Starting phenix.real_space_refine on Wed Sep 17 11:22:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d0a_46448/09_2025/9d0a_46448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d0a_46448/09_2025/9d0a_46448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d0a_46448/09_2025/9d0a_46448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d0a_46448/09_2025/9d0a_46448.map" model { file = "/net/cci-nas-00/data/ceres_data/9d0a_46448/09_2025/9d0a_46448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d0a_46448/09_2025/9d0a_46448.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5398 2.51 5 N 1413 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8416 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2289 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 297} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 236 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "E" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1766 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2380 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1745 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 208} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.16, per 1000 atoms: 0.26 Number of scatterers: 8416 At special positions: 0 Unit cell: (86.48, 122.36, 135.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1550 8.00 N 1413 7.00 C 5398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.45 Conformation dependent library (CDL) restraints added in 476.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2018 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.6% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 64 through 71 removed outlier: 3.985A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU R 69 " --> pdb=" O SER R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 76 Processing helix chain 'R' and resid 76 through 102 removed outlier: 3.843A pdb=" N VAL R 88 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 108 through 127 removed outlier: 3.555A pdb=" N ILE R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR R 113 " --> pdb=" O PRO R 109 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER R 124 " --> pdb=" O ALA R 120 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL R 125 " --> pdb=" O ASP R 121 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 137 Processing helix chain 'R' and resid 144 through 174 removed outlier: 3.537A pdb=" N CYS R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 186 removed outlier: 4.050A pdb=" N ARG R 185 " --> pdb=" O GLY R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 207 Processing helix chain 'R' and resid 207 through 212 removed outlier: 3.654A pdb=" N VAL R 211 " --> pdb=" O ILE R 207 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL R 212 " --> pdb=" O PRO R 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 207 through 212' Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 231 through 238 removed outlier: 3.647A pdb=" N GLY R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 251 removed outlier: 3.583A pdb=" N TYR R 242 " --> pdb=" O ASP R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 270 Processing helix chain 'R' and resid 281 through 317 removed outlier: 3.538A pdb=" N LYS R 287 " --> pdb=" O LYS R 283 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 319 through 321 No H-bonds generated for 'chain 'R' and resid 319 through 321' Processing helix chain 'R' and resid 322 through 345 removed outlier: 3.817A pdb=" N VAL R 328 " --> pdb=" O ALA R 324 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS R 331 " --> pdb=" O ILE R 327 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU R 332 " --> pdb=" O VAL R 328 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER R 333 " --> pdb=" O ALA R 329 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS R 338 " --> pdb=" O THR R 334 " (cutoff:3.500A) Proline residue: R 341 - end of helix removed outlier: 3.505A pdb=" N TYR R 345 " --> pdb=" O PRO R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 359 removed outlier: 3.943A pdb=" N ARG R 352 " --> pdb=" O SER R 348 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP R 353 " --> pdb=" O HIS R 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 34 Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.940A pdb=" N PHE A 55 " --> pdb=" O LYS A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.703A pdb=" N GLN A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 221 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.800A pdb=" N ARG A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 305 through 323 removed outlier: 4.160A pdb=" N ALA A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 363 removed outlier: 3.709A pdb=" N ILE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.752A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.734A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.494A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 3.522A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.463A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.360A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.764A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.681A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.982A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 208 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.538A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 149 removed outlier: 3.583A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 217 through 218 Processing sheet with id=AB5, first strand: chain 'A' and resid 189 through 196 removed outlier: 3.544A pdb=" N LEU A 196 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 40 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU A 42 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL A 206 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU A 44 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LYS A 41 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 43 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 226 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N PHE A 262 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 228 