Starting phenix.real_space_refine on Sat Aug 23 17:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yox_33989/08_2025/7yox_33989.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yox_33989/08_2025/7yox_33989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yox_33989/08_2025/7yox_33989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yox_33989/08_2025/7yox_33989.map" model { file = "/net/cci-nas-00/data/ceres_data/7yox_33989/08_2025/7yox_33989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yox_33989/08_2025/7yox_33989.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 102 5.16 5 C 8745 2.51 5 N 2355 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 13878 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "B" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "C" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Chain: "D" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "E" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2206 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "F" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 15, 'TRANS': 291} Time building chain proxies: 2.60, per 1000 atoms: 0.19 Number of scatterers: 13878 At special positions: 0 Unit cell: (77.738, 138.109, 143.071, 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 102 16.00 O 2676 8.00 N 2355 7.00 C 8745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 172 " distance=2.54 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 172 " distance=2.03 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS F 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 575.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3342 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 17 sheets defined 33.5% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 91 through 106 removed outlier: 3.901A pdb=" N LYS A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 131 through 138 removed outlier: 3.639A pdb=" N THR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.537A pdb=" N GLU A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'B' and resid 2 through 21 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 61 through 84 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 140 through 148 removed outlier: 3.761A pdb=" N GLU C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 179 Processing helix chain 'C' and resid 316 through 320 Processing helix chain 'D' and resid 2 through 31 removed outlier: 3.763A pdb=" N LYS D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASP D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 51 through 61 removed outlier: 3.548A pdb=" N GLY D 55 " --> pdb=" O ASN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 84 Processing helix chain 'D' and resid 116 through 120 Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'E' and resid 3 through 26 removed outlier: 4.544A pdb=" N GLU E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR E 20 " --> pdb=" O TYR E 16 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN E 23 " --> pdb=" O GLU E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 61 through 83 Processing helix chain 'E' and resid 161 through 165 removed outlier: 3.811A pdb=" N THR E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 77 through 82 Processing helix chain 'F' and resid 90 through 108 removed outlier: 4.092A pdb=" N GLU F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASP F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 Processing helix chain 'F' and resid 125 through 131 Processing helix chain 'F' and resid 131 through 138 removed outlier: 3.704A pdb=" N THR F 135 " --> pdb=" O GLY F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 148 Processing helix chain 'F' and resid 148 through 179 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 318 through 320 No H-bonds generated for 'chain 'F' and resid 318 through 320' Processing helix chain 'F' and resid 341 through 346 Processing helix chain 'F' and resid 365 through 369 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 124 removed outlier: 5.686A pdb=" N ILE A 121 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR A 199 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 123 " --> pdb=" O TYR A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 228 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 218 through 228 current: chain 'A' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 248 through 252 current: chain 'A' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 310 through 316 current: chain 'A' and resid 352 through 364 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.784A pdb=" N TYR B 38 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ARG B 99 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 40 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N SER B 101 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 42 " --> pdb=" O SER B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 137 through 140 removed outlier: 3.546A pdb=" N GLN B 200 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 12.901A pdb=" N SER B 219 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE B 261 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 221 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 241 " --> pdb=" O ASN B 266 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 268 " --> pdb=" O THR B 239 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR B 239 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL B 130 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 205 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B 132 " --> pdb=" O LYS B 203 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 142 through 143 Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AA7, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.017A pdb=" N ILE C 121 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR C 199 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL C 123 " --> pdb=" O TYR C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 205 removed outlier: 3.873A pdb=" N ARG C 222 " --> pdb=" O THR C 205 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 218 through 225 current: chain 'C' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 248 through 252 current: chain 'C' and resid 310 through 315 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 310 through 315 current: chain 'C' and resid 356 through 363 Processing sheet with id=AA9, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 43 removed outlier: 5.483A pdb=" N TYR D 38 " --> pdb=" O HIS D 97 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG D 99 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 40 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER D 101 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL D 42 " --> pdb=" O SER D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 123 through 133 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 123 through 133 current: chain 'D' and resid 196 through 205 removed outlier: 3.605A pdb=" N GLN D 200 " --> pdb=" O LEU D 224 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 219 through 225 current: chain 'D' and resid 259 through 264 Processing sheet with id=AB3, first strand: chain 'D' and resid 142 through 147 removed outlier: 3.605A pdb=" N PHE D 154 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS D 147 " --> pdb=" O HIS D 152 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N HIS D 152 " --> pdb=" O CYS D 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 43 Processing sheet with id=AB5, first strand: chain 'E' and resid 137 through 139 removed outlier: 8.542A pdb=" N SER E 219 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LEU