Starting phenix.real_space_refine on Fri Jul 3 11:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_41710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_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_41710/07_2026/8ty1_41710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_41710.map" model { file = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_41710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_41710.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_41710.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ty1_41710/07_2026/8ty1_41710.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 chiralities: 4 Time building chain proxies: 2.80, per 1000 atoms: 0.21 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: 1.02 Conformation dependent library (CDL) restraints added in 602.9 milliseconds 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: 0.39 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: 2.62 Time building geometry restraints manager: 1.40 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 - 18.09: 6917 18.09 - 36.17: 921 36.17 - 54.26: 211 54.26 - 72.34: 38 72.34 - 90.43: 20 Dihedral angle restraints: 8107 sinusoidal: 3233 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 8104 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: 14.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.030 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 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 : 17.336 90.425 4946 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.010 0.001 ARG B 62 TYR 0.025 0.002 TYR B 88 PHE 0.033 0.002 PHE A1785 TRP 0.064 0.004 TRP C 127 HIS 0.009 0.002 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (13869) covalent geometry : angle 0.88656 / 0.45 (18816) SS BOND : bond 0.00367 / 0.25 ( 11) SS BOND : angle 1.16668 / 0.77 ( 22) hydrogen bonds : bond 0.15833 / 9.22 ( 315) hydrogen bonds : angle 8.58911 / 5.74 ( 822) link_ALPHA1-3 : bond 0.00426 / 0.17 ( 3) link_ALPHA1-3 : angle 1.71437 / 0.97 ( 9) link_BETA1-4 : bond 0.00558 / 0.32 ( 6) link_BETA1-4 : angle 2.89423 / 1.80 ( 18) link_NAG-ASN : bond 0.00594 / 0.24 ( 3) link_NAG-ASN : angle 5.34067 / 3.28 ( 9) *********************** 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 : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 HIS cc_start: 0.5257 (m-70) cc_final: 0.4894 (m-70) 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: 0.4216 (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: 0.4153 (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: 0.1042 time to fit residues: 26.1716 Evaluate side-chains 155 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 149 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 221 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.193133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.152072 restraints weight = 24128.371| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 4.25 r_work: 0.4176 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13892 Z= 0.185 Angle : 0.760 10.476 18874 Z= 0.382 Chirality : 0.048 0.259 2071 Planarity : 0.006 0.112 2379 Dihedral : 6.313 54.761 1838 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.74 % Favored : 89.84 % Rotamer: Outliers : 4.50 % Allowed : 25.38 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.20), residues: 1653 helix: -1.56 (0.54), residues: 78 sheet: -1.34 (0.22), residues: 476 loop : -2.04 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 82 TYR 0.021 0.002 TYR A 137 PHE 0.028 0.002 PHE A1785 TRP 0.026 0.002 TRP A 139 HIS 0.009 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (13869) covalent geometry : angle 0.74586 / 0.38 (18816) SS BOND : bond 0.00373 / 0.24 ( 11) SS BOND : angle 1.35456 / 0.79 ( 22) hydrogen bonds : bond 0.04120 / 2.63 ( 315) hydrogen bonds : angle 7.34400 / 4.93 ( 822) link_ALPHA1-3 : bond 0.00575 / 0.25 ( 3) link_ALPHA1-3 : angle 1.74191 / 1.06 ( 9) link_BETA1-4 : bond 0.00757 / 0.43 ( 6) link_BETA1-4 : angle 2.75617 / 1.67 ( 18) link_NAG-ASN : bond 0.00511 / 0.24 ( 3) link_NAG-ASN : angle 5.11815 / 3.22 ( 9) *********************** 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 215 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 149 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8421 (tmm) cc_final: 0.8119 (tmm) REVERT: A 279 VAL cc_start: 0.2703 (OUTLIER) cc_final: 0.2462 (t) REVERT: A 292 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6000 (mp) REVERT: A 313 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 324 HIS cc_start: 0.5901 (m-70) cc_final: 0.5475 (m-70) REVERT: A 1711 MET cc_start: 0.3085 (mpp) cc_final: 0.2691 (mpp) REVERT: A 1794 ASP cc_start: 0.5792 (t0) cc_final: 0.4989 (p0) REVERT: A 2167 MET cc_start: 0.6002 (mmt) cc_final: 0.5613 (mmt) REVERT: A 2180 MET cc_start: 0.7769 (tpt) cc_final: 0.7448 (tpt) REVERT: A 2238 MET cc_start: 0.4567 (mmm) cc_final: 0.4320 (mmm) REVERT: C 1 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6987 (pt0) REVERT: C 57 TRP cc_start: 0.8263 (OUTLIER) cc_final: 0.7663 (t60) outliers start: 66 outliers final: 31 residues processed: 201 average time/residue: 0.0895 time to fit residues: 27.6144 Evaluate side-chains 172 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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 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 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 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1882 ILE 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 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 132 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 116 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 A1957 HIS ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2087 GLN A2091 GLN ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.195073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.150858 restraints weight = 24314.480| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 4.06 r_work: 0.4202 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13892 Z= 0.161 Angle : 0.719 9.478 18874 Z= 0.361 Chirality : 0.048 0.259 2071 Planarity : 0.005 0.083 2379 Dihedral : 5.772 48.106 1829 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.44 % Favored : 90.14 % Rotamer: Outliers : 5.25 % Allowed : 25.44 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1653 helix: -1.51 (0.55), residues: 78 sheet: -1.34 (0.22), residues: 479 loop : -2.00 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.017 0.002 TYR B 92 PHE 0.025 0.002 PHE A1785 TRP 0.027 0.002 TRP C 127 HIS 0.007 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (13869) covalent geometry : angle 0.70472 / 0.36 (18816) SS BOND : bond 0.00571 / 0.32 ( 11) SS BOND : angle 1.25157 / 0.73 ( 22) hydrogen bonds : bond 0.03639 / 2.31 ( 315) hydrogen bonds : angle 7.11450 / 4.79 ( 822) link_ALPHA1-3 : bond 0.00687 / 0.27 ( 3) link_ALPHA1-3 : angle 1.47427 / 0.86 ( 9) link_BETA1-4 : bond 0.00679 / 0.43 ( 6) link_BETA1-4 : angle 2.70786 / 1.63 ( 18) link_NAG-ASN : bond 0.00552 / 0.22 ( 3) link_NAG-ASN : angle 5.15711 / 3.25 ( 9) *********************** 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 220 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 143 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8378 (tmm) cc_final: 0.8090 (tmm) REVERT: A 279 VAL cc_start: 0.2599 (OUTLIER) cc_final: 0.2367 (t) REVERT: A 292 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.5797 (mp) REVERT: A 324 HIS cc_start: 0.5847 (m-70) cc_final: 0.5395 (m-70) REVERT: A 407 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5131 (t80) REVERT: A 666 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6913 (t0) REVERT: A 1794 ASP cc_start: 0.5818 (t0) cc_final: 0.5029 (p0) REVERT: A 1818 LYS cc_start: 0.8076 (tptt) cc_final: 0.7867 (tptt) REVERT: A 2010 MET cc_start: 0.8018 (tpp) cc_final: 0.7776 (mpp) REVERT: A 2167 MET cc_start: 0.5888 (mmt) cc_final: 0.5477 (mmt) REVERT: A 2180 MET cc_start: 0.7695 (tpt) cc_final: 0.7239 (tpt) REVERT: A 2238 MET cc_start: 0.5147 (mmm) cc_final: 0.4876 (tpp) REVERT: C 1 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: C 57 TRP cc_start: 0.8289 (OUTLIER) cc_final: 0.7629 (t60) outliers start: 77 outliers final: 44 residues processed: 205 average time/residue: 0.0924 time to fit residues: 28.6899 Evaluate side-chains 183 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 133 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 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 1784 SER 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 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 B residue 76 ILE 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 1 GLN 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 83 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 128 optimal weight: 0.0570 chunk 105 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2235 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.195184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.151859 restraints weight = 24306.505| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 4.34 r_work: 0.4242 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6152 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13892 Z= 0.132 Angle : 0.699 9.538 18874 Z= 0.347 Chirality : 0.047 0.260 2071 Planarity : 0.005 0.073 2379 Dihedral : 5.591 50.132 1829 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.71 % Favored : 90.93 % Rotamer: Outliers : 4.91 % Allowed : 25.