Starting phenix.real_space_refine on Wed Feb 4 06:36:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kt8_62559/02_2026/9kt8_62559.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kt8_62559/02_2026/9kt8_62559.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kt8_62559/02_2026/9kt8_62559.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kt8_62559/02_2026/9kt8_62559.map" model { file = "/net/cci-nas-00/data/ceres_data/9kt8_62559/02_2026/9kt8_62559.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kt8_62559/02_2026/9kt8_62559.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 70 5.16 5 C 5800 2.51 5 N 1548 2.21 5 O 1675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9093 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1830 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2404 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain: "R" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'P9X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.23 Number of scatterers: 9093 At special positions: 0 Unit cell: (91.057, 119.14, 133.607, 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 70 16.00 O 1675 8.00 N 1548 7.00 C 5800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " 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=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 214.6 milliseconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 37.8% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.592A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.796A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 271 through 281 removed outlier: 4.346A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.825A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.537A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.319A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.039A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 55 removed outlier: 3.661A pdb=" N LYS R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 60 through 79 removed outlier: 3.503A pdb=" N ILE R 64 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 removed outlier: 3.698A pdb=" N ARG R 89 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 131 removed outlier: 3.539A pdb=" N ARG R 101 " --> pdb=" O ASP R 97 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N MET R 103 " --> pdb=" O PRO R 99 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN R 112 " --> pdb=" O ALA R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 138 Processing helix chain 'R' and resid 140 through 160 removed outlier: 3.701A pdb=" N ALA R 144 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 145 " --> pdb=" O ASN R 141 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 164 removed outlier: 3.629A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 164' Processing helix chain 'R' and resid 187 through 218 removed outlier: 3.714A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU R 199 " --> pdb=" O LEU R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.568A pdb=" N ILE R 211 " --> pdb=" O CYS R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 261 removed outlier: 3.755A pdb=" N VAL R 236 " --> pdb=" O PHE R 232 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 269 through 280 Processing helix chain 'R' and resid 280 through 295 removed outlier: 4.082A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER R 287 " --> pdb=" O THR R 283 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.938A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.691A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.557A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.903A 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: 6.928A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.844A 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 151 removed outlier: 