E 263 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS E 221 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ALA E 265 " --> pdb=" O LYS E 221 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE E 223 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR E 267 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N GLU E 225 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN E 269 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE E 261 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 247 " --> pdb=" O ILE E 261 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E 263 " --> pdb=" O MET E 245 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET E 245 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA E 265 " --> pdb=" O ILE E 243 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 243 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 130 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLN E 205 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 132 " --> pdb=" O LYS E 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 142 through 146 removed outlier: 4.224A pdb=" N ARG E 143 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE E 156 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 120 through 124 Processing sheet with id=AB8, first strand: chain 'F' and resid 218 through 221 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 218 through 221 current: chain 'F' and resid 248 through 252 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 248 through 252 current: chain 'F' and resid 310 through 316 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 310 through 316 current: chain 'F' and resid 355 through 358 No H-bonds generated for sheet with id=AB8 434 hydrogen bonds defined for protein. 1254 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3992 1.33 - 1.45: 1993 1.45 - 1.57: 8001 1.57 - 1.69: 0 1.69 - 1.81: 147 Bond restraints: 14133 Sorted by residual: bond pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 1.526 1.493 0.033 1.28e-02 6.10e+03 6.61e+00 bond pdb=" CA ARG E 247 " pdb=" C ARG E 247 " ideal model delta sigma weight residual 1.521 1.492 0.029 1.19e-02 7.06e+03 6.10e+00 bond pdb=" C ASN D 266 " pdb=" O ASN D 266 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.79e+00 bond pdb=" C LEU F 145 " pdb=" O LEU F 145 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.33e+00 bond pdb=" C PHE E 13 " pdb=" O PHE E 13 " ideal model delta sigma weight residual 1.237 1.210 0.027 1.17e-02 7.31e+03 5.13e+00 ... (remaining 14128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 17982 2.67 - 5.34: 1013 5.34 - 8.00: 97 8.00 - 10.67: 19 10.67 - 13.34: 2 Bond angle restraints: 19113 Sorted by residual: angle pdb=" N GLN D 162 " pdb=" CA GLN D 162 " pdb=" C GLN D 162 " ideal model delta sigma weight residual 112.26 98.92 13.34 1.32e+00 5.74e-01 1.02e+02 angle pdb=" N CYS D 106 " pdb=" CA CYS D 106 " pdb=" C CYS D 106 " ideal model delta sigma weight residual 108.22 101.45 6.77 9.00e-01 1.23e+00 5.65e+01 angle pdb=" N GLY C 132 " pdb=" CA GLY C 132 " pdb=" C GLY C 132 " ideal model delta sigma weight residual 112.73 120.80 -8.07 1.20e+00 6.94e-01 4.52e+01 angle pdb=" N TYR B 20 " pdb=" CA TYR B 20 " pdb=" C TYR B 20 " ideal model delta sigma weight residual 111.36 118.63 -7.27 1.09e+00 8.42e-01 4.44e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 110.62 117.15 -6.53 1.02e+00 9.61e-01 4.10e+01 ... (remaining 19108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 6568 17.90 - 35.81: 932 35.81 - 53.71: 846 53.71 - 71.61: 334 71.61 - 89.51: 41 Dihedral angle restraints: 8721 sinusoidal: 3573 harmonic: 5148 Sorted by residual: dihedral pdb=" CB CYS F 242 " pdb=" SG CYS F 242 " pdb=" SG CYS F 245 " pdb=" CB CYS F 245 " ideal model delta sinusoidal sigma weight residual 93.00 166.91 -73.91 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" C VAL B 155 " pdb=" N VAL B 155 " pdb=" CA VAL B 155 " pdb=" CB VAL B 155 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" C PHE C 72 " pdb=" N PHE C 72 " pdb=" CA PHE C 72 " pdb=" CB PHE C 72 " ideal model delta harmonic sigma weight residual -122.60 -137.66 15.06 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 8718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1745 0.112 - 0.224: 364 0.224 - 0.335: 54 0.335 - 0.447: 12 0.447 - 0.559: 3 Chirality restraints: 2178 Sorted by residual: chirality pdb=" CA PHE C 72 " pdb=" N PHE C 72 " pdb=" C PHE C 72 " pdb=" CB PHE C 72 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA VAL B 155 " pdb=" N VAL B 155 " pdb=" C VAL B 155 " pdb=" CB VAL B 155 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA GLU F 202 " pdb=" N GLU F 202 " pdb=" C GLU F 202 " pdb=" CB GLU F 202 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 2175 not shown) Planarity restraints: 2466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 38 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO B 39 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 249 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.17e+00 pdb=" N PRO D 250 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 250 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 250 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 168 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO D 169 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 169 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 169 " 0.039 5.00e-02 4.00e+02 ... (remaining 2463 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.61: 21 1.61 - 2.43: 133 2.43 - 3.25: 14380 3.25 - 4.08: 42455 4.08 - 4.90: 68604 Warning: very small nonbonded interaction distances. Nonbonded interactions: 125593 Sorted by model distance: nonbonded pdb=" O ILE E 28 " pdb=" CB SER E 91 " model vdw 0.786 3.440 nonbonded pdb=" C ILE E 28 " pdb=" CB SER E 91 " model vdw 0.870 3.670 nonbonded pdb=" CA SER E 18 " pdb=" CE1 HIS E 21 " model vdw 0.903 3.690 nonbonded pdb=" O ILE E 28 " pdb=" OG SER E 91 " model vdw 0.918 3.040 nonbonded pdb=" O LEU B 78 " pdb=" OE1 GLN B 82 " model vdw 0.982 3.040 ... (remaining 125588 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.910 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.008 0.512 14138 Z= 0.537 Angle : 1.314 13.945 19121 Z= 0.896 Chirality : 0.095 0.559 2178 Planarity : 0.007 0.074 2466 Dihedral : 27.063 89.513 5367 Min Nonbonded Distance : 0.786 Molprobity Statistics. All-atom Clashscore : 33.58 Ramachandran Plot: Outliers : 0.17 % Allowed : 1.04 % Favored : 98.79 % Rotamer: Outliers : 46.70 % Allowed : 16.89 % Favored : 36.41 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.19), residues: 1737 helix: 3.80 (0.20), residues: 518 sheet: 1.37 (0.25), residues: 426 loop : 0.97 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 146 TYR 0.024 0.002 TYR C 86 PHE 0.031 0.003 PHE C 72 TRP 0.011 0.003 TRP F 288 HIS 0.005 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00626 (14133) covalent geometry : angle 1.30805 (19113) SS BOND : bond 0.25621 ( 4) SS BOND : angle 6.26556 ( 8) hydrogen bonds : bond 0.17087 ( 434) hydrogen bonds : angle 6.57178 ( 1254) Misc. bond : bond 0.16164 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 744 poor density : 463 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8392 (pt) REVERT: A 96 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8473 (mp) REVERT: A 97 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.9117 (tp-100) REVERT: A 112 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.7825 (tttm) REVERT: A 130 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8026 (mt-10) REVERT: A 153 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8453 (tt) REVERT: A 198 VAL cc_start: 