Starting phenix.real_space_refine on Sat Aug 23 18:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ty1_41710/08_2025/8ty1_41710.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ty1_41710/08_2025/8ty1_41710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ty1_41710/08_2025/8ty1_41710.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ty1_41710/08_2025/8ty1_41710.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ty1_41710/08_2025/8ty1_41710.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ty1_41710/08_2025/8ty1_41710.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.73, per 1000 atoms: 0.28 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: 1.24 Conformation dependent library (CDL) restraints added in 696.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.63 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: 3.23 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4283 1.34 - 1.46: 3586 1.46 - 1.59: 5896 1.59 - 1.71: 1 1.71 - 1.83: 103 Bond restraints: 13869 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.568 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" C1 MAN F 4 " pdb=" C2 MAN F 4 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" CB PRO C 209 " pdb=" CG PRO C 209 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.70e+00 bond pdb=" C5 BMA D 3 " pdb=" O5 BMA D 3 " ideal model delta sigma weight residual 1.417 1.453 -0.036 2.00e-02 2.50e+03 3.28e+00 ... (remaining 13864 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 18287 2.33 - 4.65: 440 4.65 - 6.98: 59 6.98 - 9.30: 22 9.30 - 11.63: 8 Bond angle restraints: 18816 Sorted by residual: angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 101.99 10.01 1.40e+00 5.10e-01 5.12e+01 angle pdb=" C ASN A1805 " pdb=" CA ASN A1805 " pdb=" CB ASN A1805 " ideal model delta sigma weight residual 116.54 110.18 6.36 1.15e+00 7.56e-01 3.06e+01 angle pdb=" C HIS A2315 " pdb=" N GLN A2316 " pdb=" CA GLN A2316 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" N GLN A2316 " pdb=" CA GLN A2316 " pdb=" CB GLN A2316 " ideal model delta sigma weight residual 110.49 118.97 -8.48 1.69e+00 3.50e-01 2.52e+01 angle pdb=" C VAL A2314 " pdb=" N HIS A2315 " pdb=" CA HIS A2315 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.52: 7469 23.52 - 47.03: 713 47.03 - 70.55: 105 70.55 - 94.06: 42 94.06 - 117.58: 18 Dihedral angle restraints: 8347 sinusoidal: 3473 harmonic: 4874 Sorted by residual: dihedral pdb=" CB CYS B 136 " pdb=" SG CYS B 136 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.96 -61.96 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 220 " pdb=" CB CYS C 220 " ideal model delta sinusoidal sigma weight residual 93.00 151.99 -58.99 1 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" CA CYS A 180 " pdb=" C CYS A 180 " pdb=" N ARG A 181 " pdb=" CA ARG A 181 " ideal model delta harmonic sigma weight residual -180.00 -148.81 -31.19 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1598 0.055 - 0.110: 384 0.110 - 0.164: 81 0.164 - 0.219: 5 0.219 - 0.274: 3 Chirality restraints: 2071 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 2068 not shown) Planarity restraints: 2382 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 208 " 0.119 5.00e-02 4.00e+02 1.73e-01 4.78e+01 pdb=" N PRO C 209 " -0.299 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.094 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 127 " -0.018 2.00e-02 2.50e+03 2.71e-02 1.84e+01 pdb=" CG TRP C 127 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP C 127 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 127 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 127 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 127 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 127 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP C 127 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.025 2.00e-02 2.50e+03 2.40e-02 1.45e+01 pdb=" CG TRP A 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.006 2.00e-02 2.50e+03 ... (remaining 2379 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 222 2.58 - 3.16: 11640 3.16 - 3.74: 21330 3.74 - 4.32: 29351 4.32 - 4.90: 47611 Nonbonded interactions: 110154 Sorted by model distance: nonbonded pdb=" OE2 GLU A 111 " pdb=" OH TYR A 115 " model vdw 2.005 3.040 nonbonded pdb=" O ALA A1877 " pdb=" ND2 ASN A1922 " model vdw 2.124 3.120 nonbonded pdb=" OE1 GLN A 135 " pdb=" OH TYR A 137 " model vdw 2.136 3.040 nonbonded pdb=" OG SER A 628 " pdb=" O LYS A 707 " model vdw 2.138 3.040 nonbonded pdb=" OE2 GLU A 389 " pdb=" NH2 ARG A 439 " model vdw 2.139 3.120 ... (remaining 110149 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 13892 Z= 0.232 Angle : 0.899 11.625 18874 Z= 0.454 Chirality : 0.050 0.274 2071 Planarity : 0.006 0.173 2379 Dihedral : 19.173 117.576 5186 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 22.79 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 aren 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 covalent geometry : bond 0.00527 (13869) covalent geometry : angle 0.88656 (18816) SS BOND : bond 0.00367 ( 11) SS BOND : angle 1.16668 ( 22) hydrogen bonds : bond 0.15833 ( 315) hydrogen bonds : angle 8.58911 ( 822) link_ALPHA1-3 : bond 0.00426 ( 3) link_ALPHA1-3 : angle 1.71437 ( 9) link_BETA1-4 : bond 0.00558 ( 6) link_BETA1-4 : angle 2.89423 ( 18) link_NAG-ASN : bond 0.00594 ( 3) link_NAG-ASN : angle 5.34067 ( 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 : 0.365 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: 0.1167 time to fit residues: 29.2098 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 : 0.525 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 590 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.193082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.150902 restraints weight = 24127.088| |-----------------------------------------------------------------------------| r_work (start): 0.4404 rms_B_bonded: 4.33 r_work: 0.4178 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.1030 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= 0.187 Angle : 0.769 10.463 18874 Z= 0.384 Chirality : 0.049 0.233 2071 Planarity : 0.006 0.111 2379 Dihedral : 12.731 114.434 2078 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.62 % Favored : 89.96 % Rotamer: Outliers : 4.43 % Allowed : 25.24 % Favored : 70.33 % 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 aren not related in a simple way. whole: -2.61 (0.20), residues: 1653 helix: -1.43 (0.55), residues: 75 sheet: -1.35 (0.22), residues: 481 loop : -2.03 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 418 TYR 0.021 0.002 TYR A 137 PHE 0.027 0.002 PHE A1785 TRP 0.028 0.002 TRP A 139 HIS 0.010 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00424 (13869) covalent geometry : angle 0.75290 (18816) SS BOND : bond 0.00860 ( 11) SS BOND : angle 1.20526 ( 22) hydrogen bonds : bond 0.04116 ( 315) hydrogen bonds : angle 7.32449 ( 822) link_ALPHA1-3 : bond 0.01140 ( 3) link_ALPHA1-3 : angle 2.63961 ( 9) link_BETA1-4 : bond 0.00926 ( 6) link_BETA1-4 : angle 2.96765 ( 18) link_NAG-ASN : bond 0.00653 ( 3) link_NAG-ASN : angle 5.14811 ( 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 216 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8462 (tmm) cc_final: 0.8121 (tmm) REVERT: A 279 VAL cc_start: 0.2684 (OUTLIER) cc_final: 0.2448 (t) REVERT: A 292 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.5978 (mp) REVERT: A 313 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 324 HIS cc_start: 0.5915 (m-70) cc_final: 0.5441 (m-70) REVERT: A 1711 MET cc_start: 0.3135 (mpp) cc_final: 0.2711 (mpp) REVERT: A 1794 ASP cc_start: 0.5791 (t0) cc_final: 0.4997 (p0) REVERT: A 2167 MET cc_start: 0.5984 (mmt) cc_final: 0.5571 (mmt) REVERT: A 2180 MET cc_start: 0.7819 (tpt) cc_final: 0.7509 (tpt) REVERT: A 2238 MET cc_start: 0.4600 (mmm) cc_final: 0.4335 (mmm) REVERT: C 1 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: C 57 TRP cc_start: 0.8311 (OUTLIER) cc_final: 0.7638 (t60) outliers start: 65 outliers final: 31 residues processed: 202 average time/residue: 0.1147 time to fit residues: 35.4309 Evaluate side-chains 171 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 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: 0.0980 chunk 164 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 100 optimal weight: 0.0770 chunk 116 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** 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 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 = 0.4961 r_free = 0.4961 target = 0.194700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.149872 restraints weight = 24293.611| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 3.97 r_work: 0.4181 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13892 Z= 0.168 Angle : 0.738 10.061 18874 Z= 0.367 Chirality : 0.048 0.236 2071 Planarity : 0.005 0.083 2379 Dihedral : 11.529 114.579 2069 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.56 % Favored : 90.02 % 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 aren not related in a simple way. whole: -2.60 (0.20), residues: 1653 helix: -1.51 (0.55), residues: 78 sheet: -1.35 (0.22), residues: 479 loop : -2.01 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 18 TYR 0.018 0.002 TYR A 137 PHE 0.025 0.002 PHE A1785 TRP 0.026 0.002 TRP C 127 HIS 0.007 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00384 (13869) covalent geometry : angle 0.72191 (18816) SS BOND : bond 0.00546 ( 11) SS BOND : angle 1.01307 ( 22) hydrogen bonds : bond 0.03685 ( 315) hydrogen bonds : angle 7.15334 ( 822) link_ALPHA1-3 : bond 0.01171 ( 3) link_ALPHA1-3 : angle 2.22999 ( 9) link_BETA1-4 : bond 0.00836 ( 6) link_BETA1-4 : angle 2.87545 ( 18) link_NAG-ASN : bond 0.00653 ( 3) link_NAG-ASN : angle 5.32242 ( 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 : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8350 (tmm) cc_final: 0.8136 (tmm) REVERT: A 279 VAL cc_start: 0.2643 (OUTLIER) cc_final: 0.2410 (t) REVERT: A 292 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.5925 (mp) REVERT: A 324 HIS cc_start: 0.5887 (m-70) cc_final: 0.5475 (m-70) REVERT: A 407 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5167 (t80) REVERT: A 666 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.6956 (t0) REVERT: A 1794 ASP cc_start: 0.5834 (t0) cc_final: 0.5029 (p0) REVERT: A 2010 MET cc_start: 0.8038 (tpp) cc_final: 0.7821 (mpp) REVERT: A 2167 MET cc_start: 0.6027 (mmt) cc_final: 0.5632 (mmt) REVERT: A 2180 MET cc_start: 0.7597 (tpt) cc_final: 0.7117 (tpt) REVERT: C 57 TRP cc_start: 0.8228 (OUTLIER) cc_final: 0.7682 (t60) outliers start: 77 outliers final: 44 residues processed: 204 average time/residue: 0.1069 time to fit residues: 33.0382 Evaluate side-chains 184 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 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 666 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1776 LYS Chi-restraints excluded: chain A residue 1777 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1871 VAL Chi-restraints excluded: chain A residue 1882 ILE Chi-restraints excluded: chain A residue 1926 MET Chi-restraints excluded: chain A residue 1940 ILE Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2195 TYR Chi-restraints excluded: chain A residue 2232 VAL Chi-restraints excluded: chain B residue 38 GLN 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 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 220 CYS 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: 2.9990 chunk 82 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 128 optimal weight: 0.0370 chunk 105 optimal weight: 0.0870 chunk 85 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 78 optimal weight: 0.0020 overall best weight: 0.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2235 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 221 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.197023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.154178 restraints weight = 25050.027| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 4.10 r_work: 0.4255 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13892 Z= 0.123 Angle : 0.712 10.856 18874 Z= 0.348 Chirality : 0.047 0.255 2071 Planarity : 0.005 0.073 2379 Dihedral : 10.338 113.647 2069 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.71 % Favored : 90.93 % Rotamer: Outliers : 4.57 % Allowed : 26.26 % 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 aren not related in a simple way. whole: -2.46 (0.20), residues: 1653 helix: -1.67 (0.51), residues: 91 sheet: -1.23 (0.22), residues: 479 loop : -1.90 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2307 TYR 0.023 0.001 TYR A 159 PHE 0.017 0.001 PHE A2234 TRP 0.026 0.002 TRP C 127 HIS 0.005 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00275 (13869) covalent geometry : angle 0.69574 (18816) SS BOND : bond 0.00307 ( 11) SS BOND : angle 0.91815 ( 22) hydrogen bonds : bond 0.03161 ( 315) hydrogen bonds : angle 6.84602 ( 822) link_ALPHA1-3 : bond 0.01165 ( 3) link_ALPHA1-3 : angle 2.24333 ( 9) link_BETA1-4 : bond 0.00808 ( 6) link_BETA1-4 : angle 2.72731 ( 18) link_NAG-ASN : bond 0.00600 ( 3) link_NAG-ASN : angle 5.41383 ( 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 212 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 145 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 TRP cc_start: 0.5618 (OUTLIER) cc_final: 0.5297 (m-90) REVERT: A 261 MET cc_start: 0.8293 (tmm) cc_final: 0.8027 (tmm) REVERT: A 279 VAL cc_start: 0.2866 (OUTLIER) cc_final: 0.2637 (t) REVERT: A 292 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5682 (mp) REVERT: A 302 MET cc_start: 0.4702 (tpt) cc_final: 0.4181 (mmt) REVERT: A 324 HIS cc_start: 0.5562 (m-70) cc_final: 0.5196 (m-70) REVERT: A 407 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.5141 (t80) REVERT: A 665 GLU cc_start: 0.8561 (mp0) cc_final: 0.8251 (mp0) REVERT: A 1794 ASP cc_start: 0.5756 (t0) cc_final: 0.5057 (p0) REVERT: A 2010 MET cc_start: 0.7939 (tpp) cc_final: 0.7243 (mpp) REVERT: A 2167 MET cc_start: 0.6030 (mmt) cc_final: 0.5628 (mmt) REVERT: A 2180 MET cc_start: 0.7760 (tpt) cc_final: 0.7407 (tpt) REVERT: A 2238 MET cc_start: 0.5961 (tpp) cc_final: 0.5589 (tpp) REVERT: A 2324 LEU cc_start: 0.7425 (mt) cc_final: 0.6986 (mm) REVERT: B 138 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8786 (pp) REVERT: B 141 PHE cc_start: 0.4251 (p90) cc_final: 0.3429 (p90) REVERT: C 57 TRP cc_start: 0.8235 (OUTLIER) cc_final: 0.7585 (t60) outliers start: 67 outliers final: 40 residues processed: 198 average time/residue: 0.0917 time to fit residues: 27.8457 Evaluate side-chains 186 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 118 HIS Chi-restraints excluded: chain A residue 139 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 199 LEU 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 403 ASP Chi-restraints excluded: chain A residue 407 TYR 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 1871 VAL Chi-restraints excluded: chain A residue 1889 TRP Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 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 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 