Starting phenix.real_space_refine on Thu Jul 2 06:10:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.map" model { file = "/net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xy7_33513/07_2026/7xy7_33513.cif" } resolution = 3.26 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= 0.021 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 47 5.16 5 C 4481 2.51 5 N 1231 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "R GLU 217": not complete - not flipped Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7047 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1857 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "R" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2189 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.25 Number of scatterers: 7047 At special positions: 0 Unit cell: (78.72, 101.76, 134.4, 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 47 16.00 O 1288 8.00 N 1231 7.00 C 4481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 407.1 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 46.4% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.179A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.958A pdb=" N GLN A 229 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS A 230 " --> pdb=" O TRP A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.582A pdb=" N SER A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.629A pdb=" N LEU A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 Processing helix chain 'A' and resid 296 through 299 removed outlier: 4.023A pdb=" N ALA A 299 " --> pdb=" O PRO A 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 299' Processing helix chain 'A' and resid 314 through 335 removed outlier: 3.631A pdb=" N ARG A 325 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 removed outlier: 3.671A pdb=" N TYR A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.653A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.716A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 19 removed outlier: 3.713A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.779A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.703A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'R' and resid 6 through 35 removed outlier: 4.140A pdb=" N LEU R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL R 28 " --> pdb=" O GLY R 24 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS R 29 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 70 removed outlier: 3.606A pdb=" N TYR R 44 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Proline residue: R 62 - end of helix removed outlier: 4.397A pdb=" N GLY R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 109 removed outlier: 3.584A pdb=" N LEU R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE R 80 " --> pdb=" O TYR R 76 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER R 92 " --> pdb=" O LEU R 88 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE R 93 " --> pdb=" O THR R 89 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE R 107 " --> pdb=" O ARG R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 117 removed outlier: 3.561A pdb=" N LEU R 116 " --> pdb=" O ARG R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 138 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 172 through 177 removed outlier: 3.512A pdb=" N VAL R 177 " --> pdb=" O PHE R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 183 removed outlier: 3.907A pdb=" N MET R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 183 " --> pdb=" O MET R 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 178 through 183' Processing helix chain 'R' and resid 191 through 218 removed outlier: 3.641A pdb=" N PHE R 206 " --> pdb=" O TYR R 202 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 218 " --> pdb=" O GLN R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 260 removed outlier: 3.742A pdb=" N HIS R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE R 239 " --> pdb=" O SER R 235 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE R 243 " --> pdb=" O ILE R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 260 through 266 removed outlier: 4.457A pdb=" N ASN R 266 " --> pdb=" O ALA R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 281 removed outlier: 3.801A pdb=" N ASN R 273 " --> pdb=" O LYS R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 291 removed outlier: 3.804A pdb=" N VAL R 285 " --> pdb=" O ALA R 281 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 294 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 207 removed outlier: 7.129A pdb=" N ARG A 35 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 238 