 0.03378 ( 315) hydrogen bonds : angle 7.21292 ( 822) SS BOND : bond 0.00448 ( 11) SS BOND : angle 1.73038 ( 22) covalent geometry : bond 0.00358 (13869) covalent geometry : angle 0.72622 (18816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 139 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5139 (OUTLIER) cc_final: 0.2786 (m-80) REVERT: A 209 TRP cc_start: 0.6655 (t-100) cc_final: 0.6409 (t-100) REVERT: A 261 MET cc_start: 0.8351 (tmm) cc_final: 0.8057 (tmm) REVERT: A 275 HIS cc_start: 0.3792 (OUTLIER) cc_final: 0.2979 (t-170) REVERT: A 287 LEU cc_start: 0.4339 (OUTLIER) cc_final: 0.3961 (mt) REVERT: A 292 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.5920 (mp) REVERT: A 302 MET cc_start: 0.4773 (tpt) cc_final: 0.4288 (mmt) REVERT: A 324 HIS cc_start: 0.5815 (m-70) cc_final: 0.5452 (m90) REVERT: A 407 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5465 (t80) REVERT: A 539 MET cc_start: 0.4596 (OUTLIER) cc_final: 0.3291 (tmm) REVERT: A 645 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4334 (mp10) REVERT: A 665 GLU cc_start: 0.8263 (mp0) cc_final: 0.8020 (mp0) REVERT: A 666 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.7041 (t0) REVERT: A 1794 ASP cc_start: 0.5854 (t0) cc_final: 0.5089 (p0) REVERT: A 2033 ARG cc_start: 0.7165 (ptt90) cc_final: 0.6617 (ptp-110) REVERT: A 2167 MET cc_start: 0.6257 (mmt) cc_final: 0.5835 (mmt) REVERT: A 2180 MET cc_start: 0.7540 (tpt) cc_final: 0.7243 (tpt) REVERT: A 2238 MET cc_start: 0.5193 (mmm) cc_final: 0.3819 (mmm) REVERT: A 2324 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6833 (mt) REVERT: B 138 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8753 (pp) REVERT: C 1 GLN cc_start: 0.7887 (pp30) cc_final: 0.7546 (pm20) REVERT: C 57 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.7656 (t60) outliers start: 85 outliers final: 66 residues processed: 206 average time/residue: 0.2292 time to fit residues: 71.5522 Evaluate side-chains 210 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 133 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 165 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 89 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4970 r_free = 0.4970 target = 0.195756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.154697 restraints weight = 24048.201| |-----------------------------------------------------------------------------| r_work (start): 0.4448 rms_B_bonded: 4.32 r_work: 0.4213 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13892 Z= 0.141 Angle : 0.736 11.066 18874 Z= 0.363 Chirality : 0.048 0.252 2071 Planarity : 0.005 0.082 2379 Dihedral : 8.521 102.859 2069 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.44 % Favored : 90.20 % Rotamer: Outliers : 5.66 % Allowed : 27.29 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.55 (0.20), residues: 1653 helix: -1.93 (0.50), residues: 87 sheet: -1.26 (0.23), residues: 480 loop : -1.96 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 209 HIS 0.008 0.001 HIS A2005 PHE 0.021 0.001 PHE A1785 TYR 0.043 0.002 TYR A 159 ARG 0.004 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00643 ( 3) link_NAG-ASN : angle 5.24505 ( 9) link_BETA1-4 : bond 0.00749 ( 6) link_BETA1-4 : angle 2.78664 ( 18) link_ALPHA1-3 : bond 0.01097 ( 3) link_ALPHA1-3 : angle 2.30549 ( 9) hydrogen bonds : bond 0.03203 ( 315) hydrogen bonds : angle 6.94744 ( 822) SS BOND : bond 0.00406 ( 11) SS BOND : angle 1.25563 ( 22) covalent geometry : bond 0.00323 (13869) covalent geometry : angle 0.72049 (18816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 138 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5063 (OUTLIER) cc_final: 0.2722 (m-80) REVERT: A 209 TRP cc_start: 0.6568 (t-100) cc_final: 0.6347 (t-100) REVERT: A 261 MET cc_start: 0.8255 (tmm) cc_final: 0.7989 (tmm) REVERT: A 275 HIS cc_start: 0.3728 (OUTLIER) cc_final: 0.2939 (t-170) REVERT: A 287 LEU cc_start: 0.4267 (OUTLIER) cc_final: 0.3875 (mt) REVERT: A 292 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.5939 (mp) REVERT: A 302 MET cc_start: 0.4686 (tpt) cc_final: 0.4093 (mmt) REVERT: A 324 HIS cc_start: 0.5780 (m-70) cc_final: 0.5435 (m90) REVERT: A 407 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5431 (t80) REVERT: A 539 MET cc_start: 0.4636 (OUTLIER) cc_final: 0.3336 (tmm) REVERT: A 645 GLN cc_start: 0.5232 (OUTLIER) cc_final: 0.4384 (mp10) REVERT: A 665 GLU cc_start: 0.8192 (mp0) cc_final: 0.7824 (mp0) REVERT: A 666 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7037 (t0) REVERT: A 1794 ASP cc_start: 0.5817 (t0) cc_final: 0.5093 (p0) REVERT: A 2167 MET cc_start: 0.6199 (mmt) cc_final: 0.5782 (mmt) REVERT: A 2180 MET cc_start: 0.7704 (tpt) cc_final: 0.7401 (tpt) REVERT: A 2238 MET cc_start: 0.4956 (mmm) cc_final: 0.3770 (mmm) REVERT: A 2321 MET cc_start: 0.6375 (mmm) cc_final: 0.5789 (mpp) REVERT: A 2324 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6771 (mt) REVERT: C 1 GLN cc_start: 0.7928 (pp30) cc_final: 0.7592 (pm20) REVERT: C 57 TRP cc_start: 0.8207 (OUTLIER) cc_final: 0.7614 (t60) outliers start: 83 outliers final: 65 residues processed: 205 average time/residue: 0.2360 time to fit residues: 73.2195 Evaluate side-chains 209 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1852 ILE Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 152 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 35 optimal weight: 0.0170 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 93 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 45 HIS ** 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 = 0.4959 r_free = 0.4959 target = 0.194846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.153690 restraints weight = 24076.792| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 4.56 r_work: 0.4187 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13892 Z= 0.165 Angle : 0.760 11.408 18874 Z= 0.374 Chirality : 0.048 0.245 2071 Planarity : 0.005 0.085 2379 Dihedral : 8.403 100.606 2069 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.98 % Favored : 89.66 % Rotamer: Outliers : 5.87 % Allowed : 26.88 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.53 (0.20), residues: 1653 helix: -1.91 (0.49), residues: 86 sheet: -1.24 (0.22), residues: 496 loop : -1.96 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 209 HIS 0.008 0.001 HIS A2005 PHE 0.026 0.002 PHE B 141 TYR 0.055 0.002 TYR A 159 ARG 0.003 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00665 ( 3) link_NAG-ASN : angle 5.24393 ( 9) link_BETA1-4 : bond 0.00728 ( 6) link_BETA1-4 : angle 2.82354 ( 18) link_ALPHA1-3 : bond 0.01125 ( 3) link_ALPHA1-3 : angle 2.35153 ( 9) hydrogen bonds : bond 0.03294 ( 315) hydrogen bonds : angle 6.99630 ( 822) SS BOND : bond 0.00409 ( 11) SS BOND : angle 1.12954 ( 22) covalent geometry : bond 0.00380 (13869) covalent geometry : angle 0.74416 (18816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 136 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.2739 (m-80) REVERT: A 209 TRP cc_start: 0.6617 (t-100) cc_final: 0.6378 (t-100) REVERT: A 261 MET cc_start: 0.8311 (tmm) cc_final: 0.7972 (tmm) REVERT: A 275 HIS cc_start: 0.3800 (OUTLIER) cc_final: 0.2989 (t-170) REVERT: A 287 LEU cc_start: 0.4201 (OUTLIER) cc_final: 0.3811 (mt) REVERT: A 292 