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: 9.9990 chunk 97 optimal weight: 0.8980 chunk 57 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS A 693 HIS ** A1745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1861 ASN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.195212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.153804 restraints weight = 24316.117| |-----------------------------------------------------------------------------| r_work (start): 0.4441 rms_B_bonded: 4.22 r_work: 0.4199 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 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 0.044 13892 Z= 0.169 Angle : 0.728 10.298 18874 Z= 0.358 Chirality : 0.047 0.242 2071 Planarity : 0.005 0.075 2379 Dihedral : 9.586 111.979 2069 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.80 % Favored : 89.84 % Rotamer: Outliers : 6.21 % Allowed : 25.03 % Favored : 68.76 % 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 aren not related in a simple way. whole: -2.52 (0.20), residues: 1653 helix: -1.71 (0.51), residues: 91 sheet: -1.23 (0.22), residues: 484 loop : -1.97 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 48 TYR 0.035 0.002 TYR A 159 PHE 0.025 0.002 PHE A1785 TRP 0.027 0.002 TRP A 209 HIS 0.007 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00389 (13869) covalent geometry : angle 0.70911 (18816) SS BOND : bond 0.00325 ( 11) SS BOND : angle 1.19030 ( 22) hydrogen bonds : bond 0.03421 ( 315) hydrogen bonds : angle 7.02858 ( 822) link_ALPHA1-3 : bond 0.01219 ( 3) link_ALPHA1-3 : angle 2.43311 ( 9) link_BETA1-4 : bond 0.00807 ( 6) link_BETA1-4 : angle 2.64381 ( 18) link_NAG-ASN : bond 0.00781 ( 3) link_NAG-ASN : angle 5.94800 ( 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 241 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 150 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5462 (OUTLIER) cc_final: 0.4696 (m-80) REVERT: A 261 MET cc_start: 0.8359 (tmm) cc_final: 0.8093 (tmm) REVERT: A 279 VAL cc_start: 0.2744 (OUTLIER) cc_final: 0.2453 (t) REVERT: A 287 LEU cc_start: 0.4102 (OUTLIER) cc_final: 0.3805 (mt) REVERT: A 292 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.5867 (mp) REVERT: A 302 MET cc_start: 0.4726 (tpt) cc_final: 0.4451 (tpp) REVERT: A 324 HIS cc_start: 0.5774 (m-70) cc_final: 0.5397 (m90) REVERT: A 407 TYR cc_start: 0.5958 (OUTLIER) cc_final: 0.5239 (t80) REVERT: A 539 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.3562 (tmm) REVERT: A 665 GLU cc_start: 0.8275 (mp0) cc_final: 0.7919 (mp0) REVERT: A 1794 ASP cc_start: 0.5883 (t0) cc_final: 0.5104 (p0) REVERT: A 1958 PHE cc_start: 0.5626 (OUTLIER) cc_final: 0.4834 (m-80) REVERT: A 2167 MET cc_start: 0.6136 (mmt) cc_final: 0.5752 (mmt) REVERT: A 2180 MET cc_start: 0.7576 (tpt) cc_final: 0.7237 (tpt) REVERT: A 2324 LEU cc_start: 0.7300 (mt) cc_final: 0.6861 (mm) REVERT: B 138 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8739 (pp) REVERT: B 141 PHE cc_start: 0.4056 (p90) cc_final: 0.3729 (p90) REVERT: C 57 TRP cc_start: 0.8179 (OUTLIER) cc_final: 0.7607 (t60) outliers start: 91 outliers final: 60 residues processed: 224 average time/residue: 0.0969 time to fit residues: 33.4400 Evaluate side-chains 207 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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: 0.5980 chunk 39 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 98 optimal weight: 0.0670 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1745 GLN ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.197087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.154327 restraints weight = 24059.767| |-----------------------------------------------------------------------------| r_work (start): 0.4442 rms_B_bonded: 4.05 r_work: 0.4242 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13892 Z= 0.135 Angle : 0.711 10.809 18874 Z= 0.348 Chirality : 0.047 0.250 2071 Planarity : 0.005 0.072 2379 Dihedral : 9.042 109.437 2069 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.95 % Favored : 90.68 % Rotamer: Outliers : 5.73 % Allowed : 26.06 % Favored : 68.21 % 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 aren not related in a simple way. whole: -2.43 (0.20), residues: 1653 helix: -1.65 (0.51), residues: 91 sheet: -1.21 (0.22), residues: 489 loop : -1.88 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1696 TYR 0.035 0.002 TYR A 159 PHE 0.021 0.001 PHE A1785 TRP 0.030 0.002 TRP A 209 HIS 0.005 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00305 (13869) covalent geometry : angle 0.69278 (18816) SS BOND : bond 0.00392 ( 11) SS BOND : angle 1.44683 ( 22) hydrogen bonds : bond 0.03157 ( 315) hydrogen bonds : angle 6.96996 ( 822) link_ALPHA1-3 : bond 0.01180 ( 3) link_ALPHA1-3 : angle 2.26959 ( 9) link_BETA1-4 : bond 0.00770 ( 6) link_BETA1-4 : angle 2.65442 ( 18) link_NAG-ASN : bond 0.00687 ( 3) link_NAG-ASN : angle 5.62344 ( 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 235 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 151 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 TRP