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.20), residues: 1653 helix: -1.68 (0.51), residues: 91 sheet: -1.27 (0.22), residues: 479 loop : -1.96 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 108 TYR 0.024 0.002 TYR A 159 PHE 0.026 0.001 PHE A2234 TRP 0.025 0.002 TRP C 127 HIS 0.010 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13869) covalent geometry : angle 0.68389 / 0.34 (18816) SS BOND : bond 0.00352 / 0.22 ( 11) SS BOND : angle 1.21117 / 0.70 ( 22) hydrogen bonds : bond 0.03222 / 2.09 ( 315) hydrogen bonds : angle 7.04919 / 4.72 ( 822) link_ALPHA1-3 : bond 0.00695 / 0.27 ( 3) link_ALPHA1-3 : angle 1.49424 / 0.87 ( 9) link_BETA1-4 : bond 0.00741 / 0.45 ( 6) link_BETA1-4 : angle 2.64713 / 1.60 ( 18) link_NAG-ASN : bond 0.00519 / 0.20 ( 3) link_NAG-ASN : angle 5.24030 / 3.28 ( 9) *********************** 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 220 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 148 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8318 (tmm) cc_final: 0.8036 (tmm) REVERT: A 279 VAL cc_start: 0.2726 (OUTLIER) cc_final: 0.2491 (t) REVERT: A 292 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.5643 (mp) REVERT: A 302 MET cc_start: 0.4714 (tpt) cc_final: 0.4160 (mmt) REVERT: A 313 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7680 (mp) REVERT: A 324 HIS cc_start: 0.5642 (m-70) cc_final: 0.5256 (m-70) REVERT: A 407 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.5147 (t80) REVERT: A 665 GLU cc_start: 0.8571 (mp0) cc_final: 0.8257 (mp0) REVERT: A 1794 ASP cc_start: 0.5766 (t0) cc_final: 0.5064 (p0) REVERT: A 2010 MET cc_start: 0.7984 (tpp) cc_final: 0.7261 (mpp) REVERT: A 2167 MET cc_start: 0.5977 (mmt) cc_final: 0.5555 (mmt) REVERT: A 2180 MET cc_start: 0.7761 (tpt) cc_final: 0.7405 (tpt) REVERT: A 2238 MET cc_start: 0.5299 (mmm) cc_final: 0.4777 (tpp) REVERT: A 2324 LEU cc_start: 0.7464 (mt) cc_final: 0.7011 (mm) REVERT: B 138 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (pp) REVERT: B 141 PHE cc_start: 0.4217 (p90) cc_final: 0.3369 (p90) REVERT: C 57 TRP cc_start: 0.8201 (OUTLIER) cc_final: 0.7572 (t60) outliers start: 72 outliers final: 48 residues processed: 205 average time/residue: 0.0865 time to fit residues: 27.3116 Evaluate side-chains 191 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 194 HIS 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 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 313 ILE 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 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 1784 SER 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 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 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 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 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 235 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 134 optimal weight: 0.2980 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS A 693 HIS ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 ASN ** A1961 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.194575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.151602 restraints weight = 24344.265| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 4.34 r_work: 0.4199 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13892 Z= 0.177 Angle : 0.717 10.564 18874 Z= 0.359 Chirality : 0.048 0.260 2071 Planarity : 0.005 0.077 2379 Dihedral : 5.758 52.370 1829 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.16 % Favored : 89.47 % Rotamer: Outliers : 7.09 % Allowed : 24.22 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.20), residues: 1653 helix: -1.72 (0.50), residues: 90 sheet: -1.26 (0.22), residues: 484 loop : -2.01 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2033 TYR 0.034 0.002 TYR A 159 PHE 0.049 0.002 PHE A2234 TRP 0.027 0.002 TRP A 209 HIS 0.009 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (13869) covalent geometry : angle 0.70277 / 0.36 (18816) SS BOND : bond 0.00341 / 0.24 ( 11) SS BOND : angle 0.87108 / 0.58 ( 22) hydrogen bonds : bond 0.03439 / 2.20 ( 315) hydrogen bonds : angle 7.13316 / 4.80 ( 822) link_ALPHA1-3 : bond 0.00668 / 0.25 ( 3) link_ALPHA1-3 : angle 1.52999 / 0.89 ( 9) link_BETA1-4 : bond 0.00700 / 0.43 ( 6) link_BETA1-4 : angle 2.66286 / 1.60 ( 18) link_NAG-ASN : bond 0.00551 / 0.22 ( 3) link_NAG-ASN : angle 5.27856 / 3.30 ( 9) *********************** 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 245 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 