0.6681 (OUTLIER) cc_final: 0.5909 (p) REVERT: A 218 TYR cc_start: 0.7766 (t80) cc_final: 0.7256 (t80) REVERT: A 253 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7372 (mp) REVERT: A 288 TRP cc_start: 0.8075 (t60) cc_final: 0.7193 (t60) REVERT: A 300 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.6011 (p0) REVERT: A 314 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: A 332 THR cc_start: 0.6681 (p) cc_final: 0.6045 (p) REVERT: B 21 HIS cc_start: 0.7866 (m90) cc_final: 0.7198 (m90) REVERT: B 78 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8662 (tp) REVERT: B 84 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7761 (tp) REVERT: B 92 MET cc_start: 0.7550 (pmm) cc_final: 0.6835 (tmm) REVERT: B 119 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: B 149 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (tptp) REVERT: B 189 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.4298 (pp) REVERT: B 222 VAL cc_start: 0.8842 (t) cc_final: 0.8136 (t) REVERT: B 239 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8398 (p) REVERT: C 69 LEU cc_start: 0.7215 (OUTLIER) cc_final: 0.6261 (mt) REVERT: C 78 TRP cc_start: 0.7268 (p-90) cc_final: 0.7035 (p-90) REVERT: C 112 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.6835 (mttm) REVERT: C 122 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7939 (pp) REVERT: C 152 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 163 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8274 (t) REVERT: C 187 THR cc_start: 0.4795 (OUTLIER) cc_final: 0.4257 (p) REVERT: C 258 TYR cc_start: 0.7116 (t80) cc_final: 0.6759 (t80) REVERT: C 317 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7695 (t70) REVERT: C 353 PHE cc_start: 0.8352 (m-80) cc_final: 0.8124 (m-80) REVERT: C 361 SER cc_start: 0.7776 (OUTLIER) cc_final: 0.7409 (m) REVERT: C 363 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8480 (p) REVERT: D 124 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7910 (pp) REVERT: D 143 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5538 (tpt-90) REVERT: D 145 TYR cc_start: 0.6036 (m-80) cc_final: 0.5543 (m-10) REVERT: D 163 TYR cc_start: 0.7387 (m-10) cc_final: 0.6940 (m-10) REVERT: D 172 CYS cc_start: 0.3736 (OUTLIER) cc_final: 0.1732 (t) REVERT: D 183 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7610 (m-80) REVERT: D 194 THR cc_start: 0.2664 (OUTLIER) cc_final: 0.2154 (t) REVERT: D 254 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8344 (t0) REVERT: E 26 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8290 (pp) REVERT: E 92 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4859 (pmm) REVERT: E 100 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8239 (pp) REVERT: E 120 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8525 (p) REVERT: E 206 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6984 (pt0) REVERT: E 261 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7880 (mt) REVERT: F 63 GLN cc_start: 0.0850 (OUTLIER) cc_final: -0.2437 (tp-100) REVERT: F 65 MET cc_start: 0.1756 (OUTLIER) cc_final: 0.1381 (pmm) REVERT: F 66 GLN cc_start: 0.0813 (OUTLIER) cc_final: 0.0343 (pt0) REVERT: F 69 LEU cc_start: 0.4873 (OUTLIER) cc_final: 0.4469 (mm) REVERT: F 78 TRP cc_start: 0.1562 (t-100) cc_final: 0.0666 (t-100) REVERT: F 85 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7844 (p) REVERT: F 93 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8449 (pt) REVERT: F 102 PHE cc_start: 0.8890 (t80) cc_final: 0.8584 (t80) REVERT: F 152 THR cc_start: 0.9080 (p) cc_final: 0.8750 (t) REVERT: F 167 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7053 (t0) REVERT: F 270 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6894 (ptp90) REVERT: F 282 LEU cc_start: 0.9057 (mp) cc_final: 0.8706 (tp) REVERT: F 289 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6885 (tm-30) REVERT: F 290 SER cc_start: 0.9013 (OUTLIER) cc_final: 0.8032 (t) outliers start: 744 outliers final: 178 residues processed: 980 average time/residue: 0.1187 time to fit residues: 161.3482 Evaluate side-chains 511 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 286 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 101 LYS Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 155 CYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 263 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 171 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 197 ARG Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 252 GLN Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 HIS Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 91 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 206 GLU Chi-restraints excluded: chain E residue 229 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain F residue 63 GLN Chi-restraints excluded: chain F residue 65 MET Chi-restraints excluded: chain F residue 66 GLN Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 167 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 LYS Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 270 ARG Chi-restraints excluded: chain F residue 272 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 290 SER Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 307 ILE Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 352 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.0020 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 HIS A 339 ASN A 360 ASN B 11 GLN B 43 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 272 ASN C 106 HIS C 136 ASN C 176 GLN C 195 HIS D 2 ASN D 59 ASN D 82 GLN D 209 GLN D 266 ASN D 269 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS E 207 GLN E 269 GLN E 272 ASN E 274 GLN F 176 GLN F 289 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.103557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.079722 restraints weight = 55985.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082612 restraints weight = 32961.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.084490 restraints weight = 24156.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.085698 restraints weight = 19930.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.086386 restraints weight = 17657.251| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14138 Z= 0.182 Angle : 0.803 11.437 19121 Z= 0.416 Chirality : 0.050 0.324 2178 Planarity : 0.006 0.091 2466 Dihedral : 15.934 89.623 2367 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 14.44 % Allowed : 29.88 % Favored : 55.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.19), residues: 1737 helix: 1.47 (0.21), residues: 522 sheet: 0.76 (0.25), residues: 414 loop : 0.78 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 111 TYR 0.025 0.002 TYR F 201 PHE 0.039 0.003 PHE D 69 TRP 0.019 0.002 TRP D 248 HIS 0.013 0.002 HIS F 195 Details of bonding type rmsd covalent geometry : bond 0.00397 (14133) covalent geometry : angle 0.80259 (19113) SS BOND : bond 0.00422 ( 4) SS BOND : angle 1.43682 ( 8) hydrogen bonds : bond 0.05875 ( 434) hydrogen bonds : angle 5.80969 ( 1254) Misc. bond : bond 0.00275 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 284 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7617 (mtpp) REVERT: A 198 VAL cc_start: 0.6472 (OUTLIER) cc_final: 0.5849 (p) REVERT: A 300 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.5998 (p0) REVERT: A 332 THR cc_start: 0.6371 (p) cc_final: 0.6052 (p) REVERT: B 21 HIS cc_start: 0.7954 (m90) cc_final: 0.7206 (m90) REVERT: B 28 ILE cc_start: 0.8704 (mm) cc_final: 0.8230 (mm) REVERT: B 31 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6574 (mm-30) REVERT: B 38 TYR cc_start: 0.7527 (m-80) cc_final: 0.7073 (m-80) REVERT: B 48 PHE cc_start: 0.8394 (m-80) cc_final: 0.7751 (m-80) REVERT: B 52 MET cc_start: 0.7437 (pmm) cc_final: 0.6420 (mmp) REVERT: B 69 PHE cc_start: 0.8832 (m-10) cc_final: 0.8437 (m-80) REVERT: B 84 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7946 (tp) REVERT: B 92 MET cc_start: 0.7462 (pmm) cc_final: 0.6923 (tmm) REVERT: B 99 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7428 (mpt180) REVERT: B 149 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8557 (tptp) REVERT: B 260 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7721 (mp0) REVERT: C 65 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6510 (ppp) REVERT: C 71 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7701 (tpp-160) REVERT: C 78 TRP cc_start: 0.7531 (p-90) cc_final: 0.7209 (p-90) REVERT: C 125 PHE cc_start: 0.7766 (t80) cc_final: 0.7547 (t80) REVERT: C 164 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9215 (tm) REVERT: C 302 ARG cc_start: 0.3067 (OUTLIER) cc_final: 0.2213 (pmt-80) REVERT: D 146 MET cc_start: 0.7350 (tmm) cc_final: 0.6806 (tmm) REVERT: D 254 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8906 (t0) REVERT: E 60 MET cc_start: 0.8297 (tpp) cc_final: 0.8086 (tpp) REVERT: E 157 LYS cc_start: 0.7593 (mmtm) cc_final: 0.6587 (ttpt) REVERT: E 164 TYR cc_start: 0.6258 (t80) cc_final: 0.5925 (t80) REVERT: E 187 SER cc_start: 0.3999 (OUTLIER) cc_final: 0.3638 (t) REVERT: E 202 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8408 (mt) REVERT: E 225 GLU cc_start: 0.8281 (tp30) cc_final: 0.8070 (mm-30) REVERT: F 85 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8043 (p) REVERT: F 95 LYS cc_start: 0.9329 (mtmp) cc_final: 0.9078 (mttm) REVERT: F 106 HIS cc_start: 0.8295 (m90) cc_final: 0.7945 (m90) REVERT: F 112 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8504 (mtmt) REVERT: F 146 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8654 (mtm-85) REVERT: F 238 MET cc_start: 0.8206 (tpp) cc_final: 0.7940 (tpp) REVERT: F 282 LEU cc_start: 0.9086 (mp) cc_final: 0.8612 (tp) REVERT: F 289 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7045 (tm-30) REVERT: F 291 ILE cc_start: 0.8931 (pt) cc_final: 0.8661 (pt) REVERT: F 314 GLU cc_start: 0.8350 (mp0) cc_final: 0.7794 (mp0) REVERT: F 321 ASP cc_start: 0.7909 (t70) cc_final: 0.7666 (t0) outliers start: 230 outliers final: 117 residues processed: 466 average time/residue: 0.1007 time to fit residues: 69.0476 Evaluate side-chains 362 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 227 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 30 LYS Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 149 LYS Chi-restraints excluded: chain D residue 151 LYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 22 LYS Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 161 GLU Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 187 SER Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 112 LYS Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 242 CYS Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 131 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 2 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN C 106 HIS C 200 ASN D 266 ASN D 269 GLN ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 252 GLN E 253 GLN E 266 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 200 ASN F 346 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.100586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.077808 restraints weight = 55719.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079814 restraints weight = 32649.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.080607 restraints weight = 24189.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.080855 restraints weight = 23515.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.080983 restraints weight = 20681.612| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14138 Z= 0.180 Angle : 0.735 13.005 19121 Z= 0.381 Chirality : 0.048 0.273 2178 Planarity : 0.005 0.060 2466 Dihedral : 12.173 84.491 2090 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 10.55 % Allowed : 31.07 % Favored : 58.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.19), residues: 1737 helix: 1.22 (0.22), residues: 515 sheet: 0.59 (0.26), residues: 395 loop : 0.63 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 306 TYR 0.020 0.002 TYR B 16 PHE 0.039 0.003 PHE D 69 TRP 0.015 0.002 TRP A 288 HIS 0.011 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00400 (14133) covalent geometry : angle 0.73468 (19113) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.87837 ( 8) hydrogen bonds : bond 0.05086 ( 434) hydrogen bonds : angle 5.65558 ( 1254) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 251 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7650 (ttpt) REVERT: A 195 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7214 (p90) REVERT: A 198 VAL cc_start: 0.6531 (OUTLIER) cc_final: 0.5849 (p) REVERT: A 218 TYR cc_start: 0.7810 (t80) cc_final: 0.7119 (t80) REVERT: A 332 THR cc_start: 0.6442 (p) cc_final: 0.5906 (p) REVERT: B 21 HIS cc_start: 0.7898 (m90) cc_final: 0.7048 (m90) REVERT: B 48 PHE cc_start: 0.8342 (m-80) cc_final: 0.7562 (m-80) REVERT: B 52 MET cc_start: 0.7516 (pmm) cc_final: 0.6389 (mmm) REVERT: B 69 PHE cc_start: 0.8932 (m-10) cc_final: 0.8469 (m-80) REVERT: B 84 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8091 (tp) REVERT: B 92 MET cc_start: 0.7358 (pmm) cc_final: 0.6864 (tmm) REVERT: B 161 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7994 (mm-30) REVERT: C 65 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6826 (ppp) REVERT: C 71 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7779 (tpp-160) REVERT: C 164 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9167 (tm) REVERT: C 314 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7357 (mm-30) REVERT: D 45 MET cc_start: 0.8821 (ppp) cc_final: 0.8354 (ppp) REVERT: D 97 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7755 (m170) REVERT: D 146 MET cc_start: 0.8155 (tmm) cc_final: 0.7676 (tmm) REVERT: D 205 GLN cc_start: 0.8207 (pp30) cc_final: 0.7860 (pp30) REVERT: D 237 ASP cc_start: 0.8040 (m-30) cc_final: 0.7781 (m-30) REVERT: D 254 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8832 (t0) REVERT: E 157 LYS cc_start: 0.7640 (mmtm) cc_final: 0.6888 (ttpt) REVERT: E 164 TYR cc_start: 0.6376 (t80) cc_final: 0.5840 (t80) REVERT: F 85 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8048 (p) REVERT: F 102 PHE cc_start: 0.9207 (t80) cc_final: 0.8959 (t80) REVERT: F 106 HIS cc_start: 0.8215 (m90) cc_final: 0.7887 (m90) REVERT: F 146 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8536 (mtm-85) REVERT: F 161 HIS cc_start: 0.8715 (t70) cc_final: 0.8480 (t70) REVERT: F 238 MET cc_start: 0.8001 (tpp) cc_final: 0.7750 (tpp) outliers start: 168 outliers final: 107 residues processed: 386 average time/residue: 0.0981 time to fit residues: 56.2811 Evaluate side-chains 335 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 217 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 187 THR Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 43 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 171 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN C 161 HIS ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN F 289 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.101100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.076715 restraints weight = 56743.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079443 restraints weight = 33497.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.081080 restraints weight = 24626.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082269 restraints weight = 20586.