cc_start: 0.6581 (t-100) cc_final: 0.5542 (t60) REVERT: A 261 MET cc_start: 0.8268 (tmm) cc_final: 0.8034 (tmm) REVERT: A 279 VAL cc_start: 0.2869 (OUTLIER) cc_final: 0.2602 (t) REVERT: A 292 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.5826 (mp) REVERT: A 302 MET cc_start: 0.4660 (tpt) cc_final: 0.4415 (tpp) REVERT: A 324 HIS cc_start: 0.5802 (m-70) cc_final: 0.5457 (m90) REVERT: A 407 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.5207 (t80) REVERT: A 539 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.3414 (tmm) REVERT: A 553 ILE cc_start: 0.6878 (OUTLIER) cc_final: 0.6003 (tp) REVERT: A 665 GLU cc_start: 0.8209 (mp0) cc_final: 0.7837 (mp0) REVERT: A 666 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6920 (t0) REVERT: A 1794 ASP cc_start: 0.5892 (t0) cc_final: 0.5144 (p0) REVERT: A 2167 MET cc_start: 0.6110 (mmt) cc_final: 0.5759 (mmt) REVERT: A 2180 MET cc_start: 0.7540 (tpt) cc_final: 0.7235 (tpt) REVERT: A 2324 LEU cc_start: 0.7237 (mt) cc_final: 0.6791 (mm) REVERT: B 138 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8688 (pp) REVERT: B 141 PHE cc_start: 0.4253 (p90) cc_final: 0.3719 (p90) REVERT: C 57 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7590 (t60) REVERT: C 108 ARG cc_start: 0.3616 (OUTLIER) cc_final: 0.3402 (ptt180) outliers start: 84 outliers final: 63 residues processed: 214 average time/residue: 0.0896 time to fit residues: 29.7544 Evaluate side-chains 217 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 145 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL 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 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 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 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 481 THR Chi-restraints excluded: chain A residue 531 ARG 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 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 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 1965 VAL Chi-restraints excluded: chain A residue 1975 VAL Chi-restraints excluded: chain A residue 1985 THR Chi-restraints excluded: chain A residue 2062 TRP Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2086 THR Chi-restraints excluded: chain A residue 2112 TRP Chi-restraints excluded: chain A residue 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 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 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: 6.9990 chunk 79 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 120 optimal weight: 1.9990 chunk 140 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.195491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.151991 restraints weight = 24106.938| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 4.24 r_work: 0.4183 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13892 Z= 0.163 Angle : 0.722 10.283 18874 Z= 0.356 Chirality : 0.047 0.244 2071 Planarity : 0.005 0.077 2379 Dihedral : 8.772 106.600 2069 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.04 % Favored : 89.66 % Rotamer: Outliers : 6.07 % Allowed : 26.19 % Favored : 67.74 % 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 aren not related in a simple way. whole: -2.48 (0.20), residues: 1653 helix: -1.66 (0.51), residues: 91 sheet: -1.18 (0.22), residues: 496 loop : -1.96 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2033 TYR 0.049 0.002 TYR A 159 PHE 0.026 0.002 PHE A1785 TRP 0.019 0.002 TRP A 209 HIS 0.006 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00378 (13869) covalent geometry : angle 0.70602 (18816) SS BOND : bond 0.00449 ( 11) SS BOND : angle 1.09061 ( 22) hydrogen bonds : bond 0.03261 ( 315) hydrogen bonds : angle 6.91913 ( 822) link_ALPHA1-3 : bond 0.01132 ( 3) link_ALPHA1-3 : angle 2.33194 ( 9) link_BETA1-4 : bond 0.00732 ( 6) link_BETA1-4 : angle 2.69031 ( 18) link_NAG-ASN : bond 0.00657 ( 3) link_NAG-ASN : angle 5.44018 ( 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 233 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 144 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5235 (OUTLIER) cc_final: 0.2897 (m-80) REVERT: A 209 TRP cc_start: 0.6553 (t-100) cc_final: 0.5453 (t60) REVERT: A 261 MET cc_start: 0.8405 (tmm) cc_final: 0.8098 (tmm) REVERT: A 275 HIS cc_start: 0.3821 (OUTLIER) cc_final: 0.3057 (t-170) REVERT: A 287 LEU cc_start: 0.4121 (OUTLIER) cc_final: 0.3778 (mt) REVERT: A 292 LEU cc_start: 0.6796 (OUTLIER) cc_final: 0.5805 (mp) REVERT: A 324 HIS cc_start: 0.5841 (m-70) cc_final: 0.5487 (m90) REVERT: A 407 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5357 (t80) REVERT: A 539 MET cc_start: 0.4835 (OUTLIER) cc_final: 0.3508 (tmm) REVERT: A 553 ILE cc_start: 0.7002 (OUTLIER) cc_final: 0.6229 (tp) REVERT: A 665 GLU cc_start: 0.8257 (mp0) cc_final: 0.7849 (mp0) REVERT: A 666 ASP cc_start: 0.7388 (OUTLIER) cc_final: 0.6952 (t0) REVERT: A 1794 ASP cc_start: 0.5854 (t0) cc_final: 0.5114 (p0) REVERT: A 2167 MET cc_start: 0.6202 (mmt) cc_final: 0.5795 (mmt) REVERT: A 2180 MET cc_start: 0.7574 (tpt) cc_final: 0.7255 (tpt) REVERT: A 