Starting phenix.real_space_refine on Fri Jun 6 15:59:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc8_37434/06_2025/8wc8_37434_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc8_37434/06_2025/8wc8_37434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wc8_37434/06_2025/8wc8_37434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc8_37434/06_2025/8wc8_37434.map" model { file = "/net/cci-nas-00/data/ceres_data/8wc8_37434/06_2025/8wc8_37434_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc8_37434/06_2025/8wc8_37434_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.098 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 55 5.16 5 C 5174 2.51 5 N 1372 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8062 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1695 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 218} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 7, 'PHE:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2333 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 119 Chain: "R" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2030 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "S" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1666 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "Y" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 328 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'VMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.03, per 1000 atoms: 0.62 Number of scatterers: 8062 At special positions: 0 Unit cell: (86.92, 117.26, 121.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 55 16.00 O 1460 8.00 N 1372 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.00 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " 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: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 38.5% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.563A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.655A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.932A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.990A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.280A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 16 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.585A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 51 Processing helix chain 'R' and resid 52 through 55 removed outlier: 3.772A pdb=" N HIS R 55 " --> pdb=" O LYS R 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 52 through 55' Processing helix chain 'R' and resid 56 through 86 removed outlier: 3.933A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE R 62 " --> pdb=" O THR R 58 " (cutoff:3.500A) Proline residue: R 78 - end of helix Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.543A pdb=" N ASP R 127 " --> pdb=" O TYR R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix removed outlier: 3.534A pdb=" N LEU R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 179 Processing helix chain 'R' and resid 187 through 200 removed outlier: 3.722A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 227 Processing helix chain 'R' and resid 248 through 277 removed outlier: 4.051A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 305 removed outlier: 3.679A pdb=" N GLY R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 315 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'Y' and resid 16 through 24 Processing helix chain 'Y' and resid 29 through 45 Processing helix chain 'Y' and resid 46 through 48 No H-bonds generated for 'chain 'Y' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.170A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.636A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.011A 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: 4.327A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.626A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.250A 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: 6.627A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.454A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.634A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 5.414A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.434A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.631A pdb=" N ASN S 194 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.41: 3495 1.41 - 1.65: 4668 1.65 - 1.89: 81 1.89 - 2.13: 1 2.13 - 2.37: 1 Bond restraints: 8246 Sorted by residual: bond pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 1.331 2.375 -1.044 1.46e-02 4.69e+03 5.12e+03 bond pdb=" C LEU R 289 " pdb=" O LEU R 289 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.17e-02 7.31e+03 3.33e+01 bond pdb=" C TYR R 294 " pdb=" O TYR R 294 " ideal model delta sigma weight residual 1.237 1.170 0.067 1.17e-02 7.31e+03 3.26e+01 bond pdb=" C PHE R 292 " pdb=" O PHE R 292 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.16e-02 