3.712A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.860A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.836A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.053A 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: 3.744A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.749A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.749A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.708A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.949A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 11 through 13 removed outlier: 4.057A pdb=" N ILE R 182 " --> pdb=" O CYS R 19 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 170 removed outlier: 3.913A pdb=" N ILE R 169 " --> pdb=" O LEU R 176 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1203 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: 1.01 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1468 1.31 - 1.44: 2595 1.44 - 1.56: 5127 1.56 - 1.69: 0 1.69 - 1.82: 102 Bond restraints: 9292 Sorted by residual: bond pdb=" C1 P9X R 401 " pdb=" C2 P9X R 401 " ideal model delta sigma weight residual 1.550 1.357 0.193 2.00e-02 2.50e+03 9.31e+01 bond pdb=" C4 P9X R 401 " pdb=" O1 P9X R 401 " ideal model delta sigma weight residual 1.342 1.519 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C3 P9X R 401 " pdb=" C4 P9X R 401 " ideal model delta sigma weight residual 1.357 1.465 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C1 P9X R 401 " pdb=" O1 P9X R 401 " ideal model delta sigma weight residual 1.455 1.544 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C2 P9X R 401 " pdb=" C3 P9X R 401 " ideal model delta sigma weight residual 1.436 1.359 0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 9287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 12459 2.49 - 4.99: 91 4.99 - 7.48: 15 7.48 - 9.98: 6 9.98 - 12.47: 1 Bond angle restraints: 12572 Sorted by residual: angle pdb=" N LYS R 15 " pdb=" CA LYS R 15 " pdb=" C LYS R 15 " ideal model delta sigma weight residual 114.56 108.62 5.94 1.27e+00 6.20e-01 2.19e+01 angle pdb=" C1 P9X R 401 " pdb=" C2 P9X R 401 " pdb=" C3 P9X R 401 " ideal model delta sigma weight residual 105.43 117.90 -12.47 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CA PRO R 168 " pdb=" N PRO R 168 " pdb=" CD PRO R 168 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C LYS R 15 " pdb=" N LYS R 16 " pdb=" CA LYS R 16 " ideal model delta sigma weight residual 121.87 127.81 -5.94 1.64e+00 3.72e-01 1.31e+01 angle pdb=" CA ARG A 32 " pdb=" C ARG A 32 " pdb=" N GLU A 33 " ideal model delta sigma weight residual 118.27 123.97 -5.70 1.59e+00 3.96e-01 1.29e+01 ... (remaining 12567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.54: 4974 16.54 - 33.09: 445 33.09 - 49.63: 82 49.63 - 66.17: 14 66.17 - 82.72: 12 Dihedral angle restraints: 5527 sinusoidal: 2192 harmonic: 3335 Sorted by residual: dihedral pdb=" CA MET R 167 " pdb=" C MET R 167 " pdb=" N PRO R 168 " pdb=" CA PRO R 168 " ideal model delta harmonic sigma weight residual 180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LEU R 80 " pdb=" C LEU R 80 " pdb=" N PRO R 81 " pdb=" CA PRO R 81 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -160.80 -19.20 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1142 0.051 - 0.103: 227 0.103 - 0.154: 38 0.154 - 0.206: 1 0.206 - 0.257: 2 Chirality restraints: 1410 Sorted by residual: chirality pdb=" C1 P9X R 401 " pdb=" C2 P9X R 401 " pdb=" C6 P9X R 401 " pdb=" O1 P9X R 401 " both_signs ideal model delta sigma weight residual False 2.77 2.52 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ASP R 290 " pdb=" N ASP R 290 " pdb=" C ASP R 290 " pdb=" CB ASP R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO R 168 " pdb=" N PRO R 168 " pdb=" C PRO R 168 " pdb=" CB PRO R 168 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1407 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 167 