2324 LEU cc_start: 0.7284 (mt) cc_final: 0.6843 (mm) REVERT: B 138 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8747 (pp) REVERT: B 141 PHE cc_start: 0.4406 (p90) cc_final: 0.3846 (p90) REVERT: C 57 TRP cc_start: 0.8223 (OUTLIER) cc_final: 0.7591 (t60) REVERT: C 108 ARG cc_start: 0.3758 (OUTLIER) cc_final: 0.3488 (ptt180) REVERT: C 164 CYS cc_start: 0.3861 (OUTLIER) cc_final: 0.3168 (p) outliers start: 89 outliers final: 66 residues processed: 210 average time/residue: 0.0970 time to fit residues: 31.2520 Evaluate side-chains 220 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 142 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 59 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 138 VAL 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 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 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 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 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 164 CYS Chi-restraints excluded: chain C residue 184 THR 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: 1.9990 chunk 78 optimal weight: 0.0370 chunk 140 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** 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 = 0.4962 r_free = 0.4962 target = 0.195027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.149717 restraints weight = 24096.159| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 4.07 r_work: 0.4186 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.2242 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= 0.162 Angle : 0.743 10.281 18874 Z= 0.365 Chirality : 0.047 0.247 2071 Planarity : 0.005 0.080 2379 Dihedral : 8.582 103.873 2069 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.80 % Favored : 89.90 % Rotamer: Outliers : 6.21 % Allowed : 26.53 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.20), residues: 1653 helix: -1.76 (0.49), residues: 90 sheet: -1.17 (0.22), residues: 497 loop : -1.95 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2033 TYR 0.048 0.002 TYR A 159 PHE 0.026 0.002 PHE A1785 TRP 0.017 0.002 TRP A 209 HIS 0.010 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00374 (13869) covalent geometry : angle 0.72624 (18816) SS BOND : bond 0.00481 ( 11) SS BOND : angle 1.31159 ( 22) hydrogen bonds : bond 0.03221 ( 315) hydrogen bonds : angle 6.93384 ( 822) link_ALPHA1-3 : bond 0.01115 ( 3) link_ALPHA1-3 : angle 2.31802 ( 9) link_BETA1-4 : bond 0.00733 ( 6) link_BETA1-4 : angle 2.74252 ( 18) link_NAG-ASN : bond 0.00664 ( 3) link_NAG-ASN : angle 5.38152 ( 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 236 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 145 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5236 (OUTLIER) cc_final: 0.2899 (m-80) REVERT: A 209 TRP cc_start: 0.6529 (t-100) cc_final: 0.6312 (t-100) REVERT: A 261 MET cc_start: 0.8362 (tmm) cc_final: 0.8057 (tmm) REVERT: A 275 HIS cc_start: 0.3697 (OUTLIER) cc_final: 0.2925 (t-170) REVERT: A 279 VAL cc_start: 0.2695 (OUTLIER) cc_final: 0.2430 (t) REVERT: A 287 LEU cc_start: 0.4139 (OUTLIER) cc_final: 0.3808 (mt) REVERT: A 292 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.5847 (mp) REVERT: A 302 MET cc_start: 0.4754 (tpt) cc_final: 0.4258 (mmt) REVERT: A 324 HIS cc_start: 0.5772 (m-70) cc_final: 0.5415 (m90) REVERT: A 407 TYR cc_start: 0.6156 (OUTLIER) cc_final: 0.5428 (t80) REVERT: A 539 MET cc_start: 0.4844 (OUTLIER) cc_final: 0.3551 (tmm) REVERT: A 665 GLU cc_start: 0.8253 (mp0) cc_final: 0.7864 (mp0) REVERT: A 666 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6986 (t0) REVERT: A 1794 ASP cc_start: 0.5858 (t0) cc_final: 0.5151 (p0) REVERT: A 2010 MET cc_start: 0.8087 (tpp) cc_final: 0.7723 (mpp) REVERT: A 2167 MET cc_start: 0.6144 (mmt) cc_final: 0.5779 (mmt) REVERT: A 2180 MET cc_start: 0.7753 (tpt) cc_final: 0.7459 (tpt) REVERT: A 2324 LEU cc_start: 0.7218 (mt) cc_final: 0.6803 (mm) REVERT: B 138 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8837 (pp) REVERT: B 141 PHE cc_start: 0.4582 (p90) cc_final: 0.3979 (p90) REVERT: C 57 TRP cc_start: 0.8231 (OUTLIER) cc_final: 0.7581 (t60) REVERT: C 108 ARG cc_start: 0.3666 (OUTLIER) cc_final: 0.3455 (ptt180) REVERT: C 164 CYS cc_start: 0.4286 (OUTLIER) cc_final: 0.3714 (p) outliers start: 91 outliers final: 69 residues processed: 217 average time/residue: 0.1005 time to fit residues: 33.2281 Evaluate side-chains 223 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 142 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 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 309 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 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 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 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 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 164 CYS 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: 0.0040 chunk 26 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 70 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 overall best weight: 