7.43e+03 2.94e+01 bond pdb=" C PHE R 185 " pdb=" O PHE R 185 " ideal model delta sigma weight residual 1.234 1.170 0.064 1.22e-02 6.72e+03 2.75e+01 ... (remaining 8241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.79: 11237 7.79 - 15.59: 6 15.59 - 23.38: 0 23.38 - 31.18: 0 31.18 - 38.97: 2 Bond angle restraints: 11245 Sorted by residual: angle pdb=" O GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 123.05 87.02 36.03 1.03e+00 9.43e-01 1.22e+03 angle pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta sigma weight residual 121.41 160.38 -38.97 1.96e+00 2.60e-01 3.95e+02 angle pdb=" N PRO S 236 " pdb=" CA PRO S 236 " pdb=" C PRO S 236 " ideal model delta sigma weight residual 112.47 97.97 14.50 2.06e+00 2.36e-01 4.96e+01 angle pdb=" C THR R 37 " pdb=" CA THR R 37 " pdb=" CB THR R 37 " ideal model delta sigma weight residual 110.96 100.82 10.14 1.54e+00 4.22e-01 4.33e+01 angle pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " ideal model delta sigma weight residual 114.28 123.01 -8.73 1.56e+00 4.11e-01 3.13e+01 ... (remaining 11240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4384 17.31 - 34.62: 315 34.62 - 51.93: 53 51.93 - 69.23: 5 69.23 - 86.54: 5 Dihedral angle restraints: 4762 sinusoidal: 1563 harmonic: 3199 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual -86.00 -162.39 76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" CA GLY A 320 " pdb=" C GLY A 320 " pdb=" N GLY A 322 " pdb=" CA GLY A 322 " ideal model delta harmonic sigma weight residual -180.00 -148.86 -31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" C PHE R 292 " pdb=" N PHE R 292 " pdb=" CA PHE R 292 " pdb=" CB PHE R 292 " ideal model delta harmonic sigma weight residual -122.60 -136.35 13.75 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 4759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 1293 0.136 - 0.273: 10 0.273 - 0.409: 1 0.409 - 0.546: 2 0.546 - 0.682: 4 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA LEU R 289 " pdb=" N LEU R 289 " pdb=" C LEU R 289 " pdb=" CB LEU R 289 " both_signs ideal model delta sigma weight residual False 2.51 1.83 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PHE R 292 " pdb=" N PHE R 292 " pdb=" C PHE R 292 " pdb=" CB PHE R 292 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA TRP R 291 " pdb=" N TRP R 291 " pdb=" C TRP R 291 " pdb=" CB TRP R 291 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 1307 not shown) Planarity restraints: 1417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 320 " -0.146 2.00e-02 2.50e+03 2.03e-01 4.13e+02 pdb=" C GLY A 320 " 0.347 2.00e-02 2.50e+03 pdb=" O GLY A 320 " -0.142 2.00e-02 2.50e+03 pdb=" N GLY A 322 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL S 199 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO S 200 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO S 200 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO S 200 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 56 " -0.053 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO R 57 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO R 57 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 57 " -0.044 5.00e-02 4.00e+02 ... (remaining 1414 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1841 2.78 - 3.31: 7558 3.31 - 3.84: 13764 3.84 - 4.37: 15780 4.37 - 4.90: 28412 Nonbonded interactions: 67355 Sorted by model distance: nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.252 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.258 3.040 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.288 3.040 nonbonded pdb=" O SER S 52 " pdb=" NH1 ARG S 72 " model vdw 2.295 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.297 3.040 ... (remaining 67350 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.013 1.044 8248 Z= 0.845 Angle : 0.854 38.971 11249 Z= 0.555 Chirality : 0.060 0.682 1310 Planarity : 0.008 0.203 1417 Dihedral : 12.531 86.543 2692 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.26 % Allowed : 0.26 % Favored : 99.48 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1077 helix: 2.57 (0.26), residues: 362 sheet: 0.07 (0.31), residues: 266 loop : -0.50 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 291 HIS 0.004 0.001 HIS B 225 PHE 0.036 0.002 PHE R 292 TYR 0.030 0.002 TYR S 235 ARG 0.008 0.000 ARG R 212 Details of bonding type rmsd hydrogen bonds : bond 0.12894 ( 426) hydrogen bonds : angle 5.79398 ( 1236) SS BOND : bond 0.02097 ( 2) SS BOND : angle 1.90567 ( 4) covalent geometry : bond 0.01265 ( 8246) covalent geometry : angle 0.85384 (11245) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.920 Fit side-chains REVERT: A 17 LYS cc_start: 0.7752 (mtmt) cc_final: 0.7537 (mtmt) REVERT: R 218 LYS cc_start: 0.7698 (ttpp) cc_final: 0.7218 (pttp) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 1.0470 time to fit residues: 175.4704 Evaluate side-chains 118 