Starting phenix.real_space_refine on Wed Feb 12 13:21:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wc8_37434/02_2025/8wc8_37434_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wc8_37434/02_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_37434/02_2025/8wc8_37434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wc8_37434/02_2025/8wc8_37434.map" model { file = "/net/cci-nas-00/data/ceres_data/8wc8_37434/02_2025/8wc8_37434_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wc8_37434/02_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-5592/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: 2.27 Conformation dependent library (CDL) restraints added in 1.3 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: 0.92 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: 2.45 Time building geometry restraints manager: 2.45 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: 0.820 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.750 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.640 ------------------------------------------------------------------------------- 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 8246 Z= 0.986 Angle : 0.854 38.971 11245 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 *********************** 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 : 0.821 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: 1.0808 time to fit residues: 181.2622 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 : 0.859 ------------------------------------------------------------------------------- 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 = 0.130955 restraints weight = 9554.469| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.15 r_work: 0.3385 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 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 8246 Z= 0.185 Angle : 0.529 7.309 11245 Z= 0.282 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 *********************** 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 : 0.879 Fit side-chains REVERT: A 17 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7779 (mtmt) REVERT: A 188 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8136 (mmtt) REVERT: A 237 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7956 (mm) REVERT: A 356 ARG cc_start: 0.7846 (mtm110) cc_final: 0.7634 (mtm-85) REVERT: B 52 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8307 (ptm160) REVERT: R 105 MET cc_start: 0.8515 (ttp) cc_final: 0.8255 (ttt) REVERT: R 218 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7434 (pttp) REVERT: R 290 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8039 (tp) REVERT: S 38 ARG cc_start: 0.8039 (mtm180) cc_final: 0.7836 (mtm180) REVERT: S 93 MET cc_start: 0.7429 (mmm) cc_final: 0.7217 (tpp) outliers start: 17 outliers final: 7 residues processed: 140 average time/residue: 1.2057 time to fit residues: 179.3344 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 : 0.927 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 5.9990 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: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.163724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128386 restraints weight = 9570.000| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.97 r_work: 0.3342 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8246 Z= 0.257 Angle : 0.540 7.119 11245 Z= 0.290 Chirality : 0.043 0.188 1310 Planarity : 0.005 0.060 1417 Dihedral : 4.223 22.812 1178 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.61 % Allowed : 14.36 % Favored : 83.03 % 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 197 PHE 0.015 0.001 PHE A 189 TYR 0.013 0.001 TYR A 30 ARG 0.006 0.001 ARG R 212 *********************** 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 : 0.907 Fit side-chains REVERT: A 17 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7784 (mtmt) REVERT: B 52 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8429 (ptm160) REVERT: R 65 MET cc_start: 0.8724 (ttp) cc_final: 0.8450 (ttp) REVERT: R 105 MET cc_start: 0.8528 (ttp) cc_final: 0.8301 (ttt) REVERT: R 196 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6730 (mpt) REVERT: R 218 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7416 (pttp) REVERT: S 38 ARG cc_start: 0.8124 (mtm180) cc_final: 0.7895 (ttm170) outliers start: 20 outliers final: 7 residues processed: 135 average time/residue: 1.1985 time to fit residues: 171.9808 Evaluate side-chains 128 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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: 0.5980 chunk 66 optimal weight: 0.4980 chunk 44 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.167668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128198 restraints weight = 9547.005| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.16 r_work: 0.3336 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 8246 Z= 0.154 Angle : 0.485 7.021 11245 Z= 0.261 Chirality : 0.041 0.167 1310 Planarity : 0.004 0.056 1417 Dihedral : 4.004 20.956 1178 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.26 % Allowed : 15.93 % Favored : 80.81 % 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: 