0.7472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1919 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 = 0.4993 r_free = 0.4993 target = 0.197221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.151971 restraints weight = 24000.995| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 4.06 r_work: 0.4216 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.2358 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= 0.142 Angle : 0.730 11.845 18874 Z= 0.357 Chirality : 0.047 0.249 2071 Planarity : 0.005 0.081 2379 Dihedral : 8.280 100.766 2069 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.50 % Favored : 90.20 % Rotamer: Outliers : 5.80 % Allowed : 26.74 % 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 aren not related in a simple way. whole: -2.40 (0.20), residues: 1653 helix: -1.84 (0.48), residues: 90 sheet: -1.10 (0.22), residues: 491 loop : -1.89 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 23 TYR 0.046 0.002 TYR A 159 PHE 0.022 0.001 PHE A1785 TRP 0.015 0.002 TRP A 209 HIS 0.009 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00328 (13869) covalent geometry : angle 0.71430 (18816) SS BOND : bond 0.00437 ( 11) SS BOND : angle 1.12559 ( 22) hydrogen bonds : bond 0.03091 ( 315) hydrogen bonds : angle 6.82107 ( 822) link_ALPHA1-3 : bond 0.01127 ( 3) link_ALPHA1-3 : angle 2.29578 ( 9) link_BETA1-4 : bond 0.00758 ( 6) link_BETA1-4 : angle 2.78200 ( 18) link_NAG-ASN : bond 0.00602 ( 3) link_NAG-ASN : angle 5.20526 ( 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 231 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 146 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5086 (OUTLIER) cc_final: 0.2565 (m-80) REVERT: A 209 TRP cc_start: 0.6487 (t-100) cc_final: 0.6283 (t-100) REVERT: A 261 MET cc_start: 0.8235 (tmm) cc_final: 0.7988 (tmm) REVERT: A 275 HIS cc_start: 0.3701 (OUTLIER) cc_final: 0.2896 (t-170) REVERT: A 279 VAL cc_start: 0.2661 (OUTLIER) cc_final: 0.2369 (t) REVERT: A 287 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3886 (mt) REVERT: A 292 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.5859 (mp) REVERT: A 302 MET cc_start: 0.4706 (tpt) cc_final: 0.4107 (mmt) REVERT: A 407 TYR cc_start: 0.6166 (OUTLIER) cc_final: 0.5430 (t80) REVERT: A 539 MET cc_start: 0.4788 (OUTLIER) cc_final: 0.3495 (tmm) REVERT: A 665 GLU cc_start: 0.8176 (mp0) cc_final: 0.7807 (mp0) REVERT: A 666 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6977 (t0) REVERT: A 1706 LEU cc_start: 0.5833 (tp) cc_final: 0.5588 (tp) REVERT: A 1794 ASP cc_start: 0.5908 (t0) cc_final: 0.5191 (p0) REVERT: A 2010 MET cc_start: 0.8099 (tpp) cc_final: 0.7556 (mpp) REVERT: A 2167 MET cc_start: 0.6178 (mmt) cc_final: 0.5835 (mmt) REVERT: A 2180 MET cc_start: 0.7755 (tpt) cc_final: 0.7462 (tpt) REVERT: A 2324 LEU cc_start: 0.7248 (mt) cc_final: 0.6812 (mm) REVERT: B 138 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8813 (pp) REVERT: B 141 PHE cc_start: 0.4710 (p90) cc_final: 0.4102 (p90) REVERT: C 57 TRP cc_start: 0.8217 (OUTLIER) cc_final: 0.7558 (t60) REVERT: C 164 CYS cc_start: 0.4145 (OUTLIER) cc_final: 0.3499 (p) outliers start: 85 outliers final: 68 residues processed: 212 average time/residue: 0.1072 time to fit residues: 34.8597 Evaluate side-chains 219 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 140 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 122 ARG 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 270 ILE 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 309 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 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 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 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 2086 THR 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 2250 SER 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 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 199 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 57 TRP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 164 CYS 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: 0.6980 chunk 122 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2005 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4995 r_free = 0.4995 target = 0.197093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.152928 restraints weight = 23557.529| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 4.00 r_work: 0.4219 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.2457 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= 0.161 Angle : 0.751 12.232 18874 Z= 0.369 Chirality : 0.048 0.243 2071 Planarity : 0.005 0.084 2379 Dihedral : 8.122 98.016 2069 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.22 % Favored : 89.47 % Rotamer: Outliers : 5.80 % Allowed : 26.88 % 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 aren not related in a simple way. whole: -2.45 (0.20), residues: 1653 helix: -1.96 (0.46), residues: 96 sheet: -1.08 (0.23), residues: 492 loop : -1.94 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 108 TYR 0.026 0.002 TYR A 638 PHE 0.069 0.002 PHE