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU A 37 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A 240 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 39 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASP A 242 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.800A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.886A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.749A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.121A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.659A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.926A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.834A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 72 through 73 removed outlier: 3.527A pdb=" N THR R 73 " --> pdb=" O VAL R 169 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 960 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: 1.10 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2296 1.34 - 1.46: 1024 1.46 - 1.57: 3805 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 7190 Sorted by residual: bond pdb=" C4 NEC R 501 " pdb=" C5 NEC R 501 " ideal model delta sigma weight residual 1.385 1.471 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 NEC R 501 " pdb=" C6 NEC R 501 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C8 NEC R 501 " pdb=" N7 NEC R 501 " ideal model delta sigma weight residual 1.302 1.357 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C3' NEC R 501 " pdb=" O3' NEC R 501 " ideal model delta sigma weight residual 1.393 1.433 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C2' NEC R 501 " pdb=" O2' NEC R 501 " ideal model delta sigma weight residual 1.400 1.434 -0.034 2.00e-02 2.50e+03 2.89e+00 ... (remaining 7185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9622 1.94 - 3.89: 104 3.89 - 5.83: 20 5.83 - 7.77: 3 7.77 - 9.72: 3 Bond angle restraints: 9752 Sorted by residual: angle pdb=" C2 NEC R 501 " pdb=" N3 NEC R 501 " pdb=" C4 NEC R 501 " ideal model delta sigma weight residual 111.54 120.89 -9.35 3.00e+00 1.11e-01 9.71e+00 angle pdb=" CA LEU B 198 " pdb=" CB LEU B 198 " pdb=" CG LEU B 198 " ideal model delta sigma weight residual 116.30 126.02 -9.72 3.50e+00 8.16e-02 7.70e+00 angle pdb=" C5 NEC R 501 " pdb=" C4 NEC R 501 " pdb=" N3 NEC R 501 " ideal model delta sigma weight residual 126.75 118.68 8.07 3.00e+00 1.11e-01 7.23e+00 angle pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.89e+00 angle pdb=" CB ARG A 339 " pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " ideal model delta sigma weight residual 111.30 117.23 -5.93 2.30e+00 1.89e-01 6.64e+00 ... (remaining 9747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 4160 35.44 - 70.87: 108 70.87 - 106.31: 4 106.31 - 141.74: 0 141.74 - 177.18: 1 Dihedral angle restraints: 4273 sinusoidal: 1662 harmonic: 2611 Sorted by residual: dihedral pdb=" CB CYS R 78 " pdb=" SG CYS R 78 " pdb=" SG CYS R 171 " pdb=" CB CYS R 171 " ideal model delta sinusoidal sigma weight residual 93.00 162.51 -69.51 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB GLU R 217 " pdb=" CG GLU R 217 " pdb=" CD GLU R 217 " pdb=" OE1 GLU R 217 " ideal model delta sinusoidal sigma weight residual 0.00 177.18 -177.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CA CYS R 171 " pdb=" C CYS R 171 " pdb=" N LEU R 172 " pdb=" CA LEU R 172 " ideal model delta harmonic sigma weight residual 180.00 161.32 18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 4270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 767 0.037 - 0.074: 260 0.074 - 0.111: 67 0.111 - 0.149: 23 0.149 - 0.186: 1 Chirality restraints: 1118 Sorted by residual: chirality pdb=" C2' NEC R 501 " pdb=" C1' NEC R 501 " pdb=" C3' NEC R 501 " pdb=" O2' NEC R 501 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA PRO R 249 " pdb=" N PRO R 249 " pdb=" C PRO R 249 " pdb=" CB PRO R 249 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1115 not shown) Planarity restraints: 1239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 193 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO R 194 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 314 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO A 315 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 315 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 315 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 118 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" CG ASP B 118 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP B 118 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP B 118 " 0.008 2.00e-02 2.50e+03 ... (remaining 1236 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 141 2.69 - 3.24: 6499 3.24 - 3.80: 10479 3.80 - 4.35: 13048 4.35 - 4.90: 22273 Nonbonded interactions: 52440 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.141 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE1 GLN B 175 " model vdw 2.259 3.040 nonbonded pdb=" OG SER A 6 " pdb=" OE1 GLU A 8 " model vdw 2.260 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.276 3.040 ... (remaining 52435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 7.