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO R 168 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO R 81 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " -0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO E 236 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " -0.026 5.00e-02 4.00e+02 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 968 2.75 - 3.29: 8562 3.29 - 3.83: 14670 3.83 - 4.36: 17566 4.36 - 4.90: 31135 Nonbonded interactions: 72901 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.215 3.040 nonbonded pdb=" O ALA A 203 " pdb=" NH1 ARG A 205 " model vdw 2.247 3.120 nonbonded pdb=" O GLN B 9 " pdb=" NE2 GLN B 13 " model vdw 2.247 3.120 nonbonded pdb=" OG SER R 298 " pdb=" O SER R 300 " model vdw 2.252 3.040 nonbonded pdb=" OE2 GLU A 289 " pdb=" OH TYR A 302 " model vdw 2.271 3.040 ... (remaining 72896 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: 1.770 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.920 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 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 : 0.004 0.193 9296 Z= 0.200 Angle : 0.605 12.474 12580 Z= 0.326 Chirality : 0.042 0.257 1410 Planarity : 0.005 0.113 1589 Dihedral : 13.434 82.717 3359 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % 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: 0.86 (0.25), residues: 1137 helix: 1.53 (0.28), residues: 369 sheet: 1.31 (0.30), residues: 277 loop : -0.61 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.015 0.001 TYR E 235 PHE 0.008 0.001 PHE B 199 TRP 0.015 0.001 TRP R 50 HIS 0.004 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9292) covalent geometry : angle 0.60491 (12572) SS BOND : bond 0.00318 ( 4) SS BOND : angle 1.08154 ( 8) hydrogen bonds : bond 0.18188 ( 433) hydrogen bonds : angle 6.49006 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.217 Fit side-chains REVERT: A 306 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7127 (mm110) REVERT: C 21 MET cc_start: 0.5656 (mmt) cc_final: 0.5321 (mmt) REVERT: C 62 ARG cc_start: 0.6829 (ptp90) cc_final: 0.6557 (ptp90) REVERT: E 46 GLU cc_start: 0.7810 (tt0) cc_final: 0.7603 (tt0) REVERT: R 60 LYS cc_start: 0.7038 (mttp) cc_final: 0.5868 (pttt) REVERT: R 84 MET cc_start: 0.4377 (mtp) cc_final: 0.4084 (mtp) REVERT: R 101 ARG cc_start: 0.4435 (ptt90) cc_final: 0.3676 (ptt180) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.6411 time to fit residues: 90.8999 Evaluate side-chains 120 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110108 restraints weight = 9706.521| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.75 r_work: 0.2936 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9296 Z= 0.168 Angle : 0.609 7.796 12580 Z= 0.326 Chirality : 0.045 0.213 1410 Planarity : 0.005 0.117 1589 Dihedral : 5.539 47.495 1266 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 1.61 % Allowed : 8.54 % Favored : 89.85 % 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: 0.96 (0.25), residues: 1137 helix: 1.71 (0.28), residues: 374 sheet: 1.34 (0.30), residues: 279 loop : -0.66 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.015 0.002 TYR E 190 PHE 0.015 0.002 PHE A 196 TRP 0.025 0.002 TRP R 50 HIS 0.006 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9292) covalent geometry : angle 0.60771 (12572) SS BOND : bond 0.00636 ( 4) SS BOND : angle 1.60135 ( 8) hydrogen bonds : bond 0.05188 ( 433) hydrogen bonds : angle 4.90809 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.269 Fit side-chains REVERT: A 33 GLU cc_start: 0.7725 (tt0) cc_final: 0.7388 (mt-10) REVERT: B 172 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7720 (tp30) REVERT: B 217 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6817 (pp-130) REVERT: C 21 MET cc_start: 0.5891 (mmt) cc_final: 0.5553 (mtt) REVERT: C 62 ARG cc_start: 0.6717 (ptp90) cc_final: 0.6370 (ptp90) REVERT: E 202 ARG cc_start: 0.7542 (ptp90) cc_final: 0.7327 (ptp-170) REVERT: E 234 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: R 15 LYS cc_start: 0.4869 (tmmt) cc_final: 0.4602 (tmtp) REVERT: R 84 MET cc_start: 0.4505 (mtp) cc_final: 0.4214 (mtp) REVERT: R 176 LEU cc_start: 0.3930 (OUTLIER) cc_final: 0.3659 (tt) outliers start: 16 outliers final: 9 residues processed: 128 average time/residue: 0.6858 time to fit residues: 92.1263 Evaluate side-chains 128 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 18 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 86 ASN R 141 ASN R 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.180639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3353 r_free = 0.3353 target = 0.121346 restraints weight = 9590.952| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.97 r_work: 0.3076 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 9296 Z= 0.101 Angle : 0.502 7.641 12580 Z= 0.268 Chirality : 0.042 0.203 1410 Planarity : 0.005 0.114 1589 Dihedral : 4.858 39.472 1266 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 2.01 % Allowed : 9.95 % Favored : 88.04 % 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: 1.25 (0.25), residues: 1137 helix: 2.02 (0.28), residues: 374 sheet: 1.58 (0.30), residues: 276 loop : -0.59 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 222 TYR 0.014 0.001 TYR E 190 PHE 0.010 0.001 PHE B 241 TRP 0.018 0.001 TRP R 50 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9292) covalent geometry : angle 0.50093 (12572) SS BOND : bond 0.00312 ( 4) SS BOND : angle 1.15591 ( 8) hydrogen bonds : bond 0.03808 ( 433) hydrogen bonds : angle 4.38857 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.261 Fit side-chains REVERT: A 33 GLU cc_start: 0.7422 (tt0) cc_final: 0.7109 (mt-10) REVERT: C 21 MET cc_start: 0.5942 (mmt) cc_final: 0.5581 (mtt) REVERT: C 62 ARG cc_start: 0.6787 (ptp90) cc_final: 0.6497 (ptp90) REVERT: E 202 ARG cc_start: 0.7529 (ptp90) cc_final: 0.7308 (ptp-170) REVERT: R 15 LYS cc_start: 0.4695 (tmmt) cc_final: 0.4385 (tmtp) REVERT: R 109 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.4919 (pp-130) REVERT: R 176 LEU cc_start: 0.3823 (OUTLIER) cc_final: 0.3588 (tt) outliers start: 20 outliers final: 5 residues processed: 131 average time/residue: 0.6412 time to fit residues: 88.4377 Evaluate side-chains 121 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 93 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 141 ASN R 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.179032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118676 restraints weight = 9684.460| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.06 r_work: 0.3039 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 9296 Z= 0.104 Angle : 0.505 7.640 12580 Z= 0.268 Chirality : 0.042 0.198 1410 Planarity : 0.005 0.114 1589 Dihedral : 4.724 34.018 1266 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 2.31 % Allowed : 11.86 % Favored : 85.83 % 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 (0.25), residues: 1137 helix: 2.19 (0.28), residues: 373 sheet: 1.62 (0.30), residues: 277 loop : -0.55 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.014 0.001 TYR E 190 PHE 0.010 0.001 PHE A 196 TRP 0.016 0.001 TRP R 50 HIS 0.003 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9292) covalent geometry : angle 0.50397 (12572) SS BOND : bond 0.00382 ( 4) SS BOND : angle 1.21975 ( 8) hydrogen bonds : bond 0.03720 ( 433) hydrogen bonds : angle 4.25221 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.261 Fit side-chains REVERT: A 32 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6600 (ttp-170) REVERT: A 33 GLU cc_start: 0.7330 (tt0) cc_final: 0.6916 (mm-30) REVERT: C 21 MET cc_start: 0.6104 (mmt) cc_final: 0.5717 (mtt) REVERT: C 62 ARG cc_start: 0.6721 (ptp90) cc_final: 0.6263 (ptp90) REVERT: E 46 GLU