1.05 (0.26), residues: 1079 helix: 2.64 (0.26), residues: 373 sheet: 0.42 (0.33), residues: 248 loop : -0.81 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.012 0.001 TYR S 190 ARG 0.006 0.000 ARG R 212 *********************** 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 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.961 Fit side-chains REVERT: A 17 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7677 (mtmt) REVERT: B 52 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8333 (ptm160) REVERT: B 155 ASN cc_start: 0.8492 (t0) cc_final: 0.8143 (t0) REVERT: R 123 TYR cc_start: 0.8331 (m-80) cc_final: 0.8126 (m-80) REVERT: R 158 MET cc_start: 0.7383 (ttt) cc_final: 0.6876 (ttm) REVERT: R 196 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6530 (mpt) REVERT: R 218 LYS cc_start: 0.8003 (ttpp) cc_final: 0.7272 (pttp) REVERT: R 290 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (tp) REVERT: S 38 ARG cc_start: 0.8063 (mtm180) cc_final: 0.7799 (mtm180) REVERT: S 59 TYR cc_start: 0.8428 (m-10) cc_final: 0.8160 (m-10) outliers start: 25 outliers final: 8 residues processed: 145 average time/residue: 1.1523 time to fit residues: 177.8317 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 : 1.129 ------------------------------------------------------------------------------- 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 69 THR 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: 2.9990 chunk 4 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130370 restraints weight = 9511.565| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.09 r_work: 0.3395 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8246 Z= 0.160 Angle : 0.490 7.074 11245 Z= 0.264 Chirality : 0.041 0.174 1310 Planarity : 0.004 0.058 1417 Dihedral : 3.938 21.101 1178 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.52 % Allowed : 17.75 % Favored : 78.72 % 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: 1.03 (0.26), residues: 1079 helix: 2.53 (0.26), residues: 379 sheet: 0.37 (0.33), residues: 252 loop : -0.76 (0.29), residues: 448 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 0.014 0.001 PHE A 189 TYR 0.012 0.001 TYR R 79 ARG 0.010 0.000 ARG B 134 *********************** 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 159 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.844 Fit side-chains REVERT: A 17 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7640 (mtmt) REVERT: B 52 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8352 (ptm160) REVERT: B 155 ASN cc_start: 0.8445 (t0) cc_final: 0.8096 (t0) REVERT: R 48 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6874 (mp) REVERT: R 123 TYR cc_start: 0.8299 (m-80) cc_final: 0.8076 (m-80) REVERT: R 158 MET cc_start: 0.7373 (ttt) cc_final: 0.6863 (ttm) REVERT: R 196 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6425 (mpt) REVERT: R 218 LYS cc_start: 0.7999 (ttpp) cc_final: 0.7267 (pttp) REVERT: S 38 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7808 (mtm180) REVERT: S 59 TYR cc_start: 0.8385 (m-10) cc_final: 0.8115 (m-10) outliers start: 27 outliers final: 14 residues processed: 146 average time/residue: 1.1767 time to fit residues: 182.6402 Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER 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 156 GLN 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 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: 0.5980 chunk 70 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 2 optimal weight: 0.0970 chunk 101 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 B 220 GLN S 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133815 restraints weight = 9575.577| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.93 r_work: 0.3408 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8246 Z= 0.163 Angle : 0.495 7.138 11245 Z= 0.267 Chirality : 0.041 0.184 1310 Planarity : 0.005 0.061 1417 Dihedral : 3.921 21.155 1178 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.74 % Allowed : 19.19 % Favored : 78.07 % 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: 0.98 (0.26), residues: 1079 helix: 2.49 (0.26), residues: 380 sheet: 0.34 (0.32), residues: 252 loop : -0.78 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.014 0.001 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.012 0.001 TYR A 30 ARG 0.013 0.001 ARG B 134 *********************** 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: 21 poor density : 134 time to evaluate : 0.947 Fit side-chains REVERT: A 17 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7649 (mtmt) REVERT: B 52 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8366 (ptm160) REVERT: B 155 ASN cc_start: 0.8432 (t0) cc_final: 0.8087 (t0) REVERT: B 186 ASP cc_start: 0.8387 (p0) cc_final: 0.8083 (p0) REVERT: R 48 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6853 (mp) REVERT: R 123 TYR cc_start: 0.8266 (m-80) cc_final: 0.8040 (m-80) REVERT: R 196 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6308 (mpt) REVERT: R 218 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7271 (pttp) REVERT: R 290 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8029 (tp) REVERT: S 59 TYR cc_start: 0.8391 (m-10) cc_final: 0.8149 (m-10) REVERT: S 113 GLN cc_start: 0.8308 (pt0) cc_final: 0.8092 (mp10) outliers start: 21 outliers final: 11 residues processed: 145 average time/residue: 1.1544 time to fit residues: 178.1338 Evaluate side-chains 136 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 52 ARG Chi-restraints excluded: chain B residue 234 PHE 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 138 ILE Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain S residue 204 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 B 183 HIS B 220 GLN ** S 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.164522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131576 restraints weight = 9591.751| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.87 r_work: 0.3376 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8246 Z= 0.228 Angle : 0.549 7.268 11245 Z= 0.292 Chirality : 0.043 0.198 1310 Planarity : 0.005 0.065 1417 Dihedral : 4.069 22.477 1178 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.52 % Allowed : 19.58 % Favored : 76.89 % 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: 0.93 (0.26), residues: 1079 helix: 2.48 (0.26), residues: 377 sheet: 0.14 (0.32), residues: 263 loop : -0.72 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.015 0.001 HIS B 225 PHE 0.022 0.001 PHE R 307 TYR 0.013 0.001 TYR R 79 ARG 0.008 0.000 ARG B 134 *********************** 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 157 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.903 Fit side-chains REVERT: A 17 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7722 (mtmt) REVERT: A 188 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7849 (mmtt) REVERT: B 52 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.8401 (ptm160) REVERT: B 186 ASP cc_start: 0.8467 (p0) cc_final: 0.8172 (p0) REVERT: R 48 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7036 (mp) REVERT: R 123 TYR cc_start: 0.8403 (m-80) cc_final: 0.8201 (m-80) REVERT: R 196 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6451 (mpt) REVERT: R 218 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7399 (pttp) REVERT: R 290 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8144 (tp) REVERT: S 46 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7593 (tp30) outliers start: 27 outliers final: 14 residues processed: 146 average time/residue: 1.1381 time to fit residues: 177.1810 Evaluate side-chains 146 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER 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 234 PHE 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 46 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 84 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 B 183 HIS B 220 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 = 0.3888 r_free = 0.3888 target = 0.165110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131233 restraints weight = 9630.172| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.87 r_work: 0.3387 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8246 Z= 0.192 Angle : 0.527 8.608 11245 Z= 0.282 Chirality : 0.042 0.209 1310 Planarity : 0.005 0.067 1417 Dihedral : 4.026 20.879 1178 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.00 % Allowed : 20.50 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.26), residues: 1079 helix: 2.46 (0.26), residues: 378 sheet: 0.12 (0.32), residues: 252 loop : -0.80 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.014 0.001 HIS B 225 PHE 0.019 0.001 PHE R 307 TYR 0.012 0.001 TYR A 30 ARG 0.007 0.000 ARG B 134 *********************** 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 155 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.888 Fit side-chains REVERT: A 17 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7645 (mtmt) REVERT: B 52 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8385 (ptm160) REVERT: B 96 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8363 (mpp80) REVERT: B 186 ASP cc_start: 0.8385 (p0) cc_final: 0.8048 (p0) REVERT: R 48 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6875 (mp) REVERT: R 123 TYR cc_start: 0.8372 (m-80) cc_final: 0.8113 (m-80) REVERT: R 196 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6282 (mpt) REVERT: R 218 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7344 (pttp) REVERT: R 290 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8062 (tp) REVERT: S 18 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7101 (ptp-110) outliers start: 23 outliers final: 14 residues processed: 148 average time/residue: 1.1135 time to fit residues: 175.7345 Evaluate side-chains 141 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 243 ILE 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 234 PHE 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 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: 0.9990 chunk 104 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 213 GLN A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 220 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 = 0.3886 r_free = 0.3886 target = 0.164768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131921 