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.5908 (mp) REVERT: A 302 MET cc_start: 0.4635 (tpt) cc_final: 0.4329 (tpt) REVERT: A 324 HIS cc_start: 0.5831 (m-70) cc_final: 0.5466 (m90) REVERT: A 407 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5483 (t80) REVERT: A 539 MET cc_start: 0.4608 (OUTLIER) cc_final: 0.3339 (tmm) REVERT: A 645 GLN cc_start: 0.5232 (OUTLIER) cc_final: 0.4455 (mp10) REVERT: A 665 GLU cc_start: 0.8220 (mp0) cc_final: 0.7956 (mp0) REVERT: A 666 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6985 (t0) REVERT: A 1794 ASP cc_start: 0.5829 (t0) cc_final: 0.5090 (p0) REVERT: A 2033 ARG cc_start: 0.7174 (ptt90) cc_final: 0.6598 (ptp-110) REVERT: A 2167 MET cc_start: 0.6189 (mmt) cc_final: 0.5797 (mmt) REVERT: A 2180 MET cc_start: 0.7585 (tpt) cc_final: 0.7268 (tpt) REVERT: A 2238 MET cc_start: 0.4982 (mmm) cc_final: 0.3861 (mmm) REVERT: A 2321 MET cc_start: 0.6075 (mmm) cc_final: 0.5607 (mpp) REVERT: A 2324 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6856 (mt) REVERT: C 1 GLN cc_start: 0.7801 (pp30) cc_final: 0.7528 (pm20) REVERT: C 57 TRP cc_start: 0.8258 (OUTLIER) cc_final: 0.7635 (t60) outliers start: 86 outliers final: 67 residues processed: 206 average time/residue: 0.2399 time to fit residues: 75.7159 Evaluate side-chains 211 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 134 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 194 HIS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 540 GLU Chi-restraints excluded: chain A residue 586 TYR Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 632 HIS Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1847 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2082 HIS Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2124 MET Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2196 PHE Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain A residue 2257 VAL Chi-restraints excluded: chain A residue 2324 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 235 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 13 optimal weight: 0.5980 chunk 162 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 78 optimal weight: 0.0020 chunk 126 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.198616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.154951 restraints weight = 23458.103| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 4.04 r_work: 0.4257 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13892 Z= 0.134 Angle : 0.749 13.412 18874 Z= 0.366 Chirality : 0.048 0.250 2071 Planarity : 0.005 0.083 2379 Dihedral : 8.155 98.530 2069 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.95 % Favored : 90.74 % Rotamer: Outliers : 5.39 % Allowed : 27.22 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.43 (0.20), residues: 1653 helix: -1.97 (0.49), residues: 86 sheet: -1.20 (0.22), residues: 500 loop : -1.86 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1817 HIS 0.009 0.001 HIS A2005 PHE 0.026 0.001 PHE B 141 TYR 0.052 0.002 TYR A 159 ARG 0.004 0.000 ARG A 531 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 3) link_NAG-ASN : angle 5.11742 ( 9) link_BETA1-4 : bond 0.00774 ( 6) link_BETA1-4 : angle 2.82350 ( 18) link_ALPHA1-3 : bond 0.01186 ( 3) link_ALPHA1-3 : angle 2.30955 ( 9) hydrogen bonds : bond 0.03100 ( 315) hydrogen bonds : angle 6.85505 ( 822) SS BOND : bond 0.00753 ( 11) SS BOND : angle 1.53817 ( 22) covalent geometry : bond 0.00307 (13869) covalent geometry : angle 0.73251 (18816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9042.89 seconds wall clock time: 157 minutes 45.35 seconds (9465.35 seconds total)