141 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5428 (OUTLIER) cc_final: 0.4863 (m-80) REVERT: A 261 MET cc_start: 0.8367 (tmm) cc_final: 0.8094 (tmm) REVERT: A 279 VAL cc_start: 0.2698 (OUTLIER) cc_final: 0.2431 (t) REVERT: A 287 LEU cc_start: 0.4187 (OUTLIER) cc_final: 0.3879 (mt) REVERT: A 292 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.5784 (mp) REVERT: A 302 MET cc_start: 0.4703 (tpt) cc_final: 0.4427 (tpp) REVERT: A 324 HIS cc_start: 0.5901 (m-70) cc_final: 0.5417 (m-70) REVERT: A 407 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5288 (t80) REVERT: A 539 MET cc_start: 0.4885 (OUTLIER) cc_final: 0.3531 (tmm) REVERT: A 665 GLU cc_start: 0.8252 (mp0) cc_final: 0.7879 (mp0) REVERT: A 666 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7013 (t0) REVERT: A 1794 ASP cc_start: 0.5846 (t0) cc_final: 0.5085 (p0) REVERT: A 1958 PHE cc_start: 0.5562 (OUTLIER) cc_final: 0.4785 (m-80) REVERT: A 2167 MET cc_start: 0.6084 (mmt) cc_final: 0.5712 (mmt) REVERT: A 2180 MET cc_start: 0.7797 (tpt) cc_final: 0.7468 (tpt) REVERT: A 2324 LEU cc_start: 0.7346 (mt) cc_final: 0.6921 (mm) REVERT: B 138 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8833 (pp) REVERT: B 141 PHE cc_start: 0.4067 (p90) cc_final: 0.3747 (p90) REVERT: C 57 TRP cc_start: 0.8269 (OUTLIER) cc_final: 0.7631 (t60) outliers start: 104 outliers final: 65 residues processed: 224 average time/residue: 0.0864 time to fit residues: 30.1453 Evaluate side-chains 210 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 135 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 92 MET Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 138 VAL 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 239 VAL 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 539 MET 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 1871 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 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 2232 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 86 ILE Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 184 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 68 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1745 GLN ** 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 = 0.4959 r_free = 0.4959 target = 0.194594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.150105 restraints weight = 24084.106| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 4.47 r_work: 0.4161 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13892 Z= 0.171 Angle : 0.725 11.018 18874 Z= 0.361 Chirality : 0.048 0.256 2071 Planarity : 0.005 0.075 2379 Dihedral : 5.795 53.830 1829 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.92 % Favored : 89.72 % Rotamer: Outliers : 6.34 % Allowed : 25.85 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.20), residues: 1653 helix: -1.67 (0.50), residues: 90 sheet: -1.30 (0.22), residues: 495 loop : -2.00 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2033 TYR 0.038 0.002 TYR A 159 PHE 0.032 0.002 PHE A2234 TRP 0.030 0.002 TRP A 209 HIS 0.009 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (13869) covalent geometry : angle 0.70981 / 0.36 (18816) SS BOND : bond 0.00794 / 0.32 ( 11) SS BOND : angle 1.33397 / 0.77 ( 22) hydrogen bonds : bond 0.03375 / 2.17 ( 315) hydrogen bonds : angle 7.11771 / 4.78 ( 822) link_ALPHA1-3 : bond 0.00658 / 0.24 ( 3) link_ALPHA1-3 : angle 1.50224 / 0.87 ( 9) link_BETA1-4 : bond 0.00700 / 0.43 ( 6) link_BETA1-4 : angle 2.65911 / 1.60 ( 18) link_NAG-ASN : bond 0.00574 / 0.23 ( 3) link_NAG-ASN : angle 5.30915 / 3.32 ( 9) *********************** 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 232 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 139 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.4974 (m-80) REVERT: A 209 TRP cc_start: 0.6754 (t-100) cc_final: 0.5614 (t60) REVERT: A 261 MET cc_start: 0.8398 (tmm) cc_final: 0.8152 (tmm) REVERT: A 275 HIS cc_start: 0.3860 (OUTLIER) cc_final: 0.3074 (t-170) REVERT: A 279 VAL cc_start: 0.2676 (OUTLIER) cc_final: 0.2410 (t) REVERT: A 287 LEU cc_start: 0.4307 (OUTLIER) cc_final: 0.3990 (mt) REVERT: A 292 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.5789 (mp) REVERT: A 302 MET cc_start: 0.4688 (tpt) cc_final: 0.4464 (tpp) REVERT: A 324 HIS cc_start: 0.5981 (m-70) cc_final: 0.5610 (m90) REVERT: A 407 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5365 (t80) REVERT: A 539 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.3510 (tmm) REVERT: A 665 GLU cc_start: 0.8284 (mp0) cc_final: 0.8062 (mp0) REVERT: A 666 ASP cc_start: 0.7463 (OUTLIER) cc_final: 0.7040 (t0) REVERT: A 1794 ASP cc_start: 0.5847 (t0) cc_final: 0.5091 (p0) REVERT: A 