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 259 GLN S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.130954 restraints weight = 9554.540| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.15 r_work: 0.3373 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8248 Z= 0.126 Angle : 0.529 7.308 11249 Z= 0.283 Chirality : 0.042 0.167 1310 Planarity : 0.005 0.066 1417 Dihedral : 4.188 24.664 1178 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.22 % Allowed : 11.36 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1079 helix: 2.71 (0.26), residues: 368 sheet: 0.33 (0.32), residues: 255 loop : -0.68 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.004 0.001 HIS R 113 PHE 0.016 0.001 PHE S 29 TYR 0.012 0.001 TYR S 190 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 426) hydrogen bonds : angle 4.80790 ( 1236) SS BOND : bond 0.00443 ( 2) SS BOND : angle 1.11921 ( 4) covalent geometry : bond 0.00282 ( 8246) covalent geometry : angle 0.52878 (11245) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.838 Fit side-chains REVERT: A 17 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7764 (mtmt) REVERT: A 188 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8131 (mmtt) REVERT: A 237 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7938 (mm) REVERT: A 356 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7622 (mtm-85) REVERT: B 52 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8292 (ptm160) REVERT: R 105 MET cc_start: 0.8512 (ttp) cc_final: 0.8253 (ttt) REVERT: R 218 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7418 (pttp) REVERT: R 290 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8038 (tp) REVERT: S 38 ARG cc_start: 0.8031 (mtm180) cc_final: 0.7824 (mtm180) REVERT: S 93 MET cc_start: 0.7413 (mmm) cc_final: 0.7200 (tpp) outliers start: 17 outliers final: 7 residues processed: 140 average time/residue: 1.1604 time to fit residues: 172.6501 Evaluate side-chains 133 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain Y residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 259 GLN R 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.163753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128443 restraints weight = 9571.197| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.97 r_work: 0.3342 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8248 Z= 0.163 Angle : 0.538 7.115 11249 Z= 0.289 Chirality : 0.043 0.188 1310 Planarity : 0.005 0.060 1417 Dihedral : 4.223 22.838 1178 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.61 % Allowed : 14.62 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1079 helix: 2.57 (0.26), residues: 371 sheet: 0.20 (0.32), residues: 266 loop : -0.78 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.005 0.001 HIS A 324 PHE 0.015 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.006 0.001 ARG R 212 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 426) hydrogen bonds : angle 4.79800 ( 1236) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.05411 ( 4) covalent geometry : bond 0.00384 ( 8246) covalent geometry : angle 0.53783 (11245) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.933 Fit side-chains REVERT: A 17 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7777 (mtmt) REVERT: B 52 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8387 (ptm160) REVERT: R 65 MET cc_start: 0.8711 (ttp) cc_final: 0.8434 (ttp) REVERT: R 105 MET cc_start: 0.8527 (ttp) cc_final: 0.8301 (ttt) REVERT: R 196 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6724 (mpt) REVERT: R 218 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7415 (pttp) REVERT: S 38 ARG cc_start: 0.8121 (mtm180) cc_final: 0.7893 (ttm170) outliers start: 20 outliers final: 7 residues processed: 135 average time/residue: 1.2121 time to fit residues: 174.1223 Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 0.0270 chunk 66 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.133316 restraints weight = 9551.686| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.96 r_work: 0.3371 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8248 Z= 0.111 Angle : 0.492 7.010 11249 Z= 0.264 Chirality : 0.041 0.167 1310 Planarity : 0.004 0.055 1417 Dihedral : 4.040 21.249 1178 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.26 % Allowed : 16.06 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1079 helix: 2.62 (0.26), residues: 373 sheet: 0.40 (0.33), residues: 248 loop : -0.82 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.006 0.000 ARG R 212 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 426) hydrogen bonds : angle 4.61148 ( 1236) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.58248 ( 4) covalent geometry : bond 0.00254 ( 8246) covalent geometry : angle 0.49157 (11245) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.905 Fit side-chains REVERT: A 17 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7737 (mtmt) REVERT: B 52 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8332 (ptm160) REVERT: R 158 MET cc_start: 0.7421 (ttt) cc_final: 0.6907 (ttm) REVERT: R 196 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6680 (mpt) REVERT: R 218 LYS cc_start: 0.8011 (ttpp) cc_final: 0.7305 (pttp) REVERT: R 290 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8049 (tp) REVERT: S 38 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7820 (mtm180) REVERT: S 59 TYR cc_start: 0.8388 (m-10) cc_final: 0.8141 (m-10) REVERT: S 113 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8115 (mm-40) outliers start: 25 outliers final: 9 residues processed: 147 average time/residue: 1.1158 time to fit residues: 175.0210 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 9 optimal weight: 0.0870 chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 7 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 237 ASN R 59 ASN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.167501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132995 restraints weight = 9534.834| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.96 r_work: 0.3400 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8248 Z= 0.104 Angle : 0.496 7.024 11249 Z= 0.265 Chirality : 0.041 0.178 1310 Planarity : 0.004 0.057 1417 Dihedral : 3.931 20.591 1178 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.13 % Allowed : 18.54 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1079 helix: 2.50 (0.26), residues: 380 sheet: 0.42 (0.33), residues: 246 loop : -0.82 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.012 0.001 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR R 79 ARG 0.011 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 426) hydrogen bonds : angle 4.52908 ( 1236) SS BOND : bond 0.00259 ( 2) SS BOND : angle 0.45297 ( 4) covalent geometry : bond 0.00227 ( 8246) covalent geometry : angle 0.49588 (11245) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.899 Fit side-chains REVERT: A 17 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7739 (mtmt) REVERT: B 52 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8357 (ptm160) REVERT: B 155 ASN cc_start: 0.8509 (t0) cc_final: 0.8196 (t0) REVERT: R 48 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.7023 (mp) REVERT: R 123 TYR cc_start: 0.8401 (m-80) cc_final: 0.8167 (m-80) REVERT: R 158 MET cc_start: 0.7394 (ttt) cc_final: 0.6863 (ttm) REVERT: R 196 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6525 (mpt) REVERT: R 218 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7346 (pttp) REVERT: R 290 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8066 (tp) REVERT: S 38 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7846 (mtm180) REVERT: S 59 TYR cc_start: 0.8407 (m-10) cc_final: 0.8134 (m-10) REVERT: S 113 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8094 (mm-40) outliers start: 24 outliers final: 11 residues processed: 149 average time/residue: 1.1488 time to fit residues: 182.0083 Evaluate side-chains 138 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 213 GLN A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 GLN S 39 GLN S 194 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.160402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126071 restraints weight = 9535.423| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.96 r_work: 0.3305 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8248 Z= 0.222 Angle : 0.593 7.461 11249 Z= 0.319 Chirality : 0.045 0.200 1310 Planarity : 0.005 0.064 1417 Dihedral : 4.341 25.841 1178 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.39 % Allowed : 18.80 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1079 helix: 2.27 (0.26), residues: 378 sheet: 0.02 (0.31), residues: 266 loop : -0.81 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 291 HIS 0.018 0.002 HIS B 225 PHE 0.016 0.002 PHE S 68 TYR 0.014 0.002 TYR A 30 ARG 0.010 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 426) hydrogen bonds : angle 4.87879 ( 1236) SS BOND : bond 0.00557 ( 2) SS BOND : angle 0.86728 ( 4) covalent geometry : bond 0.00529 ( 8246) covalent geometry : angle 0.59291 (11245) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.972 Fit side-chains REVERT: A 17 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7730 (mtmt) REVERT: B 186 ASP cc_start: 0.8468 (p0) cc_final: 0.8091 (p0) REVERT: R 196 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6517 (mpt) REVERT: R 218 LYS cc_start: 0.8128 (ttpp) cc_final: 0.7394 (pttp) REVERT: S 38 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7888 (ttm170) REVERT: S 113 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8092 (mp10) REVERT: S 245 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7677 (mp) outliers start: 26 outliers final: 13 residues processed: 144 average time/residue: 1.0606 time to fit residues: 