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082895 restraints weight = 18319.034| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14138 Z= 0.140 Angle : 0.706 13.241 19121 Z= 0.358 Chirality : 0.047 0.270 2178 Planarity : 0.004 0.055 2466 Dihedral : 10.230 84.127 2019 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 9.04 % Allowed : 31.58 % Favored : 59.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.19), residues: 1737 helix: 0.97 (0.22), residues: 519 sheet: 0.32 (0.25), residues: 386 loop : 0.57 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 105 TYR 0.031 0.002 TYR F 356 PHE 0.051 0.002 PHE D 69 TRP 0.008 0.001 TRP A 288 HIS 0.013 0.001 HIS A 193 Details of bonding type rmsd covalent geometry : bond 0.00310 (14133) covalent geometry : angle 0.70298 (19113) SS BOND : bond 0.00442 ( 4) SS BOND : angle 3.26176 ( 8) hydrogen bonds : bond 0.04568 ( 434) hydrogen bonds : angle 5.49892 ( 1254) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 238 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7566 (ttpt) REVERT: A 195 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7857 (p90) REVERT: A 198 VAL cc_start: 0.6395 (OUTLIER) cc_final: 0.5685 (p) REVERT: A 218 TYR cc_start: 0.7811 (t80) cc_final: 0.7067 (t80) REVERT: A 219 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (pt) REVERT: A 286 MET cc_start: 0.8610 (tpp) cc_final: 0.8396 (tpp) REVERT: A 297 MET cc_start: 0.6551 (mmm) cc_final: 0.6344 (mmm) REVERT: A 300 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.6183 (p0) REVERT: A 332 THR cc_start: 0.6099 (p) cc_final: 0.5690 (p) REVERT: B 20 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7724 (m-10) REVERT: B 21 HIS cc_start: 0.8007 (m90) cc_final: 0.7200 (m90) REVERT: B 48 PHE cc_start: 0.8265 (m-80) cc_final: 0.7733 (m-10) REVERT: B 52 MET cc_start: 0.7426 (pmm) cc_final: 0.6453 (mmm) REVERT: B 69 PHE cc_start: 0.8918 (m-10) cc_final: 0.8535 (m-80) REVERT: B 92 MET cc_start: 0.7376 (pmm) cc_final: 0.6925 (ppp) REVERT: B 149 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8510 (tptp) REVERT: C 65 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6871 (ppp) REVERT: C 71 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7742 (tpp-160) REVERT: C 107 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8739 (mt) REVERT: C 164 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9179 (tm) REVERT: C 238 MET cc_start: 0.8100 (tpp) cc_final: 0.7590 (tpp) REVERT: C 287 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8272 (p0) REVERT: C 302 ARG cc_start: 0.3467 (OUTLIER) cc_final: 0.2527 (pmt-80) REVERT: C 354 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8015 (mm) REVERT: D 45 MET cc_start: 0.8814 (ppp) cc_final: 0.8491 (ppp) REVERT: D 205 GLN cc_start: 0.8267 (pp30) cc_final: 0.7868 (pp30) REVERT: D 237 ASP cc_start: 0.8013 (m-30) cc_final: 0.7684 (m-30) REVERT: E 157 LYS cc_start: 0.7418 (mmtm) cc_final: 0.6728 (ttpt) REVERT: E 164 TYR cc_start: 0.6038 (t80) cc_final: 0.4955 (t80) REVERT: E 198 ASP cc_start: 0.8356 (p0) cc_final: 0.7826 (p0) REVERT: F 102 PHE cc_start: 0.9203 (t80) cc_final: 0.8964 (t80) REVERT: F 106 HIS cc_start: 0.8230 (m90) cc_final: 0.7967 (m90) REVERT: F 146 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8556 (mtm-85) REVERT: F 161 HIS cc_start: 0.8754 (t70) cc_final: 0.8414 (t70) REVERT: F 238 MET cc_start: 0.7967 (tpp) cc_final: 0.7747 (tpp) REVERT: F 352 MET cc_start: 0.7035 (pmm) cc_final: 0.6397 (pmm) outliers start: 144 outliers final: 103 residues processed: 347 average time/residue: 0.0881 time to fit residues: 47.2771 Evaluate side-chains 327 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 209 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 80 optimal weight: 0.0000 chunk 150 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 GLN B 272 ASN C 317 HIS ** D 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 289 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.096014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.072820 restraints weight = 58842.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.074393 restraints weight = 38136.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.074646 restraints weight = 30535.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.074832 restraints weight = 28373.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.075017 restraints weight = 26488.874| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14138 Z= 0.241 Angle : 0.745 12.664 19121 Z= 0.389 Chirality : 0.048 0.261 2178 Planarity : 0.005 0.046 2466 Dihedral : 9.925 87.754 2002 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 28.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 9.54 % Allowed : 33.02 % Favored : 57.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.20), residues: 1737 helix: 0.64 (0.22), residues: 519 sheet: -0.13 (0.26), residues: 384 loop : 0.34 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 197 TYR 0.033 0.003 TYR E 267 PHE 0.051 0.003 PHE D 69 TRP 0.014 0.003 TRP E 248 HIS 0.007 0.002 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00518 (14133) covalent geometry : angle 0.74342 (19113) SS BOND : bond 0.00453 ( 4) SS BOND : angle 2.48772 ( 8) hydrogen bonds : bond 0.04840 ( 434) hydrogen bonds : angle 5.72958 ( 1254) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 209 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7636 (ttpt) REVERT: A 195 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7665 (p90) REVERT: B 11 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8671 (pp30) REVERT: B 20 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: B 21 HIS cc_start: 0.7956 (m90) cc_final: 0.7169 (m90) REVERT: B 32 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6576 (ptp90) REVERT: B 38 TYR cc_start: 0.7751 (m-80) cc_final: 0.7468 (m-80) REVERT: B 48 PHE cc_start: 0.8340 (m-80) cc_final: 0.7580 (m-80) REVERT: B 52 MET cc_start: 0.7653 (pmm) cc_final: 0.6473 (mmt) REVERT: B 69 PHE cc_start: 0.9095 (m-10) cc_final: 0.8828 (m-80) REVERT: B 92 MET cc_start: 0.7334 (pmm) cc_final: 0.6872 (ppp) REVERT: B 139 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 149 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8497 (tptp) REVERT: B 161 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 164 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 246 GLN cc_start: 0.8291 (mm110) cc_final: 0.7691 (mm110) REVERT: C 65 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6966 (ppp) REVERT: C 102 PHE cc_start: 0.8951 (t80) cc_final: 0.8732 (t80) REVERT: C 107 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8883 (mt) REVERT: C 156 MET cc_start: 0.8602 (mmm) cc_final: 0.8392 (mmm) REVERT: C 164 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9191 (tm) REVERT: C 247 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7327 (mm-30) REVERT: C 287 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.7780 (p0) REVERT: C 288 TRP cc_start: 0.8382 (OUTLIER) cc_final: 0.7301 (t60) REVERT: C 297 MET cc_start: 0.6242 (mmt) cc_final: 0.5295 (mmt) REVERT: C 302 ARG cc_start: 0.4111 (OUTLIER) cc_final: 0.0896 (pmt-80) REVERT: C 313 CYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7575 (m) REVERT: C 320 VAL cc_start: 0.8945 (p) cc_final: 0.8610 (p) REVERT: D 45 MET cc_start: 0.8942 (ppp) cc_final: 0.8479 (ppp) REVERT: D 164 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.8287 (m-10) REVERT: D 237 ASP cc_start: 0.8373 (m-30) cc_final: 0.8021 (m-30) REVERT: E 157 LYS cc_start: 0.7873 (mmtm) cc_final: 0.7201 (ttmt) REVERT: E 164 TYR cc_start: 0.7049 (t80) cc_final: 0.6064 (t80) REVERT: E 198 ASP cc_start: 0.8621 (p0) cc_final: 0.8206 (p0) REVERT: F 106 HIS cc_start: 0.8436 (m90) cc_final: 0.6944 (m90) REVERT: F 110 TYR cc_start: 0.8254 (m-80) cc_final: 0.7730 (m-80) REVERT: F 161 HIS cc_start: 0.8904 (t70) cc_final: 0.8684 (t-90) outliers start: 152 outliers final: 112 residues processed: 335 average time/residue: 0.0921 time to fit residues: 47.5539 Evaluate side-chains 326 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 197 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 313 CYS Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 154 PHE Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 199 TYR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 GLN Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 146 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 45 optimal weight: 30.0000 chunk 164 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 HIS ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.096479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.072286 restraints weight = 57665.