1958 PHE cc_start: 0.5494 (OUTLIER) cc_final: 0.4703 (m-80) REVERT: A 2167 MET cc_start: 0.6155 (mmt) cc_final: 0.5762 (mmt) REVERT: A 2180 MET cc_start: 0.7795 (tpt) cc_final: 0.7485 (tpt) REVERT: B 138 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8900 (pp) REVERT: B 141 PHE cc_start: 0.4609 (p90) cc_final: 0.3912 (p90) REVERT: C 57 TRP cc_start: 0.8254 (OUTLIER) cc_final: 0.7622 (t60) outliers start: 93 outliers final: 66 residues processed: 215 average time/residue: 0.0854 time to fit residues: 28.4464 Evaluate side-chains 208 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 131 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 73 LEU 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 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 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 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 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 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 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 86 ILE Chi-restraints excluded: chain C residue 108 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 34 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 4 optimal weight: 0.0870 chunk 120 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4934 r_free = 0.4934 target = 0.191573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.149542 restraints weight = 24125.618| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 4.04 r_work: 0.4172 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13892 Z= 0.217 Angle : 0.769 10.961 18874 Z= 0.386 Chirality : 0.049 0.299 2071 Planarity : 0.005 0.079 2379 Dihedral : 6.057 55.523 1829 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.13 % Favored : 88.51 % Rotamer: Outliers : 6.34 % Allowed : 26.19 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.20), residues: 1653 helix: -1.96 (0.47), residues: 96 sheet: -1.29 (0.22), residues: 486 loop : -2.15 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2033 TYR 0.051 0.002 TYR A 159 PHE 0.034 0.002 PHE A1785 TRP 0.020 0.002 TRP A 209 HIS 0.010 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 (13869) covalent geometry : angle 0.75410 / 0.38 (18816) SS BOND : bond 0.00516 / 0.32 ( 11) SS BOND : angle 1.53605 / 0.86 ( 22) hydrogen bonds : bond 0.03710 / 2.37 ( 315) hydrogen bonds : angle 7.31336 / 4.92 ( 822) link_ALPHA1-3 : bond 0.00671 / 0.24 ( 3) link_ALPHA1-3 : angle 1.53906 / 0.90 ( 9) link_BETA1-4 : bond 0.00579 / 0.38 ( 6) link_BETA1-4 : angle 2.73395 / 1.64 ( 18) link_NAG-ASN : bond 0.00614 / 0.25 ( 3) link_NAG-ASN : angle 5.41974 / 3.38 ( 9) *********************** 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 228 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 135 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5268 (OUTLIER) cc_final: 0.3269 (m-80) REVERT: A 124 LYS cc_start: 0.6677 (tptp) cc_final: 0.6213 (tppt) REVERT: A 209 TRP cc_start: 0.6653 (t-100) cc_final: 0.6414 (t-100) REVERT: A 261 MET cc_start: 0.8410 (tmm) cc_final: 0.8124 (tmm) REVERT: A 275 HIS cc_start: 0.3825 (OUTLIER) cc_final: 0.3032 (t-170) REVERT: A 287 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.4002 (mt) REVERT: A 292 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.5965 (mp) REVERT: A 324 HIS cc_start: 0.5866 (m-70) cc_final: 0.5414 (m90) REVERT: A 407 TYR cc_start: 0.6260 (OUTLIER) cc_final: 0.5498 (t80) REVERT: A 539 MET cc_start: 0.4964 (OUTLIER) cc_final: 0.3740 (tmm) REVERT: A 665 GLU cc_start: 0.8266 (mp0) cc_final: 0.7990 (mp0) REVERT: A 666 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7041 (t0) REVERT: A 1772 MET cc_start: 0.6887 (tmm) cc_final: 0.6673 (tmm) REVERT: A 1794 ASP cc_start: 0.5823 (t0) cc_final: 0.5085 (p0) REVERT: A 1811 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: A 2033 ARG cc_start: 0.7325 (ptt90) cc_final: 0.6713 (ptp-110) REVERT: A 2167 MET cc_start: 0.6169 (mmt) cc_final: 0.5741 (mmt) REVERT: A 2180 MET cc_start: 0.7710 (tpt) cc_final: 0.7376 (tpt) REVERT: A 2219 TRP cc_start: 0.5010 (t60) cc_final: 0.3910 (p-90) REVERT: B 138 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8833 (pp) REVERT: B 141 PHE cc_start: 0.4617 (p90) cc_final: 0.3975 (p90) REVERT: C 57 TRP cc_start: 0.8299 (OUTLIER) cc_final: 0.7624 (t60) outliers start: 93 outliers final: 77 residues processed: 206 average time/residue: 0.0924 time to fit residues: 29.3087 Evaluate side-chains 219 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 132 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 73 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 92 MET 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 