162.8919 Evaluate side-chains 140 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 0.0570 chunk 94 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 171 ASN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.158073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123089 restraints weight = 9575.918| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.98 r_work: 0.3276 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8248 Z= 0.247 Angle : 0.618 8.445 11249 Z= 0.333 Chirality : 0.046 0.229 1310 Planarity : 0.005 0.066 1417 Dihedral : 4.535 23.378 1178 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.92 % Allowed : 18.93 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1079 helix: 2.10 (0.26), residues: 375 sheet: -0.33 (0.30), residues: 282 loop : -0.79 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 211 HIS 0.016 0.002 HIS B 225 PHE 0.020 0.002 PHE S 68 TYR 0.015 0.002 TYR R 79 ARG 0.009 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 426) hydrogen bonds : angle 5.02974 ( 1236) SS BOND : bond 0.00479 ( 2) SS BOND : angle 0.73836 ( 4) covalent geometry : bond 0.00592 ( 8246) covalent geometry : angle 0.61809 (11245) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.836 Fit side-chains REVERT: A 17 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7284 (mtmt) REVERT: A 188 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7873 (mmtt) REVERT: R 196 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6076 (mpt) REVERT: R 218 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7170 (pttp) REVERT: R 290 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7997 (tp) REVERT: S 38 ARG cc_start: 0.7998 (mtm180) cc_final: 0.7438 (mtp85) REVERT: S 113 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: S 245 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7386 (mp) outliers start: 30 outliers final: 16 residues processed: 151 average time/residue: 1.1006 time to fit residues: 177.1406 Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 113 GLN Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 15 optimal weight: 0.0570 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 171 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.162735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.128493 restraints weight = 9633.810| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.97 r_work: 0.3352 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8248 Z= 0.122 Angle : 0.533 7.335 11249 Z= 0.287 Chirality : 0.043 0.227 1310 Planarity : 0.005 0.070 1417 Dihedral : 4.230 20.813 1178 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.39 % Allowed : 20.50 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1079 helix: 2.23 (0.26), residues: 378 sheet: -0.02 (0.31), residues: 255 loop : -0.83 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.013 0.001 HIS B 225 PHE 0.018 0.001 PHE S 68 TYR 0.012 0.001 TYR S 190 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 426) hydrogen bonds : angle 4.72493 ( 1236) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.54506 ( 4) covalent geometry : bond 0.00277 ( 8246) covalent geometry : angle 0.53276 (11245) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.907 Fit side-chains REVERT: A 17 LYS cc_start: 0.7461 (mtmt) cc_final: 0.7209 (mtmt) REVERT: A 188 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7919 (mmtt) REVERT: A 213 GLN cc_start: 0.8453 (mt0) cc_final: 0.8231 (mt0) REVERT: B 124 TYR cc_start: 0.8447 (m-80) cc_final: 0.8200 (m-80) REVERT: B 186 ASP cc_start: 0.8212 (p0) cc_final: 0.7772 (p0) REVERT: R 123 TYR cc_start: 0.8228 (m-80) cc_final: 0.7930 (m-80) REVERT: R 196 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.5956 (mpt) REVERT: R 218 LYS cc_start: 0.7882 (ttpp) cc_final: 0.7140 (pttp) REVERT: R 290 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7832 (tp) REVERT: S 60 TYR cc_start: 0.8476 (m-80) cc_final: 0.8275 (m-80) REVERT: Y 31 SER cc_start: 0.8433 (t) cc_final: 0.7834 (m) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 1.0736 time to fit residues: 169.6523 Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 41 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.162249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.127711 restraints weight = 9748.657| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.99 r_work: 0.3344 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8248 Z= 0.137 Angle : 0.547 7.723 11249 Z= 0.294 Chirality : 0.043 0.224 1310 Planarity : 0.005 0.068 1417 Dihedral : 4.219 20.718 1178 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.74 % Allowed : 21.28 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.26), residues: 1079 helix: 2.27 (0.26), residues: 378 sheet: -0.08 (0.31), residues: 260 loop : -0.81 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.015 0.001 HIS B 225 PHE 0.020 0.001 PHE S 68 TYR 0.014 0.001 TYR R 79 