cc_start: 0.8424 (tt0) cc_final: 0.8160 (tt0) REVERT: E 202 ARG cc_start: 0.7500 (ptp90) cc_final: 0.7256 (ptp-170) REVERT: E 234 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7278 (mm-30) REVERT: R 83 LEU cc_start: 0.5024 (OUTLIER) cc_final: 0.4722 (tm) REVERT: R 84 MET cc_start: 0.4298 (mtp) cc_final: 0.4025 (mtp) REVERT: R 101 ARG cc_start: 0.4081 (ptt90) cc_final: 0.3501 (ptt90) REVERT: R 109 MET cc_start: 0.6281 (ttp) cc_final: 0.5523 (ppp) REVERT: R 176 LEU cc_start: 0.3844 (OUTLIER) cc_final: 0.3595 (tt) outliers start: 23 outliers final: 8 residues processed: 131 average time/residue: 0.6761 time to fit residues: 93.2357 Evaluate side-chains 126 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 9.9990 chunk 32 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN R 141 ASN R 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.177374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115245 restraints weight = 9610.796| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.75 r_work: 0.2913 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9296 Z= 0.125 Angle : 0.549 12.389 12580 Z= 0.287 Chirality : 0.043 0.198 1410 Planarity : 0.005 0.115 1589 Dihedral : 4.863 31.750 1266 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.90 % Favored : 97.01 % Rotamer: Outliers : 2.51 % Allowed : 12.26 % Favored : 85.23 % 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: 1.36 (0.25), residues: 1137 helix: 2.20 (0.28), residues: 374 sheet: 1.58 (0.30), residues: 278 loop : -0.57 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.014 0.001 TYR E 190 PHE 0.012 0.001 PHE A 196 TRP 0.016 0.001 TRP R 50 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9292) covalent geometry : angle 0.54775 (12572) SS BOND : bond 0.00489 ( 4) SS BOND : angle 1.41869 ( 8) hydrogen bonds : bond 0.04051 ( 433) hydrogen bonds : angle 4.33653 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.373 Fit side-chains REVERT: A 32 ARG cc_start: 0.7471 (ttp80) cc_final: 0.6748 (ttp-170) REVERT: A 33 GLU cc_start: 0.7629 (tt0) cc_final: 0.7167 (mm-30) REVERT: B 172 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7760 (tp30) REVERT: C 21 MET cc_start: 0.6133 (mmt) cc_final: 0.5758 (mtt) REVERT: C 62 ARG cc_start: 0.6729 (ptp90) cc_final: 0.6207 (ptp90) REVERT: E 46 GLU cc_start: 0.8567 (tt0) cc_final: 0.8306 (tt0) REVERT: E 202 ARG cc_start: 0.7535 (ptp90) cc_final: 0.7257 (ptp-170) REVERT: E 234 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7490 (mm-30) REVERT: R 83 LEU cc_start: 0.5168 (OUTLIER) cc_final: 0.4854 (tm) REVERT: R 84 MET cc_start: 0.4175 (mtp) cc_final: 0.3903 (mtp) REVERT: R 109 MET cc_start: 0.6353 (ttp) cc_final: 0.5718 (ppp) REVERT: R 176 LEU cc_start: 0.4035 (OUTLIER) cc_final: 0.3800 (tt) REVERT: R 234 MET cc_start: 0.6718 (mmm) cc_final: 0.6256 (mtp) outliers start: 25 outliers final: 9 residues processed: 131 average time/residue: 0.6304 time to fit residues: 87.3098 Evaluate side-chains 126 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN E 3 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.175944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116986 restraints weight = 9497.873| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.20 r_work: 0.2985 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9296 Z= 0.162 Angle : 0.600 11.929 12580 Z= 0.317 Chirality : 0.045 0.201 1410 Planarity : 0.005 0.115 1589 Dihedral : 5.206 31.769 1266 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.01 % Allowed : 13.07 % Favored : 84.92 % 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: 1.21 (0.25), residues: 1137 helix: 2.06 (0.28), residues: 374 sheet: 1.49 (0.30), residues: 280 loop : -0.64 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 222 TYR 0.013 0.002 TYR E 103 PHE 0.017 0.002 PHE A 196 TRP 0.018 0.002 TRP R 50 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9292) covalent