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 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 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 1811 GLU 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 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 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 2062 TRP 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 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 175 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 159 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.191870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.150818 restraints weight = 24139.749| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 4.09 r_work: 0.4166 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13892 Z= 0.217 Angle : 0.782 10.954 18874 Z= 0.391 Chirality : 0.049 0.270 2071 Planarity : 0.005 0.083 2379 Dihedral : 6.151 56.566 1829 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.71 % Favored : 88.93 % Rotamer: Outliers : 6.68 % Allowed : 26.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.19), residues: 1653 helix: -2.17 (0.45), residues: 96 sheet: -1.35 (0.23), residues: 486 loop : -2.19 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 531 TYR 0.048 0.002 TYR A 159 PHE 0.033 0.002 PHE A1785 TRP 0.016 0.002 TRP A 209 HIS 0.010 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (13869) covalent geometry : angle 0.76673 / 0.39 (18816) SS BOND : bond 0.00463 / 0.29 ( 11) SS BOND : angle 1.56240 / 0.91 ( 22) hydrogen bonds : bond 0.03707 / 2.37 ( 315) hydrogen bonds : angle 7.37666 / 4.94 ( 822) link_ALPHA1-3 : bond 0.00638 / 0.23 ( 3) link_ALPHA1-3 : angle 1.53444 / 0.90 ( 9) link_BETA1-4 : bond 0.00690 / 0.43 ( 6) link_BETA1-4 : angle 2.73827 / 1.64 ( 18) link_NAG-ASN : bond 0.00659 / 0.27 ( 3) link_NAG-ASN : angle 5.55159 / 3.44 ( 9) *********************** 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 231 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 133 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5323 (OUTLIER) cc_final: 0.3262 (m-80) REVERT: A 124 LYS cc_start: 0.6753 (tptp) cc_final: 0.6294 (tppt) REVERT: A 209 TRP cc_start: 0.6730 (t-100) cc_final: 0.6496 (t-100) REVERT: A 261 MET cc_start: 0.8372 (tmm) cc_final: 0.8111 (tmm) REVERT: A 275 HIS cc_start: 0.3876 (OUTLIER) cc_final: 0.3080 (t-170) REVERT: A 287 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.4020 (mt) REVERT: A 292 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6021 (mp) REVERT: A 302 MET cc_start: 0.4733 (tpt) cc_final: 0.4348 (tpt) REVERT: A 321 MET cc_start: 0.6931 (ttp) cc_final: 0.6629 (ttt) REVERT: A 407 TYR cc_start: 0.6389 (OUTLIER) cc_final: 0.5594 (t80) REVERT: A 539 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.3773 (tmm) REVERT: A 665 GLU cc_start: 0.8280 (mp0) cc_final: 0.7991 (mp0) REVERT: A 666 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7069 (t0) REVERT: A 1772 MET cc_start: 0.6910 (tmm) cc_final: 0.6329 (tmm) REVERT: A 1811 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: A 2033 ARG cc_start: 0.7318 (ptt90) cc_final: 0.6721 (ptp-110) REVERT: A 2167 MET cc_start: 0.6137 (mmt) cc_final: 0.5705 (mmt) REVERT: A 2180 MET cc_start: 0.7659 (tpt) cc_final: 0.7318 (tpt) REVERT: A 2238 MET cc_start: 0.5233 (mmm) cc_final: 0.3897 (mmm) REVERT: B 138 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8855 (pp) REVERT: B 141 PHE cc_start: 0.4644 (p90) cc_final: 0.3980 (p90) REVERT: C 57 TRP cc_start: 0.8305 (OUTLIER) cc_final: 0.7623 (t60) outliers start: 98 outliers final: 77 residues processed: 212 average time/residue: 0.0975 time to fit residues: 32.0032 Evaluate side-chains 218 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 131 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 92 MET 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 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 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 1811 GLU 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 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 1986 VAL 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 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 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 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 228 ASN 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 55 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 HIS ** 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 = 0.4963 r_free = 0.4963 target = 0.195156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.153540 restraints weight = 24214.446| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 4.44 r_work: 0.4189 