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.074665 restraints weight = 35841.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.076149 restraints weight = 27162.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.077002 restraints weight = 23084.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.077618 restraints weight = 20999.387| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14138 Z= 0.184 Angle : 0.702 14.050 19121 Z= 0.360 Chirality : 0.047 0.257 2178 Planarity : 0.005 0.059 2466 Dihedral : 9.488 90.628 1993 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 9.04 % Allowed : 33.71 % Favored : 57.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.20), residues: 1737 helix: 0.62 (0.22), residues: 520 sheet: -0.22 (0.26), residues: 394 loop : 0.29 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 197 TYR 0.021 0.002 TYR E 267 PHE 0.044 0.003 PHE D 69 TRP 0.017 0.002 TRP D 248 HIS 0.007 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00403 (14133) covalent geometry : angle 0.70044 (19113) SS BOND : bond 0.00400 ( 4) SS BOND : angle 2.11414 ( 8) hydrogen bonds : bond 0.04557 ( 434) hydrogen bonds : angle 5.62721 ( 1254) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 212 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7604 (ttpt) REVERT: A 195 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7699 (p90) REVERT: B 11 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8628 (pp30) REVERT: B 20 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: B 21 HIS cc_start: 0.7871 (m90) cc_final: 0.7190 (m90) REVERT: B 32 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7131 (ptp90) REVERT: B 38 TYR cc_start: 0.7701 (m-80) cc_final: 0.7449 (m-80) REVERT: B 48 PHE cc_start: 0.8133 (m-80) cc_final: 0.7330 (m-10) REVERT: B 51 ASN cc_start: 0.7512 (t0) cc_final: 0.7202 (t0) REVERT: B 52 MET cc_start: 0.7581 (pmm) cc_final: 0.6626 (mmt) REVERT: B 69 PHE cc_start: 0.9046 (m-10) cc_final: 0.8720 (m-80) REVERT: B 92 MET cc_start: 0.7461 (pmm) cc_final: 0.7032 (ppp) REVERT: B 149 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8429 (tptp) REVERT: B 161 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7884 (mm-30) REVERT: B 164 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 246 GLN cc_start: 0.8302 (mm110) cc_final: 0.7848 (mm110) REVERT: C 65 MET cc_start: 0.7475 (mtm) cc_final: 0.7011 (ppp) REVERT: C 102 PHE cc_start: 0.8885 (t80) cc_final: 0.8521 (t80) REVERT: C 107 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8812 (mt) REVERT: C 156 MET cc_start: 0.8735 (mmm) cc_final: 0.8530 (mmm) REVERT: C 164 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9212 (tm) REVERT: C 238 MET cc_start: 0.8283 (tpp) cc_final: 0.7809 (tpp) REVERT: C 287 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8140 (p0) REVERT: C 293 ILE cc_start: 0.8920 (mt) cc_final: 0.8650 (mp) REVERT: C 302 ARG cc_start: 0.3895 (OUTLIER) cc_final: 0.0407 (pmt-80) REVERT: C 314 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: C 320 VAL cc_start: 0.8726 (p) cc_final: 0.8357 (p) REVERT: D 45 MET cc_start: 0.8824 (ppp) cc_final: 0.8399 (ppp) REVERT: D 64 GLU cc_start: 0.8443 (pt0) cc_final: 0.8169 (pm20) REVERT: D 222 VAL cc_start: 0.9232 (OUTLIER) cc_final: 0.8987 (m) REVERT: E 157 LYS cc_start: 0.7722 (mmtm) cc_final: 0.7081 (ttmt) REVERT: E 164 TYR cc_start: 0.6830 (t80) cc_final: 0.5911 (t80) REVERT: E 198 ASP cc_start: 0.8606 (p0) cc_final: 0.8320 (p0) REVERT: F 110 TYR cc_start: 0.8259 (m-80) cc_final: 0.8052 (m-80) outliers start: 144 outliers final: 108 residues processed: 329 average time/residue: 0.0873 time to fit residues: 44.0119 Evaluate side-chains 314 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 193 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 82 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 153 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 230 ASN Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 161 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 69 optimal weight: 40.0000 chunk 75 optimal weight: 8.9990 chunk 114 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 ASN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.097096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073135 restraints weight = 57106.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075390 restraints weight = 35889.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.076877 restraints weight = 27375.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.077809 restraints weight = 23222.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.078314 restraints weight = 21002.935| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14138 Z= 0.156 Angle : 0.693 13.345 19121 Z= 0.351 Chirality : 0.047 0.320 2178 Planarity : 0.004 0.069 2466 Dihedral : 8.702 59.485 1981 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 8.79 % Allowed : 33.90 % Favored : 57.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1737 helix: 0.64 (0.22), residues: 512 sheet: -0.28 (0.26), residues: 407 loop : 0.27 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 197 TYR 0.017 0.002 TYR D 199 PHE 0.040 0.003 PHE E 69 TRP 0.011 0.002 TRP D 248 HIS 0.017 0.001 HIS F 171 Details of bonding type rmsd covalent geometry : bond 0.00350 (14133) covalent geometry : angle 0.69135 (19113) SS BOND : bond 0.00416 ( 4) SS BOND : angle 2.10011 ( 8) hydrogen bonds : bond 0.04377 ( 434) hydrogen bonds : angle 5.53881 ( 1254) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 207 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.7586 (ttpt) REVERT: A 195 HIS cc_start: 0.8102 (OUTLIER) cc_final: 0.7880 (p90) REVERT: A 297 MET cc_start: 0.6582 (mmm) cc_final: 0.6270 (mmm) REVERT: B 16 TYR cc_start: 0.8797 (t80) cc_final: 0.8508 (t80) REVERT: B 20 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: B 21 HIS cc_start: 0.7870 (m90) cc_final: 0.7209 (m90) REVERT: B 32 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7459 (ptp90) REVERT: B 38 TYR cc_start: 0.7757 (m-80) cc_final: 0.7525 (m-80) REVERT: B 48 PHE cc_start: 0.8021 (m-80) cc_final: 0.7175 (m-10) REVERT: B 51 ASN cc_start: 0.7478 (t0) cc_final: 0.7193 (t0) REVERT: B 52 MET cc_start: 0.7506 (pmm) cc_final: 0.6699 (mmt) REVERT: B 69 PHE cc_start: 0.9067 (m-10) cc_final: 0.8796 (m-80) REVERT: B 92 MET cc_start: 0.7511 (pmm) cc_final: 0.7085 (ppp) REVERT: B 149 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8466 (tptp) REVERT: B 161 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 164 TYR cc_start: 0.8252 (OUTLIER) cc_final: 0.7784 (t80) REVERT: B 246 GLN cc_start: 0.8323 (mm110) cc_final: 0.7930 (mm110) REVERT: C 65 MET cc_start: 0.7406 (mtm) cc_final: 0.7013 (ppp) REVERT: C 107 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8878 (mt) REVERT: C 164 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9194 (tm) REVERT: C 238 MET