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 0.003 0.086 7191 Z= 0.159 Angle : 0.576 9.715 9754 Z= 0.307 Chirality : 0.042 0.186 1118 Planarity : 0.004 0.041 1239 Dihedral : 15.701 177.175 2576 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.40 % Allowed : 17.72 % Favored : 81.88 % 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 are not related in a simple way. whole: 1.03 (0.29), residues: 881 helix: 1.98 (0.28), residues: 369 sheet: 0.61 (0.43), residues: 168 loop : -0.72 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 49 TYR 0.008 0.001 TYR R 104 PHE 0.020 0.001 PHE A 215 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 7190) covalent geometry : angle 0.57611 / 0.31 ( 9752) SS BOND : bond 0.00507 / 0.27 ( 1) SS BOND : angle 1.12481 / 0.56 ( 2) hydrogen bonds : bond 0.15533 / 10.34 ( 328) hydrogen bonds : angle 5.16484 / 3.61 ( 960) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.292 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 171 average time/residue: 0.1226 time to fit residues: 26.0830 Evaluate side-chains 166 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 0.3980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115902 restraints weight = 10687.124| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.49 r_work: 0.3350 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7191 Z= 0.118 Angle : 0.487 7.238 9754 Z= 0.263 Chirality : 0.041 0.130 1118 Planarity : 0.004 0.049 1239 Dihedral : 3.797 17.469 979 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.04 % Allowed : 15.61 % Favored : 81.35 % 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 are not related in a simple way. whole: 1.35 (0.29), residues: 881 helix: 2.27 (0.27), residues: 381 sheet: 0.73 (0.43), residues: 166 loop : -0.66 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.007 0.001 TYR A 322 PHE 0.013 0.001 PHE B 199 TRP 0.007 0.001 TRP B 99 HIS 0.002 0.001 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7190) covalent geometry : angle 0.48711 / 0.26 ( 9752) SS BOND : bond 0.00065 / 0.03 ( 1) SS BOND : angle 0.80650 / 0.38 ( 2) hydrogen bonds : bond 0.04810 / 3.24 ( 328) hydrogen bonds : angle 3.94085 / 2.77 ( 960) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.7221 (ttm170) REVERT: B 239 ASN cc_start: 0.7788 (m-40) cc_final: 0.7553 (m-40) REVERT: B 245 SER cc_start: 0.8479 (p) cc_final: 0.8214 (m) REVERT: B 298 ASP cc_start: 0.7612 (t70) cc_final: 0.7346 (t70) REVERT: R 272 MET cc_start: 0.7302 (mmm) cc_final: 0.7032 (tmm) outliers start: 23 outliers final: 16 residues processed: 173 average time/residue: 0.1182 time to fit residues: 25.3064 Evaluate side-chains 179 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 279 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 chunk 16 optimal weight: 0.1980 chunk 48 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115104 restraints weight = 10469.719| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.42 r_work: 0.3354 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7191 Z= 0.119 Angle : 0.469 8.009 9754 Z= 0.253 Chirality : 0.041 0.130 1118 Planarity : 0.004 0.041 1239 Dihedral : 3.679 17.659 975 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.31 % Allowed : 16.27 % Favored : 80.42 % 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 are not related in a simple way. whole: 1.51 (0.29), residues: 881 helix: 2.39 (0.27), residues: 381 sheet: 0.97 (0.44), residues: 158 loop : -0.60 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 215 TYR 0.008 0.001 TYR A 322 PHE 0.011 0.001 PHE A 215 TRP 0.008 0.001 TRP B 211 HIS 0.002 0.000 HIS R 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 7190) covalent geometry : angle 0.46929 / 0.25 ( 9752) SS BOND : bond 0.00050 / 0.03 ( 1) SS BOND : angle 1.04549 / 0.49 ( 2) hydrogen bonds : bond 0.04791 / 3.23 ( 328) hydrogen bonds : angle 3.82392 / 2.67 ( 960) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.7170 (ttm170) REVERT: B 197 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7284 (tpp80) REVERT: B 239 ASN cc_start: 0.7809 (m-40) cc_final: 0.7552 (m-40) REVERT: B 249 THR cc_start: 0.8411 (p) cc_final: 0.8193 (p) REVERT: B 273 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7666 (tt) REVERT: B 298 ASP cc_start: 0.7485 (t70) cc_final: 0.7134 (t70) REVERT: B 303 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: R 272 MET cc_start: 0.7288 (mmm) cc_final: 0.7005 (mmm) outliers start: 25 outliers final: 20 residues processed: 178 average time/residue: 0.1191 time to fit residues: 26.6663 Evaluate side-chains 190 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114057 restraints weight = 10623.225| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.44 r_work: 0.3334 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7191 Z= 0.138 Angle : 0.478 8.326 9754 Z= 0.258 Chirality : 0.041 0.127 1118 Planarity : 0.004 0.042 1239 Dihedral : 3.742 17.558 975 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.84 % Allowed : 16.40 % Favored : 79.76 % 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 are not related in a simple way. whole: 1.51 (0.29), residues: 881 helix: 2.40 (0.27), residues: 382 sheet: 0.95 (0.45), residues: 155 loop : -0.61 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 215 TYR 0.009 0.001 TYR A 322 PHE 0.013 0.001 PHE B 235 TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7190) covalent geometry : angle 0.47788 / 0.26 ( 9752) SS BOND : bond 0.00174 / 0.09 ( 1) SS BOND : angle 1.18453 / 0.55 ( 2) hydrogen bonds : bond 0.05159 / 3.47 ( 328) hydrogen bonds : angle 3.84614 / 2.68 ( 960) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 330 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.7124 (ttm170) REVERT: B 239 ASN cc_start: 0.7834 (m-40) cc_final: 0.7587 (m-40) REVERT: B 298 ASP cc_start: 0.7535 (t70) cc_final: 0.7150 (t70) REVERT: R 177 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7710 (m) REVERT: R 274 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7796 (mmm) outliers start: 29 outliers final: 24 residues processed: 184 average time/residue: 0.1243 time to fit residues: 28.2293 Evaluate side-chains 198 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 274 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 72 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 0.0870 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113993 restraints weight = 10609.991| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.46 r_work: 0.3337 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7191 Z= 0.128 Angle : 0.484 8.618 9754 Z= 0.258 Chirality : 0.041 0.125 1118 Planarity : 0.003 0.040 1239 Dihedral : 3.712 17.526 975 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.84 % Allowed : 17.20 % Favored : 78.97 % 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 are not related in a simple way. whole: 1.51 (0.29), residues: 881 helix: 2.44 (0.27), residues: 381 sheet: 0.91 (0.44), residues: 155 loop : -0.62 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.009 0.001 TYR A 322 PHE 0.014 0.001 PHE A 215 TRP 0.010 0.001 TRP B 339 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7190) covalent geometry : angle 0.48336 / 0.26 ( 9752) SS BOND : bond 0.00096 / 0.05 ( 1) SS BOND : angle 1.12038 / 0.52 ( 2) hydrogen bonds : bond 0.04862 / 3.27 ( 328) hydrogen bonds : angle 3.78836 / 2.63 ( 960) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7859 (ttm) REVERT: A 330 ARG cc_start: 0.7424 (ttm-80) cc_final: 0.7205 (ttm170) REVERT: B 210 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7416 (tp) REVERT: B 214 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7956 (mtt180) REVERT: B 228 ASP cc_start: 0.7595 (m-30) cc_final: 0.7190 (t0) REVERT: B 239 ASN cc_start: 0.7769 (m-40) cc_final: 0.7553 (m-40) REVERT: B 273 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8095 (mt) REVERT: B 298 ASP cc_start: 0.7554 (t70) cc_final: 0.7183 (t70) REVERT: R 177 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7731 (m) outliers start: 29 outliers final: 23 residues processed: 174 average time/residue: 0.1184 time to fit residues: 25.6804 Evaluate side-chains 194 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 274 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 5 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 33 optimal weight: 0.0270 chunk 68 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.134200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114880 restraints weight = 10592.450| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.46 r_work: 0.3350 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7191 Z= 0.110 Angle : 0.468 8.551 9754 Z= 0.250 Chirality : 0.041 0.127 1118 Planarity : 0.003 0.039 1239 Dihedral : 3.597 16.829 975 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.70 % Allowed : 18.39 