geometry : angle 0.59889 (12572) SS BOND : bond 0.00659 ( 4) SS BOND : angle 1.62646 ( 8) hydrogen bonds : bond 0.04647 ( 433) hydrogen bonds : angle 4.54314 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.291 Fit side-chains REVERT: A 32 ARG cc_start: 0.7510 (ttp80) cc_final: 0.6789 (ttp-170) REVERT: A 33 GLU cc_start: 0.7508 (tt0) cc_final: 0.7102 (mm-30) REVERT: B 258 ASP cc_start: 0.7264 (m-30) cc_final: 0.6945 (t70) REVERT: C 21 MET cc_start: 0.6117 (mmt) cc_final: 0.5652 (mtt) REVERT: C 62 ARG cc_start: 0.6659 (ptp90) cc_final: 0.6303 (ptp90) REVERT: E 202 ARG cc_start: 0.7470 (ptp90) cc_final: 0.7156 (ptp-170) REVERT: E 234 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: R 83 LEU cc_start: 0.5221 (OUTLIER) cc_final: 0.4936 (tm) REVERT: R 101 ARG cc_start: 0.4169 (ptt90) cc_final: 0.3619 (ptt90) REVERT: R 176 LEU cc_start: 0.3972 (OUTLIER) cc_final: 0.3751 (tt) outliers start: 20 outliers final: 13 residues processed: 134 average time/residue: 0.7178 time to fit residues: 101.2170 Evaluate side-chains 133 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 192 MET Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN R 141 ASN R 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112097 restraints weight = 9519.394| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.09 r_work: 0.2893 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9296 Z= 0.130 Angle : 0.570 10.209 12580 Z= 0.301 Chirality : 0.043 0.199 1410 Planarity : 0.005 0.115 1589 Dihedral : 5.000 32.622 1266 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.19 % Rotamer: Outliers : 2.21 % Allowed : 14.07 % Favored : 83.72 % 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: 1.23 (0.25), residues: 1137 helix: 2.14 (0.28), residues: 374 sheet: 1.45 (0.30), residues: 278 loop : -0.66 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.014 0.001 TYR E 190 PHE 0.013 0.001 PHE A 196 TRP 0.016 0.001 TRP R 50 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9292) covalent geometry : angle 0.56908 (12572) SS BOND : bond 0.00526 ( 4) SS BOND : angle 1.51928 ( 8) hydrogen bonds : bond 0.04209 ( 433) hydrogen bonds : angle 4.44616 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.379 Fit side-chains REVERT: A 32 ARG cc_start: 0.7465 (ttp80) cc_final: 0.6712 (ttp-170) REVERT: A 33 GLU cc_start: 0.7633 (tt0) cc_final: 0.7159 (mm-30) REVERT: A 289 GLU cc_start: 0.6419 (pm20) cc_final: 0.5899 (pp20) REVERT: B 258 ASP cc_start: 0.7398 (m-30) cc_final: 0.7082 (t70) REVERT: C 21 MET cc_start: 0.6124 (mmt) cc_final: 0.5650 (mtt) REVERT: C 62 ARG cc_start: 0.6569 (ptp90) cc_final: 0.6193 (ptp90) REVERT: E 202 ARG cc_start: 0.7439 (ptp90) cc_final: 0.7113 (ptp-170) REVERT: E 234 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: R 83 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.4966 (tm) REVERT: R 84 MET cc_start: 0.4165 (mtp) cc_final: 0.3847 (mtp) REVERT: R 101 ARG cc_start: 0.4140 (ptt90) cc_final: 0.3627 (ptt90) REVERT: R 109 MET cc_start: 0.6201 (ttp) cc_final: 0.5567 (ppp) REVERT: R 176 LEU cc_start: 0.3829 (OUTLIER) cc_final: 0.3627 (tt) REVERT: R 234 MET cc_start: 0.6696 (mmm) cc_final: 0.6256 (mtp) outliers start: 22 outliers final: 10 residues processed: 130 average time/residue: 0.6723 time to fit residues: 92.0368 Evaluate side-chains 128 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116273 restraints weight = 9448.736| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.96 r_work: 0.3017 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9296 Z= 0.179 Angle : 0.632 10.230 12580 Z= 0.333 Chirality : 0.046 0.199 1410 Planarity : 0.005 0.116 1589 Dihedral : 5.309 32.288 1266 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.25 % Favored : 96.66 % Rotamer: Outliers : 2.31 % Allowed : 14.77 % Favored : 82.91 % 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: 1.09 (0.25), residues: 1137 helix: 1.94 (0.27), residues: 377 sheet: 1.38 (0.30), residues: 280 loop : -0.68 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.014 0.002 TYR E 103 PHE 0.016 0.002 PHE A 196 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS R 161 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 9292) covalent geometry : angle 0.63083 (12572) SS BOND : bond 0.00714 ( 4) SS BOND : angle 1.79703 ( 8) hydrogen bonds : bond 0.04847 ( 433) hydrogen bonds : angle 4.61301 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.301 Fit side-chains REVERT: A 32 ARG cc_start: 0.7580 (ttp80) cc_final: 0.6865 (ttp-170) REVERT: A 33 GLU cc_start: 0.7439 (tt0) cc_final: 0.7035 (mm-30) REVERT: B 258 ASP cc_start: 0.7307 (m-30) cc_final: 0.7007 (t70) REVERT: C 21 MET cc_start: 0.6221 (mmt) cc_final: 0.5777 (mtt) REVERT: C 62 ARG cc_start: 0.6608 (ptp90) cc_final: 0.6238 (ptp90) REVERT: E 3 GLN cc_start: 0.8523 (tt0) cc_final: 0.8279 (mt0) REVERT: E 234 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7406 (mm-30) REVERT: R 25 PHE cc_start: 0.5028 (m-80) cc_final: 0.4427 (m-80) REVERT: R 83 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4999 (tm) REVERT: R 109 MET cc_start: 0.6293 (ttp) cc_final: 0.5501 (ppp) REVERT: R 158 LEU cc_start: 0.6761 (mt) cc_final: 0.6469 (mp) REVERT: R 176 LEU cc_start: 0.3871 (OUTLIER) cc_final: 0.3661 (tt) REVERT: R 220 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.4873 (mtm) outliers start: 23 outliers final: 13 residues processed: 132 average time/residue: 0.6779 time to fit residues: 94.5006 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 167 MET Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 220 MET Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.177370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.114025 restraints weight = 9496.110| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.77 r_work: 0.2920 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 9296 Z= 0.113 Angle : 0.546 9.093 12580 Z= 0.287 Chirality : 0.042 0.200 1410 Planarity : 0.005 0.115 1589 Dihedral : 4.887 34.086 1266 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Rotamer: Outliers : 1.51 % Allowed : 15.58 % Favored : 82.91 % 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: 1.25 (0.25), residues: 1137 helix: 2.18 (0.28), residues: 377 sheet: 1.43 (0.30), residues: 275 loop : -0.64 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.015 0.001 TYR E 190 PHE 0.011 0.001 PHE A 196 TRP 0.016 0.001 TRP R 50 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9292) covalent geometry : angle 0.54485 (12572) SS BOND : bond 0.00464 ( 4) SS BOND : angle 1.47006 ( 8) hydrogen bonds : bond 0.03932 ( 433) hydrogen bonds : angle 4.36988 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.364 Fit side-chains REVERT: A 32 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6660 (ttp-170) REVERT: A 33 GLU cc_start: 0.7618 (tt0) cc_final: 0.7181 (mm-30) REVERT: A 289 GLU cc_start: 0.6403 (pm20) cc_final: 0.5906 (pp20) REVERT: B 172 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7747 (tp30) REVERT: B 258 ASP cc_start: 0.7404 (m-30) cc_final: 0.7102 (t70) REVERT: C 21 MET cc_start: 0.6151 (mmt) cc_final: 0.5663 (mtt) REVERT: C 62 ARG cc_start: 0.6517 (ptp90) cc_final: 0.6146 (ptp90) REVERT: E 46 GLU cc_start: 0.8576 (tt0) cc_final: 0.8312 (tt0) REVERT: E 202 ARG cc_start: 0.7566 (ptp-170) cc_final: 0.7365 (ptp-170) REVERT: E 234 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: R 25 PHE cc_start: 0.5055 (m-80) cc_final: 0.4585 (m-80) REVERT: R 28 LYS cc_start: 0.4348 (mttm) cc_final: 0.4135 (ptmt) REVERT: R 57 LYS cc_start: 0.4582 (mtmm) cc_final: 0.3871 (tmtm) REVERT: R 83 LEU cc_start: 0.5267 (OUTLIER) cc_final: 0.4946 (tm) REVERT: R 109 MET cc_start: 0.6210 (ttp) cc_final: 0.5521 (ppp) REVERT: R 158 LEU cc_start: 0.6765 (mt) cc_final: 0.6459 (mp) REVERT: R 176 LEU cc_start: 0.3689 (OUTLIER) cc_final: 0.3481 (tt) outliers start: 15 outliers final: 8 residues processed: 132 average time/residue: 0.7291 time to fit residues: 101.2140 Evaluate side-chains 131 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 99 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.178005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 109)---------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116305 restraints weight = 9578.043| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.06 r_work: 0.3007 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 9296 Z= 0.111 Angle : 0.544 9.667 12580 Z= 0.284 Chirality : 0.042 0.201 1410 Planarity : 0.005 0.115 1589 Dihedral : 4.757 36.776 1266 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 1.51 % Allowed : 15.98 % Favored : 82.51 % 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 (0.25), residues: 1137 helix: 2.24 (0.28), residues: 377 sheet: 1.51 (0.30), residues: 273 loop : -0.57 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.014 0.001 TYR E 190 PHE 0.010 0.001 PHE A 196 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9292) covalent geometry : angle 0.54317 (12572) SS BOND : bond 0.00455 ( 4) SS BOND : angle 1.41927 ( 8) hydrogen bonds : bond 0.03783 ( 433) hydrogen bonds : angle 4.29171 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.297 Fit side-chains REVERT: A 32 ARG cc_start: 0.7373 (ttp80) cc_final: 0.6611 (ttp-170) REVERT: A 33 GLU cc_start: 0.7481 (tt0) cc_final: 0.7060 (mm-30) REVERT: A 289 GLU cc_start: 0.6388 (pm20) cc_final: 0.5902 (pp20) REVERT: B 258 ASP cc_start: 0.7286 (m-30) cc_final: 0.7010 (t70) REVERT: C 21 MET cc_start: 0.6326 (mmt) cc_final: 0.5844 (mtt) REVERT: C 62 ARG cc_start: 0.6519 (ptp90) cc_final: 0.6197 (ptp90) REVERT: E 46 GLU cc_start: 0.8485 (tt0) cc_final: 0.8224 (tt0) REVERT: E 93 MET cc_start: 0.8724 (ttm) cc_final: 0.8451 (mmm) REVERT: E 234 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: R 25 PHE cc_start: 0.5180 (m-80) cc_final: 0.4562 (m-80) REVERT: R 57 LYS cc_start: 0.4604 (mtmm) cc_final: 0.3916 (tmtm) REVERT: R 83 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.4954 (tm) REVERT: R 94 LYS cc_start: 0.4873 (pptt) cc_final: 0.3951 (ptmm) REVERT: R 109 MET cc_start: 0.6160 (ttp) cc_final: 0.5552 (ppp) REVERT: R 158 LEU cc_start: 0.6684 (mt) cc_final: 0.6368 (mp) outliers start: 15 outliers final: 8 residues processed: 132 average time/residue: 0.6708 time to fit residues: 93.3551 Evaluate side-chains 130 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 231 THR Chi-restraints excluded: chain R residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 141 ASN R 217 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.175535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117412 restraints weight = 9374.018| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.81 r_work: 0.2997 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9296 Z= 0.177 Angle : 0.628 9.183 12580 Z= 0.329 Chirality : 0.045 0.198 1410 Planarity : 0.005 0.115 1589 Dihedral : 5.219 32.683 1266 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.17 % Favored : 96.75 % Rotamer: Outliers : 1.61 % Allowed : 16.18 % Favored : 82.21 % 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: 1.18 (0.25), residues: 1137 helix: 2.03 (0.27), residues: 377 sheet: 1.38 (0.30), residues: 280 loop : -0.61 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 222 TYR 0.013 0.002 TYR E 103 PHE 0.017 0.002 PHE A 196 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9292) covalent geometry : angle 0.62617 (12572) SS BOND : bond 0.00692 ( 4) SS BOND : angle 1.78478 ( 8) hydrogen bonds : bond 0.04696 ( 433) hydrogen bonds : angle 4.55749 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.71 seconds wall clock time: 66 minutes 54.62 seconds (4014.62 seconds total)