cc_start: 0.8211 (tpp) cc_final: 0.7775 (tpp) REVERT: C 287 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8452 (p0) REVERT: C 288 TRP cc_start: 0.8360 (OUTLIER) cc_final: 0.7090 (t60) REVERT: C 302 ARG cc_start: 0.3735 (OUTLIER) cc_final: 0.0320 (pmt-80) REVERT: C 320 VAL cc_start: 0.8627 (p) cc_final: 0.8403 (p) REVERT: C 358 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7818 (tm-30) REVERT: D 45 MET cc_start: 0.8737 (ppp) cc_final: 0.8333 (ppp) REVERT: D 222 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.9023 (m) REVERT: D 254 ASP cc_start: 0.8806 (t0) cc_final: 0.8489 (t0) REVERT: E 60 MET cc_start: 0.8522 (tpp) cc_final: 0.8299 (tpp) REVERT: E 157 LYS cc_start: 0.7709 (mmtm) cc_final: 0.7149 (ttmt) REVERT: E 164 TYR cc_start: 0.6740 (t80) cc_final: 0.5831 (t80) REVERT: E 198 ASP cc_start: 0.8591 (p0) cc_final: 0.8303 (p0) REVERT: F 106 HIS cc_start: 0.8477 (m90) cc_final: 0.8020 (m90) outliers start: 140 outliers final: 104 residues processed: 322 average time/residue: 0.0836 time to fit residues: 41.2808 Evaluate side-chains 304 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 188 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 288 TRP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 30 LYS Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 131 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 GLN ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.099470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.075343 restraints weight = 58083.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.077903 restraints weight = 35338.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079485 restraints weight = 26521.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.080542 restraints weight = 22348.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081188 restraints weight = 20092.036| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14138 Z= 0.125 Angle : 0.708 14.639 19121 Z= 0.357 Chirality : 0.047 0.232 2178 Planarity : 0.004 0.070 2466 Dihedral : 7.987 59.148 1967 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 6.91 % Allowed : 36.03 % Favored : 57.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1737 helix: 0.59 (0.22), residues: 513 sheet: -0.27 (0.26), residues: 377 loop : 0.21 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 197 TYR 0.027 0.002 TYR E 199 PHE 0.050 0.003 PHE D 69 TRP 0.013 0.002 TRP A 78 HIS 0.014 0.001 HIS F 171 Details of bonding type rmsd covalent geometry : bond 0.00272 (14133) covalent geometry : angle 0.70728 (19113) SS BOND : bond 0.00436 ( 4) SS BOND : angle 2.04166 ( 8) hydrogen bonds : bond 0.04228 ( 434) hydrogen bonds : angle 5.45334 ( 1254) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 216 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.7688 (ttpt) REVERT: A 195 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7761 (p90) REVERT: A 297 MET cc_start: 0.6135 (mmm) cc_final: 0.5738 (mmm) REVERT: A 306 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6853 (tpp80) REVERT: B 16 TYR cc_start: 0.8716 (t80) cc_final: 0.8286 (t80) REVERT: B 21 HIS cc_start: 0.7885 (m90) cc_final: 0.7192 (m90) REVERT: B 32 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7429 (ptp90) REVERT: B 48 PHE cc_start: 0.7926 (m-80) cc_final: 0.6929 (m-10) REVERT: B 51 ASN cc_start: 0.7524 (t0) cc_final: 0.7027 (t0) REVERT: B 52 MET cc_start: 0.7449 (pmm) cc_final: 0.6803 (mmt) REVERT: B 69 PHE cc_start: 0.9059 (m-10) cc_final: 0.8822 (m-80) REVERT: B 92 MET cc_start: 0.7471 (pmm) cc_final: 0.7017 (ppp) REVERT: B 146 MET cc_start: 0.8034 (tpt) cc_final: 0.7834 (tpp) REVERT: B 149 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8494 (tptp) REVERT: B 161 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7985 (mm-30) REVERT: B 163 TYR cc_start: 0.8424 (m-80) cc_final: 0.8024 (m-80) REVERT: B 246 GLN cc_start: 0.8285 (mm110) cc_final: 0.7987 (mm-40) REVERT: C 65 MET cc_start: 0.7407 (mtm) cc_final: 0.7066 (ppp) REVERT: C 78 TRP cc_start: 0.7394 (p-90) cc_final: 0.7002 (p-90) REVERT: C 238 MET cc_start: 0.8127 (tpp) cc_final: 0.7714 (tpp) REVERT: C 287 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8231 (p0) REVERT: C 320 VAL cc_start: 0.8452 (p) cc_final: 0.8154 (p) REVERT: C 353 PHE cc_start: 0.8211 (m-80) cc_final: 0.7840 (m-10) REVERT: D 45 MET cc_start: 0.8731 (ppp) cc_final: 0.8441 (ppp) REVERT: D 222 VAL cc_start: 0.9175 (OUTLIER) cc_final: 0.8953 (m) REVERT: D 254 ASP cc_start: 0.8833 (t0) cc_final: 0.8490 (t0) REVERT: E 141 PHE cc_start: 0.7195 (t80) cc_final: 0.6567 (t80) REVERT: E 157 LYS cc_start: 0.7487 (mmtm) cc_final: 0.6906 (ttmt) REVERT: E 164 TYR cc_start: 0.6367 (t80) cc_final: 0.5428 (t80) REVERT: E 198 ASP cc_start: 0.8534 (p0) cc_final: 0.8323 (p0) REVERT: E 225 GLU cc_start: 0.8445 (tp30) cc_final: 0.7651 (tp30) REVERT: F 106 HIS cc_start: 0.8472 (m90) cc_final: 0.8021 (m90) REVERT: F 297 MET cc_start: 0.7015 (mpp) cc_final: 0.6691 (mpp) REVERT: F 314 GLU cc_start: 0.7967 (mp0) cc_final: 0.7693 (mp0) outliers start: 110 outliers final: 84 residues processed: 306 average time/residue: 0.0895 time to fit residues: 42.4149 Evaluate side-chains 292 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 201 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 61 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 287 ASP Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 150 CYS Chi-restraints excluded: chain E residue 184 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 117 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 66 optimal weight: 0.0970 chunk 107 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 67 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.099385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.075164 restraints weight = 57962.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.077723 restraints weight = 34844.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079377 restraints weight = 25830.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.080393 restraints weight = 21584.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081062 restraints weight = 19340.337| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.7517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14138 Z= 0.127 Angle : 0.727 15.097 19121 Z= 0.362 Chirality : 0.047 0.251 2178 Planarity : 0.004 0.085 2466 Dihedral : 7.430 57.735 1955 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 6.03 % Allowed : 36.41 % Favored : 57.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1737 helix: 0.60 (0.22), residues: 513 sheet: -0.24 (0.27), residues: 392 loop : 0.21 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 197 TYR 0.028 0.002 TYR E 267 PHE 0.048 0.002 PHE D 69 TRP 0.008 0.002 TRP F 288 HIS 0.015 0.001 HIS F 171 Details of bonding type rmsd covalent geometry : bond 0.00288 (14133) covalent geometry : angle 0.72644 (19113) SS BOND : bond 0.00392 ( 4) SS BOND : angle 1.92012 ( 8) hydrogen bonds : bond 0.04159 ( 434) hydrogen bonds : angle 5.41329 ( 1254) Misc. bond : bond 0.00018 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 205 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7716 (ttpt) REVERT: A 195 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7655 (p90) REVERT: A 306 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6816 (tpp80) REVERT: A 307 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8553 (mm) REVERT: B 21 HIS cc_start: 0.7872 (m90) cc_final: 0.7214 (m90) REVERT: B 32 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6485 (ptp90) REVERT: B 48 PHE cc_start: 0.7891 (m-80) cc_final: 0.6946 (m-10) REVERT: B 51 ASN cc_start: 0.7626 (t0) cc_final: 0.7311 (t0) REVERT: B 52 MET cc_start: 0.7411 (pmm) cc_final: 