restraints weight = 9775.335| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.88 r_work: 0.3383 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8246 Z= 0.202 Angle : 0.531 8.629 11245 Z= 0.284 Chirality : 0.043 0.216 1310 Planarity : 0.005 0.069 1417 Dihedral : 4.046 21.181 1178 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.74 % Allowed : 20.76 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.26), residues: 1079 helix: 2.44 (0.26), residues: 379 sheet: 0.07 (0.32), residues: 255 loop : -0.75 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.012 0.001 HIS B 225 PHE 0.018 0.001 PHE R 307 TYR 0.015 0.001 TYR R 79 ARG 0.007 0.000 ARG R 212 *********************** 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 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.822 Fit side-chains REVERT: A 17 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7661 (mtmt) REVERT: B 52 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8403 (ptm160) REVERT: B 186 ASP cc_start: 0.8391 (p0) cc_final: 0.8059 (p0) REVERT: R 48 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6859 (mp) REVERT: R 123 TYR cc_start: 0.8381 (m-80) cc_final: 0.8113 (m-80) REVERT: R 196 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6270 (mpt) REVERT: R 218 LYS cc_start: 0.8065 (ttpp) cc_final: 0.7343 (pttp) REVERT: R 290 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8070 (tp) REVERT: S 245 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7633 (mp) outliers start: 21 outliers final: 17 residues processed: 142 average time/residue: 1.0664 time to fit residues: 162.1859 Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER 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 234 PHE 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 271 THR Chi-restraints excluded: chain R residue 277 LEU 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 194 ASN 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: 0.7980 chunk 82 optimal weight: 0.0030 chunk 34 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 0.0040 chunk 78 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- 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 183 HIS B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.133209 restraints weight = 9543.622| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.87 r_work: 0.3414 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 8246 Z= 0.152 Angle : 0.518 8.426 11245 Z= 0.277 Chirality : 0.042 0.233 1310 Planarity : 0.005 0.070 1417 Dihedral : 4.000 19.420 1178 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.74 % Allowed : 21.15 % 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: 0.88 (0.26), residues: 1079 helix: 2.47 (0.26), residues: 379 sheet: 0.02 (0.31), residues: 256 loop : -0.73 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.011 0.001 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.011 0.001 TYR S 190 ARG 0.009 0.001 ARG S 18 ********************** 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 148 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.826 Fit side-chains REVERT: A 17 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7652 (mtmt) REVERT: A 188 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7847 (mmtt) REVERT: A 213 GLN cc_start: 0.8560 (mt0) cc_final: 0.8351 (mt0) REVERT: B 52 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8362 (ptm160) REVERT: B 186 ASP cc_start: 0.8340 (p0) cc_final: 0.8038 (p0) REVERT: R 123 TYR cc_start: 0.8312 (m-80) cc_final: 0.8054 (m-80) REVERT: R 196 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6261 (mpt) REVERT: R 218 LYS cc_start: 0.8067 (ttpp) cc_final: 0.7351 (pttp) REVERT: R 290 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8029 (tp) REVERT: S 245 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7620 (mp) outliers start: 21 outliers final: 13 residues processed: 141 average time/residue: 1.0906 time to fit residues: 164.4053 Evaluate side-chains 139 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 52 ARG 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 277 LEU 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: 5.9990 chunk 98 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 183 HIS B 220 GLN R 41 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 = 0.3895 r_free = 0.3895 target = 0.165744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131528 restraints weight = 9698.167| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.90 r_work: 0.3376 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8246 Z= 0.193 Angle : 0.537 8.542 11245 Z= 0.286 Chirality : 0.043 0.232 1310 Planarity : 0.005 0.069 1417 Dihedral : 4.047 20.692 1178 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.61 % Allowed : 21.67 % 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: 0.85 (0.26), residues: 1079 helix: 2.45 (0.26), residues: 379 sheet: -0.05 (0.31), residues: 260 loop : -0.72 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.011 0.001 HIS B 225 PHE 0.015 0.001 PHE A 189 TYR 0.015 0.001 TYR R 79 ARG 0.015 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6483.09 seconds wall clock time: 114 minutes 59.72 seconds (6899.72 seconds total)