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.29), residues: 881 helix: 2.44 (0.27), residues: 382 sheet: 0.97 (0.45), residues: 154 loop : -0.62 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.008 0.001 TYR A 322 PHE 0.014 0.001 PHE A 215 TRP 0.008 0.001 TRP B 339 HIS 0.002 0.000 HIS G 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 7190) covalent geometry : angle 0.46735 / 0.25 ( 9752) SS BOND : bond 0.00022 / 0.01 ( 1) SS BOND : angle 0.97157 / 0.46 ( 2) hydrogen bonds : bond 0.04363 / 2.93 ( 328) hydrogen bonds : angle 3.67470 / 2.55 ( 960) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7858 (ttm) REVERT: B 210 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7399 (tp) REVERT: B 298 ASP cc_start: 0.7657 (t70) cc_final: 0.7135 (t70) REVERT: R 177 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7703 (m) outliers start: 28 outliers final: 22 residues processed: 173 average time/residue: 0.1127 time to fit residues: 24.4531 Evaluate side-chains 186 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 274 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0060 chunk 3 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.132843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.113548 restraints weight = 10558.945| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.46 r_work: 0.3320 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7191 Z= 0.151 Angle : 0.496 8.750 9754 Z= 0.266 Chirality : 0.042 0.122 1118 Planarity : 0.003 0.039 1239 Dihedral : 3.751 16.441 975 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.76 % Allowed : 16.93 % Favored : 78.31 % 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 are not related in a simple way. whole: 1.48 (0.29), residues: 881 helix: 2.38 (0.27), residues: 382 sheet: 0.93 (0.45), residues: 154 loop : -0.62 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.009 0.001 TYR R 10 PHE 0.017 0.002 PHE A 215 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7190) covalent geometry : angle 0.49609 / 0.27 ( 9752) SS BOND : bond 0.00216 / 0.11 ( 1) SS BOND : angle 1.25876 / 0.59 ( 2) hydrogen bonds : bond 0.05342 / 3.60 ( 328) hydrogen bonds : angle 3.83166 / 2.66 ( 960) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7844 (ttm) REVERT: B 214 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7751 (mtm-85) REVERT: B 228 ASP cc_start: 0.7640 (m-30) cc_final: 0.7280 (t0) REVERT: B 273 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8083 (mt) REVERT: B 298 ASP cc_start: 0.7723 (t70) cc_final: 0.7130 (t70) REVERT: R 177 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7760 (m) outliers start: 36 outliers final: 26 residues processed: 191 average time/residue: 0.1161 time to fit residues: 27.5227 Evaluate side-chains 205 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 84 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 5 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114077 restraints weight = 10585.576| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.45 r_work: 0.3336 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7191 Z= 0.124 Angle : 0.487 8.804 9754 Z= 0.261 Chirality : 0.041 0.126 1118 Planarity : 0.003 0.043 1239 Dihedral : 3.672 16.324 975 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.97 % Allowed : 17.46 % Favored : 78.57 % 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 are not related in a simple way. whole: 1.52 (0.29), residues: 881 helix: 2.39 (0.27), residues: 382 sheet: 1.03 (0.45), residues: 152 loop : -0.61 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.008 0.001 TYR A 322 PHE 0.017 0.001 PHE A 215 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7190) covalent geometry : angle 0.48711 / 0.26 ( 9752) SS BOND : bond 0.00053 / 0.03 ( 1) SS BOND : angle 1.05203 / 0.49 ( 2) hydrogen bonds : bond 0.04745 / 3.18 ( 328) hydrogen bonds : angle 3.74324 / 2.60 ( 960) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7834 (ttp-170) REVERT: A 214 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7873 (ttm) REVERT: B 228 ASP cc_start: 0.7612 (m-30) cc_final: 0.7172 (t0) REVERT: B 245 SER cc_start: 0.8479 (p) cc_final: 0.8164 (m) REVERT: B 298 ASP cc_start: 0.7690 (t70) cc_final: 0.7072 (t70) REVERT: R 177 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7730 (m) outliers start: 30 outliers final: 25 residues processed: 180 average time/residue: 0.1233 time to fit residues: 27.4688 Evaluate side-chains 195 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 27 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 4 optimal weight: 0.0050 chunk 48 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113931 restraints weight = 