0.6757 (mmt) REVERT: B 92 MET cc_start: 0.7398 (pmm) cc_final: 0.6811 (ppp) REVERT: B 149 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8482 (tptp) REVERT: B 161 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7929 (mm-30) REVERT: B 164 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7707 (t80) REVERT: B 246 GLN cc_start: 0.8280 (mm110) cc_final: 0.7980 (mm-40) REVERT: C 65 MET cc_start: 0.7480 (mtm) cc_final: 0.7119 (ppp) REVERT: C 238 MET cc_start: 0.8192 (tpp) cc_final: 0.7686 (tpp) REVERT: C 353 PHE cc_start: 0.8159 (m-80) cc_final: 0.7783 (m-10) REVERT: D 45 MET cc_start: 0.8681 (ppp) cc_final: 0.8396 (ppp) REVERT: D 222 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8904 (m) REVERT: D 254 ASP cc_start: 0.8798 (t0) cc_final: 0.8454 (t0) REVERT: E 141 PHE cc_start: 0.7227 (t80) cc_final: 0.6644 (t80) REVERT: E 157 LYS cc_start: 0.7429 (mmtm) cc_final: 0.6924 (ttmt) REVERT: E 164 TYR cc_start: 0.6366 (t80) cc_final: 0.5430 (t80) REVERT: E 198 ASP cc_start: 0.8540 (p0) cc_final: 0.8330 (p0) REVERT: F 106 HIS cc_start: 0.8463 (m90) cc_final: 0.8024 (m90) REVERT: F 297 MET cc_start: 0.6926 (mpp) cc_final: 0.6560 (mpp) REVERT: F 314 GLU cc_start: 0.8007 (mp0) cc_final: 0.7760 (mp0) outliers start: 96 outliers final: 80 residues processed: 281 average time/residue: 0.0849 time to fit residues: 37.2368 Evaluate side-chains 284 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain D residue 3 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 44 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 28 optimal weight: 30.0000 chunk 159 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.097702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.073068 restraints weight = 58712.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.075466 restraints weight = 36545.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.077029 restraints weight = 27646.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.077983 restraints weight = 23386.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.078477 restraints weight = 21141.003| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14138 Z= 0.165 Angle : 0.757 15.599 19121 Z= 0.378 Chirality : 0.047 0.317 2178 Planarity : 0.005 0.083 2466 Dihedral : 7.476 59.193 1951 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 22.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.84 % Allowed : 36.53 % Favored : 57.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.20), residues: 1737 helix: 0.61 (0.22), residues: 513 sheet: -0.36 (0.26), residues: 403 loop : 0.19 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 197 TYR 0.018 0.002 TYR E 199 PHE 0.045 0.003 PHE D 69 TRP 0.016 0.002 TRP D 248 HIS 0.014 0.002 HIS F 171 Details of bonding type rmsd covalent geometry : bond 0.00372 (14133) covalent geometry : angle 0.75656 (19113) SS BOND : bond 0.00354 ( 4) SS BOND : angle 1.86532 ( 8) hydrogen bonds : bond 0.04324 ( 434) hydrogen bonds : angle 5.55293 ( 1254) Misc. bond : bond 0.00051 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3474 Ramachandran restraints generated. 1737 Oldfield, 0 Emsley, 1737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7760 (ttpt) REVERT: A 195 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7809 (p90) REVERT: A 297 MET cc_start: 0.6395 (mmm) cc_final: 0.6176 (mmm) REVERT: A 306 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.6878 (tpp80) REVERT: B 20 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: B 21 HIS cc_start: 0.7997 (m90) cc_final: 0.7314 (m90) REVERT: B 32 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7459 (ptp90) REVERT: B 48 PHE cc_start: 0.7871 (m-80) cc_final: 0.6915 (m-80) REVERT: B 52 MET cc_start: 0.7500 (pmm) cc_final: 0.6783 (mmt) REVERT: B 161 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 164 TYR cc_start: 0.8249 (OUTLIER) cc_final: 0.7898 (t80) REVERT: B 246 GLN cc_start: 0.8364 (mm110) cc_final: 0.7984 (mm110) REVERT: C 65 MET cc_start: 0.7380 (mtm) cc_final: 0.6959 (ppp) REVERT: C 164 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9193 (tm) REVERT: C 353 PHE cc_start: 0.8202 (m-80) cc_final: 0.7816 (m-10) REVERT: D 45 MET cc_start: 0.8674 (ppp) cc_final: 0.8340 (ppp) REVERT: D 164 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.8105 (m-10) REVERT: D 222 VAL cc_start: 0.9230 (OUTLIER) cc_final: 0.8944 (m) REVERT: D 254 ASP cc_start: 0.8818 (t0) cc_final: 0.8521 (t0) REVERT: E 141 PHE cc_start: 0.7351 (t80) cc_final: 0.6813 (t80) REVERT: E 157 LYS cc_start: 0.7741 (mmtm) cc_final: 0.7119 (ttpt) REVERT: E 164 TYR cc_start: 0.6730 (t80) cc_final: 0.5888 (t80) REVERT: E 198 ASP cc_start: 0.8553 (p0) cc_final: 0.8295 (p0) REVERT: F 106 HIS cc_start: 0.8487 (m90) cc_final: 0.8033 (m90) REVERT: F 297 MET cc_start: 0.6987 (mpp) cc_final: 0.6607 (mpp) REVERT: F 314 GLU cc_start: 0.8097 (mp0) cc_final: 0.7832 (mp0) outliers start: 93 outliers final: 79 residues processed: 276 average time/residue: 0.0917 time to fit residues: 38.9585 Evaluate side-chains 276 residues out of total 1593 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 188 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 TYR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 193 HIS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 20 TYR Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 32 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 113 HIS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 164 TYR Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 110 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 LYS Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 215 TYR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 323 CYS Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 110 VAL Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 147 CYS Chi-restraints excluded: chain D residue 164 TYR Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 176 GLU Chi-restraints excluded: chain D residue 183 PHE Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 97 HIS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 189 VAL Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 334 ILE Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 0.0770 chunk 115 optimal weight: 0.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.097025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.073043 restraints weight = 58851.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.075035 restraints weight = 38193.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.075426 restraints weight = 29154.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075503 restraints weight = 26993.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.075593 restraints weight = 25321.387| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14138 Z= 0.174 Angle : 0.763 14.604 19121 Z= 0.381 Chirality : 0.047 0.252 2178 Planarity : 0.005 0.078 2466 Dihedral : 7.423 59.888 1946 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.15 % Allowed : 36.22 % Favored : 57.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1737 helix: 0.58 (0.22), residues: 514 sheet: -0.51 (0.25), residues: 421 loop : 0.27 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 197 TYR 0.025 0.002 TYR E 267 PHE 0.048 0.003 PHE D 69 TRP 0.016 0.002 TRP D 248 HIS 0.014 0.002 HIS F 171 Details of bonding type rmsd covalent geometry : bond 0.00390 (14133) covalent geometry : angle 0.76205 (19113) SS BOND : bond 0.00338 ( 4) SS BOND : angle 1.89828 ( 8) hydrogen bonds : bond 0.04291 ( 434) hydrogen bonds : angle 5.60370 ( 1254) Misc. bond : bond 0.00064 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2673.56 seconds wall clock time: 47 minutes 3.87 seconds (2823.87 seconds total)