ARG 0.008 0.001 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 426) hydrogen bonds : angle 4.72315 ( 1236) SS BOND : bond 0.00345 ( 2) SS BOND : angle 0.47259 ( 4) covalent geometry : bond 0.00319 ( 8246) covalent geometry : angle 0.54736 (11245) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.856 Fit side-chains REVERT: A 17 LYS cc_start: 0.7510 (mtmt) cc_final: 0.7231 (mtmt) REVERT: A 53 MET cc_start: 0.7096 (mtp) cc_final: 0.6777 (mtt) REVERT: A 188 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7885 (mmtt) REVERT: A 213 GLN cc_start: 0.8469 (mt0) cc_final: 0.8234 (mt0) REVERT: B 186 ASP cc_start: 0.8232 (p0) cc_final: 0.7742 (p0) REVERT: R 123 TYR cc_start: 0.8265 (m-80) cc_final: 0.7925 (m-80) REVERT: R 196 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5926 (mpt) REVERT: R 218 LYS cc_start: 0.7897 (ttpp) cc_final: 0.7148 (pttp) REVERT: R 290 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7853 (tp) REVERT: S 245 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7412 (mp) outliers start: 21 outliers final: 11 residues processed: 137 average time/residue: 1.0645 time to fit residues: 155.8684 Evaluate side-chains 139 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 0.0980 chunk 82 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 78 optimal weight: 0.0070 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 171 ASN S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.165267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130856 restraints weight = 9503.968| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.96 r_work: 0.3398 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 8248 Z= 0.109 Angle : 0.519 7.898 11249 Z= 0.279 Chirality : 0.042 0.216 1310 Planarity : 0.005 0.071 1417 Dihedral : 4.079 19.390 1178 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.87 % Allowed : 21.41 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1079 helix: 2.31 (0.26), residues: 379 sheet: -0.03 (0.31), residues: 255 loop : -0.81 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.010 0.001 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.009 0.001 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 426) hydrogen bonds : angle 4.61209 ( 1236) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.27265 ( 4) covalent geometry : bond 0.00247 ( 8246) covalent geometry : angle 0.51892 (11245) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2158 Ramachandran restraints generated. 1079 Oldfield, 0 Emsley, 1079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.935 Fit side-chains REVERT: A 17 LYS cc_start: 0.7475 (mtmt) cc_final: 0.7188 (mtmt) REVERT: A 53 MET cc_start: 0.7176 (mtp) cc_final: 0.6858 (mtt) REVERT: A 188 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7874 (mmtt) REVERT: A 213 GLN cc_start: 0.8444 (mt0) cc_final: 0.8197 (mt0) REVERT: B 96 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8138 (mpp80) REVERT: B 124 TYR cc_start: 0.8341 (m-80) cc_final: 0.8124 (m-80) REVERT: B 186 ASP cc_start: 0.8128 (p0) cc_final: 0.7694 (p0) REVERT: R 123 TYR cc_start: 0.8200 (m-80) cc_final: 0.7894 (m-80) REVERT: R 196 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.5847 (mpt) REVERT: R 218 LYS cc_start: 0.7866 (ttpp) cc_final: 0.7117 (pttp) REVERT: R 290 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7835 (tp) REVERT: S 245 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7426 (mp) outliers start: 22 outliers final: 12 residues processed: 143 average time/residue: 1.0181 time to fit residues: 155.9129 Evaluate side-chains 141 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain S residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 0.0170 chunk 98 optimal weight: 0.0170 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.1980 chunk 35 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134023 restraints weight = 9680.965| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.95 r_work: 0.3438 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 8248 Z= 0.100 Angle : 0.508 8.101 11249 Z= 0.274 Chirality : 0.041 0.211 1310 Planarity : 0.005 0.078 1417 Dihedral : 3.934 20.117 1178 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.09 % Allowed : 22.32 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1079 helix: 2.39 (0.26), residues: 377 sheet: 0.24 (0.32), residues: 243 loop : -0.89 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 211 HIS 0.008 0.001 HIS B 225 PHE 0.021 0.001 PHE R 307 TYR 0.015 0.001 TYR R 79 ARG 0.008 0.001 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03050 ( 426) hydrogen bonds : angle 4.50478 ( 1236) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.27745 ( 4) covalent geometry : bond 0.00219 ( 8246) covalent geometry : angle 0.50773 (11245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6686.06 seconds wall clock time: 115 minutes 13.19 seconds (6913.19 seconds total)