10535.821| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.46 r_work: 0.3336 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7191 Z= 0.125 Angle : 0.501 8.788 9754 Z= 0.265 Chirality : 0.041 0.138 1118 Planarity : 0.003 0.038 1239 Dihedral : 3.646 15.327 975 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.70 % Allowed : 18.25 % Favored : 78.04 % 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 are not related in a simple way. whole: 1.49 (0.29), residues: 881 helix: 2.39 (0.27), residues: 382 sheet: 0.95 (0.43), residues: 157 loop : -0.64 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.008 0.001 TYR A 322 PHE 0.018 0.001 PHE A 215 TRP 0.009 0.001 TRP B 339 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 7190) covalent geometry : angle 0.50102 / 0.26 ( 9752) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 1.09710 / 0.52 ( 2) hydrogen bonds : bond 0.04735 / 3.18 ( 328) hydrogen bonds : angle 3.73574 / 2.60 ( 960) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7798 (ttp-170) REVERT: B 49 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7990 (mtt180) REVERT: B 197 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7408 (tpp80) REVERT: B 214 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7752 (mtt180) REVERT: B 228 ASP cc_start: 0.7648 (m-30) cc_final: 0.7218 (t0) REVERT: B 245 SER cc_start: 0.8480 (p) cc_final: 0.8224 (m) REVERT: B 298 ASP cc_start: 0.7720 (t70) cc_final: 0.7058 (t70) REVERT: G 47 GLU cc_start: 0.8273 (mp0) cc_final: 0.8030 (mp0) REVERT: R 177 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7726 (m) outliers start: 28 outliers final: 24 residues processed: 178 average time/residue: 0.1052 time to fit residues: 23.2344 Evaluate side-chains 193 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112298 restraints weight = 10539.642| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.44 r_work: 0.3316 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7191 Z= 0.164 Angle : 0.531 8.747 9754 Z= 0.282 Chirality : 0.042 0.136 1118 Planarity : 0.004 0.039 1239 Dihedral : 3.839 15.419 975 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.31 % Allowed : 18.65 % Favored : 78.04 % 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 are not related in a simple way. whole: 1.38 (0.29), residues: 881 helix: 2.28 (0.27), residues: 382 sheet: 0.87 (0.43), residues: 158 loop : -0.67 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.010 0.001 TYR R 10 PHE 0.024 0.002 PHE A 215 TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 7190) covalent geometry : angle 0.53077 / 0.28 ( 9752) SS BOND : bond 0.00217 / 0.11 ( 1) SS BOND : angle 1.23887 / 0.58 ( 2) hydrogen bonds : bond 0.05582 / 3.76 ( 328) hydrogen bonds : angle 3.89494 / 2.71 ( 960) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.7882 (ttp-170) REVERT: B 228 ASP cc_start: 0.7639 (m-30) cc_final: 0.7228 (t0) REVERT: B 245 SER cc_start: 0.8641 (p) cc_final: 0.8263 (m) REVERT: B 298 ASP cc_start: 0.7756 (t70) cc_final: 0.7114 (t70) REVERT: G 47 GLU cc_start: 0.8292 (mp0) cc_final: 0.8004 (mp0) REVERT: R 177 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7733 (m) outliers start: 25 outliers final: 24 residues processed: 183 average time/residue: 0.1162 time to fit residues: 26.1597 Evaluate side-chains 197 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 78 CYS Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 171 CYS Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 182 MET Chi-restraints excluded: chain R residue 238 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112285 restraints weight = 10493.865| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.43 r_work: 0.3314 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7191 Z= 0.169 Angle : 0.530 8.232 9754 Z= 0.283 Chirality : 0.043 0.132 1118 Planarity : 0.004 0.039 1239 Dihedral : 3.881 15.431 975 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.44 % Allowed : 19.18 % Favored : 77.38 % 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 are not related in a simple way. whole: 1.34 (0.29), residues: 881 helix: 2.24 (0.27), residues: 382 sheet: 0.84 (0.43), residues: 158 loop : -0.66 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.010 0.001 TYR R 10 PHE 0.026 0.002 PHE A 215 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 7190) covalent geometry : angle 0.52973 / 0.28 ( 9752) SS BOND : bond 0.00239 / 0.13 ( 1) SS BOND : angle 1.29854 / 0.61 ( 2) hydrogen bonds : bond 0.05568 / 3.75 ( 328) hydrogen bonds : angle 3.92225 / 2.73 ( 960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.30 seconds wall clock time: 36 minutes 10.03 seconds (2170.03 seconds total)