A2234 TRP 0.015 0.002 TRP A 209 HIS 0.009 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00375 (13869) covalent geometry : angle 0.73535 (18816) SS BOND : bond 0.00395 ( 11) SS BOND : angle 1.07697 ( 22) hydrogen bonds : bond 0.03185 ( 315) hydrogen bonds : angle 6.89165 ( 822) link_ALPHA1-3 : bond 0.01160 ( 3) link_ALPHA1-3 : angle 2.33627 ( 9) link_BETA1-4 : bond 0.00744 ( 6) link_BETA1-4 : angle 2.82286 ( 18) link_NAG-ASN : bond 0.00618 ( 3) link_NAG-ASN : angle 5.15398 ( 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 224 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 139 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.2795 (m-80) REVERT: A 124 LYS cc_start: 0.6570 (tptp) cc_final: 0.6246 (tppt) REVERT: A 209 TRP cc_start: 0.6512 (t-100) cc_final: 0.6302 (t-100) REVERT: A 261 MET cc_start: 0.8228 (tmm) cc_final: 0.7955 (tmm) REVERT: A 275 HIS cc_start: 0.3715 (OUTLIER) cc_final: 0.2945 (t-170) REVERT: A 279 VAL cc_start: 0.2636 (OUTLIER) cc_final: 0.2351 (t) REVERT: A 287 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3918 (mt) REVERT: A 292 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.5800 (mp) REVERT: A 302 MET cc_start: 0.4632 (tpt) cc_final: 0.4319 (tpt) REVERT: A 407 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5539 (t80) REVERT: A 539 MET cc_start: 0.4875 (OUTLIER) cc_final: 0.3619 (tmm) REVERT: A 665 GLU cc_start: 0.8179 (mp0) cc_final: 0.7787 (mp0) REVERT: A 666 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6997 (t0) REVERT: A 1706 LEU cc_start: 0.5917 (tp) cc_final: 0.5684 (tp) REVERT: A 1772 MET cc_start: 0.6534 (tmm) cc_final: 0.6125 (ttp) REVERT: A 1794 ASP cc_start: 0.5892 (t0) cc_final: 0.5173 (p0) REVERT: A 1934 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6491 (ptp) REVERT: A 1952 ASN cc_start: 0.8013 (t0) cc_final: 0.7622 (t0) REVERT: A 2033 ARG cc_start: 0.7086 (ptt90) cc_final: 0.6574 (ptp-110) REVERT: A 2167 MET cc_start: 0.6179 (mmt) cc_final: 0.5804 (mmt) REVERT: A 2180 MET cc_start: 0.7698 (tpt) cc_final: 0.7417 (tpt) REVERT: A 2324 LEU cc_start: 0.7139 (mt) cc_final: 0.6690 (mm) REVERT: B 138 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 141 PHE cc_start: 0.4637 (p90) cc_final: 0.4212 (p90) REVERT: C 57 TRP cc_start: 0.8247 (OUTLIER) cc_final: 0.7599 (t60) REVERT: C 164 CYS cc_start: 0.4055 (OUTLIER) cc_final: 0.3508 (p) outliers start: 85 outliers final: 69 residues processed: 205 average time/residue: 0.0974 time to fit residues: 30.1898 Evaluate side-chains 219 residues out of total 1467 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 138 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 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 270 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 309 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 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 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 1934 MET Chi-restraints excluded: chain A residue 1940 ILE 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 2086 THR 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 2250 SER 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 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 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 164 CYS 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: 1.9990 chunk 38 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 0.0370 chunk 94 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1919 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1952 ASN ** 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 = 0.5010 r_free = 0.5010 target = 0.198763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.156637 restraints weight = 23929.991| |-----------------------------------------------------------------------------| r_work (start): 0.4480 rms_B_bonded: 3.84 r_work: 0.4278 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13892 Z= 0.131 Angle : 0.723 14.042 18874 Z= 0.354 Chirality : 0.047 0.246 2071 Planarity : 0.005 0.083 2379 Dihedral : 7.680 94.083 2069 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.20 % Favored : 90.50 % Rotamer: Outliers : 5.18 % Allowed : 27.42 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.20), residues: 1653 helix: -1.83 (0.48), residues: 89 sheet: -1.03 (0.23), residues: 489 loop : -1.86 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1941 TYR 0.023 0.001 TYR A 638 PHE 0.058 0.001 PHE A2234 TRP 0.015 0.002 TRP A2229 HIS 0.007 0.001 HIS A2005 Details of bonding type rmsd covalent geometry : bond 0.00298 (13869) covalent geometry : angle 0.70847 (18816) SS BOND : bond 0.00385 ( 11) SS BOND : angle 0.97983 ( 22) hydrogen bonds : bond 0.02985 ( 315) hydrogen bonds : angle 6.69528 ( 822) link_ALPHA1-3 : bond 0.01213 ( 3) link_ALPHA1-3 : angle 2.10991 ( 9) link_BETA1-4 : bond 0.00740 ( 6) link_BETA1-4 : angle 2.83336 ( 18) link_NAG-ASN : bond 0.00498 ( 3) link_NAG-ASN : angle 4.86420 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4345.34 seconds wall clock time: 75 minutes 15.91 seconds (4515.91 seconds total)