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13892 Z= 0.144 Angle : 0.735 11.268 18874 Z= 0.364 Chirality : 0.047 0.263 2071 Planarity : 0.005 0.081 2379 Dihedral : 5.852 57.314 1829 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.32 % Favored : 90.32 % Rotamer: Outliers : 5.18 % Allowed : 27.49 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.20), residues: 1653 helix: -2.10 (0.45), residues: 96 sheet: -1.32 (0.22), residues: 491 loop : -2.08 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.044 0.002 TYR A 159 PHE 0.021 0.001 PHE A1785 TRP 0.014 0.002 TRP A 209 HIS 0.005 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13869) covalent geometry : angle 0.71930 / 0.36 (18816) SS BOND : bond 0.00440 / 0.25 ( 11) SS BOND : angle 1.47291 / 0.89 ( 22) hydrogen bonds : bond 0.03141 / 2.03 ( 315) hydrogen bonds : angle 7.02718 / 4.69 ( 822) link_ALPHA1-3 : bond 0.00633 / 0.24 ( 3) link_ALPHA1-3 : angle 1.52769 / 0.88 ( 9) link_BETA1-4 : bond 0.00712 / 0.44 ( 6) link_BETA1-4 : angle 2.65091 / 1.59 ( 18) link_NAG-ASN : bond 0.00618 / 0.25 ( 3) link_NAG-ASN : angle 5.31027 / 3.29 ( 9) *********************** 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 212 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 136 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5312 (OUTLIER) cc_final: 0.2963 (m-80) REVERT: A 124 LYS cc_start: 0.6553 (tptp) cc_final: 0.6220 (tppt) REVERT: A 209 TRP cc_start: 0.6673 (t-100) cc_final: 0.6461 (t-100) REVERT: A 261 MET cc_start: 0.8331 (tmm) cc_final: 0.8128 (tmm) REVERT: A 275 HIS cc_start: 0.3882 (OUTLIER) cc_final: 0.3102 (t-170) REVERT: A 287 LEU cc_start: 0.4301 (OUTLIER) cc_final: 0.3929 (mt) REVERT: A 292 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.5933 (mp) REVERT: A 324 HIS cc_start: 0.5612 (m-70) cc_final: 0.5337 (m-70) REVERT: A 407 TYR cc_start: 0.6300 (OUTLIER) cc_final: 0.5537 (t80) REVERT: A 539 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.3626 (tmm) REVERT: A 665 GLU cc_start: 0.8247 (mp0) cc_final: 0.7976 (mp0) REVERT: A 1772 MET cc_start: 0.6778 (tmm) cc_final: 0.6574 (tmm) REVERT: A 1794 ASP cc_start: 0.5690 (t0) cc_final: 0.4960 (p0) REVERT: A 2033 ARG cc_start: 0.7139 (ptt90) cc_final: 0.6560 (ptp-110) REVERT: A 2167 MET cc_start: 0.6214 (mmt) cc_final: 0.5769 (mmt) REVERT: A 2180 MET cc_start: 0.7672 (tpt) cc_final: 0.7361 (tpt) REVERT: A 2238 MET cc_start: 0.5200 (mmm) cc_final: 0.4132 (mmm) REVERT: B 138 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8872 (pp) REVERT: B 141 PHE cc_start: 0.4782 (p90) cc_final: 0.4072 (p90) REVERT: C 57 TRP cc_start: 0.8233 (OUTLIER) cc_final: 0.7568 (t60) outliers start: 76 outliers final: 59 residues processed: 195 average time/residue: 0.1065 time to fit residues: 31.5292 Evaluate side-chains 197 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 130 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 118 HIS Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU 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 194 HIS Chi-restraints excluded: chain A residue 199 LEU 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 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 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 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 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 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 C residue 18 VAL 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 86 ILE 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 27 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 123 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.196626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.154971 restraints weight = 23744.029| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 4.50 r_work: 0.4233 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13892 Z= 0.145 Angle : 0.749 13.748 18874 Z= 0.367 Chirality : 0.048 0.263 2071 Planarity : 0.005 0.084 2379 Dihedral : 5.790 57.794 1829 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.38 % Favored : 90.32 % Rotamer: Outliers : 5.18 % Allowed : 27.69 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.20), residues: 1653 helix: -1.87 (0.48), residues: 89 sheet: -1.26 (0.22), residues: 490 loop : -2.00 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 531 TYR 0.050 0.002 TYR A 159 PHE 0.021 0.001 PHE A1785 TRP 0.014 0.002 TRP A 209 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (13869) covalent geometry : angle 0.73463 / 0.36 (18816) SS BOND : bond 0.00503 / 0.33 ( 11) SS BOND : angle 1.44512 / 0.89 ( 22) hydrogen bonds : bond 0.03133 / 2.03 ( 315) hydrogen bonds : angle 6.96768 / 4.66 ( 822) link_ALPHA1-3 : bond 0.00622 / 0.23 ( 3) link_ALPHA1-3 : angle 1.53054 / 0.89 ( 9) link_BETA1-4 : bond 0.00712 / 0.44 ( 6) link_BETA1-4 : angle 2.62294 / 1.57 ( 18) link_NAG-ASN : bond 0.00572 / 0.22 ( 3) link_NAG-ASN : angle 5.20056 / 3.21 ( 9) ********************** 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 207 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 131 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5199 (OUTLIER) cc_final: 0.2999 (m-80) REVERT: A 124 LYS cc_start: 0.6548 (tptp) cc_final: 0.6184 (tppt) REVERT: A 209 TRP cc_start: 0.6613 (t-100) cc_final: 0.6402 (t-100) REVERT: A 261 MET cc_start: 0.8219 (tmm) cc_final: 0.7959 (tmm) REVERT: A 275 HIS cc_start: 0.3784 (OUTLIER) cc_final: 0.2975 (t-170) REVERT: A 279 VAL cc_start: 0.2641 (OUTLIER) cc_final: 0.2364 (t) REVERT: A 287 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.3919 (mt) REVERT: A 292 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6024 (mp) REVERT: A 324 HIS cc_start: 0.5546 (m-70) cc_final: 0.5248 (m90) REVERT: A 407 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5535 (t80) REVERT: A 539 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.3615 (tmm) REVERT: A 553 ILE cc_start: 0.7174 (OUTLIER) cc_final: 0.6464 (tp) REVERT: A 665 GLU cc_start: 0.8201 (mp0) cc_final: 0.7900 (mp0) REVERT: A 679 PHE cc_start: 0.6614 (m-80) cc_final: 0.6185 (m-10) REVERT: A 1772 MET cc_start: 0.6766 (tmm) cc_final: 0.6540 (tmm) REVERT: A 1794 ASP cc_start: 0.5691 (t0) cc_final: 0.4991 (p0) REVERT: A 2033 ARG cc_start: 0.7158 (ptt90) cc_final: 0.6578 (ptp-110) REVERT: A 2167 MET cc_start: 0.6167 (mmt) cc_final: 0.5717 (mmt) REVERT: A 2180 MET cc_start: 0.7709 (tpt) cc_final: 0.7411 (tpt) REVERT: A 2238 MET cc_start: 0.5115 (mmm) cc_final: 0.3890 (mmm) REVERT: A 2321 MET cc_start: 0.6403 (mmm) cc_final: 0.5895 (mpp) REVERT: B 138 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8848 (pp) REVERT: B 141 PHE cc_start: 0.5024 (p90) cc_final: 0.4250 (p90) REVERT: C 57 TRP cc_start: 0.8232 (OUTLIER) cc_final: 0.7563 (t60) REVERT: C 103 MET cc_start: 0.5390 (mmm) cc_final: 0.4969 (mtp) outliers start: 76 outliers final: 63 residues processed: 190 average time/residue: 0.1002 time to fit residues: 29.1317 Evaluate side-chains 203 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 130 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 88 THR Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 HIS Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU 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 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 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 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 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 2012 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 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 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 C residue 18 VAL 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 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 110 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.0020 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4998 r_free = 0.4998 target = 0.197728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.157504 restraints weight = 23605.017| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 4.30 r_work: 0.4263 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2605 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= 0.135 Angle : 0.732 13.491 18874 Z= 0.359 Chirality : 0.047 0.265 2071 Planarity : 0.005 0.083 2379 Dihedral : 5.686 57.941 1829 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.56 % Favored : 90.14 % Rotamer: Outliers : 5.39 % Allowed : 27.69 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.20), residues: 1653 helix: -1.84 (0.48), residues: 89 sheet: -1.21 (0.23), residues: 490 loop : -1.96 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 531 TYR 0.056 0.002 TYR A 159 PHE 0.019 0.001 PHE A1785 TRP 0.015 0.002 TRP A2229 HIS 0.005 0.001 HIS A2005 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (13869) covalent geometry : angle 0.71808 / 0.36 (18816) SS BOND : bond 0.00402 / 0.25 ( 11) SS BOND : angle 1.24007 / 0.78 ( 22) hydrogen bonds : bond 0.03018 / 1.95 ( 315) hydrogen bonds : angle 6.82097 / 4.57 ( 822) link_ALPHA1-3 : bond 0.00611 / 0.23 ( 3) link_ALPHA1-3 : angle 1.52705 / 0.89 ( 9) link_BETA1-4 : bond 0.00706 / 0.43 ( 6) link_BETA1-4 : angle 2.57987 / 1.55 ( 18) link_NAG-ASN : bond 0.00528 / 0.20 ( 3) link_NAG-ASN : angle 5.16526 / 3.19 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4006.79 seconds wall clock time: 69 minutes 30.17 seconds (4170.17 seconds total)