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASN A 264 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL A 230 " --> pdb=" O ASN A 264 " (cutoff:3.500A) 388 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2683 1.34 - 1.46: 2158 1.46 - 1.58: 3686 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8608 Sorted by residual: bond pdb=" N ASP B 38 " pdb=" CA ASP B 38 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N SER A 12 " pdb=" CA SER A 12 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ASP E 1 " pdb=" CA ASP E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N VAL G 30 " pdb=" CA VAL G 30 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N SER R 37 " pdb=" CA SER R 37 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 ... (remaining 8603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 11344 1.32 - 2.65: 268 2.65 - 3.97: 53 3.97 - 5.29: 17 5.29 - 6.61: 2 Bond angle restraints: 11684 Sorted by residual: angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" C MET E 192 " ideal model delta sigma weight residual 110.80 117.41 -6.61 2.13e+00 2.20e-01 9.64e+00 angle pdb=" CA LYS R 281 " pdb=" CB LYS R 281 " pdb=" CG LYS R 281 " ideal model delta sigma weight residual 114.10 119.03 -4.93 2.00e+00 2.50e-01 6.07e+00 angle pdb=" CA GLU R 145 " pdb=" CB GLU R 145 " pdb=" CG GLU R 145 " ideal model delta sigma weight residual 114.10 118.97 -4.87 2.00e+00 2.50e-01 5.93e+00 angle pdb=" C MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta sigma weight residual 110.42 106.00 4.42 1.99e+00 2.53e-01 4.93e+00 angle pdb=" N GLY E 54 " pdb=" CA GLY E 54 " pdb=" C GLY E 54 " ideal model delta sigma weight residual 113.18 107.93 5.25 2.37e+00 1.78e-01 4.90e+00 ... (remaining 11679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 4483 16.34 - 32.69: 430 32.69 - 49.03: 114 49.03 - 65.37: 22 65.37 - 81.71: 5 Dihedral angle restraints: 5054 sinusoidal: 1917 harmonic: 3137 Sorted by residual: dihedral pdb=" CA THR R 224 " pdb=" C THR R 224 " pdb=" N THR R 225 " pdb=" CA THR R 225 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE E 239 " pdb=" C PHE E 239 " pdb=" N GLY E 240 " pdb=" CA GLY E 240 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG R 173 " pdb=" C ARG R 173 " pdb=" N TYR R 174 " pdb=" CA TYR R 174 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 782 0.028 - 0.055: 363 0.055 - 0.083: 96 0.083 - 0.111: 56 0.111 - 0.138: 31 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA ILE E 189 " pdb=" N ILE E 189 " pdb=" C ILE E 189 " pdb=" CB ILE E 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA VAL G 30 " pdb=" N VAL G 30 " pdb=" C VAL G 30 " pdb=" CB VAL G 30 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE R 218 " pdb=" N ILE R 218 " pdb=" C ILE R 218 " pdb=" CB ILE R 218 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1325 not shown) Planarity restraints: 1470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.046 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO G 49 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 253 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO R 254 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 254 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 254 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 212 " 0.015 2.00e-02 2.50e+03 1.15e-02 2.33e+00 pdb=" CG PHE E 212 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE E 212 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE E 212 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE E 212 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 212 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 212 " 0.013 2.00e-02 2.50e+03 ... (remaining 1467 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2161 2.79 - 3.32: 8272 3.32 - 3.85: 13728 3.85 - 4.37: 16857 4.37 - 4.90: 28252 Nonbonded interactions: 69270 Sorted by model distance: nonbonded pdb=" OD1 ASP B 290 " pdb=" NH1 ARG B 314 " model vdw 2.264 3.120 nonbonded pdb=" NE2 HIS E 35 " pdb=" OG SER E 99 " model vdw 2.271 3.120 nonbonded pdb=" O LEU R 269 " pdb=" NH1 ARG R 282 " model vdw 2.272 3.120 nonbonded pdb=" OH TYR R 134 " pdb=" OG1 THR R 225 " model vdw 2.277 3.040 nonbonded pdb=" O ASP E 201 " pdb=" OD1 ASP E 201 " model vdw 2.287 3.040 ... (remaining 69265 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: 1.150 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8611 Z= 0.122 Angle : 0.532 6.614 11690 Z= 0.281 Chirality : 0.040 0.138 1328 Planarity : 0.004 0.070 1470 Dihedral : 14.267 81.714 3027 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.26), residues: 1063 helix: 0.22 (0.30), residues: 303 sheet: -0.36 (0.30), residues: 287 loop : -0.76 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.011 0.001 TYR B 145 PHE 0.023 0.001 PHE E 212 TRP 0.011 0.001 TRP R 141 HIS 0.008 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8608) covalent geometry : angle 0.53181 (11684) SS BOND : bond 0.00558 ( 3) SS BOND : angle 0.95647 ( 6) hydrogen bonds : bond 0.23619 ( 383) hydrogen bonds : angle 9.06118 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 241 PHE cc_start: 0.7704 (p90) cc_final: 0.7452 (p90) REVERT: E 173 TYR cc_start: 0.8113 (m-80) cc_final: 0.7516 (m-80) REVERT: R 82 TYR cc_start: 0.7903 (m-80) cc_final: 0.7686 (m-80) REVERT: R 174 TYR cc_start: 0.7762 (t80) cc_final: 0.7386 (t80) REVERT: R 202 ILE cc_start: 0.7883 (tp) cc_final: 0.7535 (tp) REVERT: R 330 LEU cc_start: 0.8497 (tp) cc_final: 0.8286 (tt) REVERT: R 340 ASP cc_start: 0.7135 (m-30) cc_final: 0.6703 (m-30) REVERT: A 267 ASP cc_start: 0.7369 (m-30) cc_final: 0.7075 (m-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.0941 time to fit residues: 25.3126 Evaluate side-chains 188 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 38 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 110 ASN B 183 HIS E 82 GLN E 171 ASN A 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.150370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.132172 restraints weight = 13767.593| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.69 r_work: 0.3698 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8611 Z= 0.177 Angle : 0.652 8.735 11690 Z= 0.346 Chirality : 0.046 0.187 1328 Planarity : 0.005 0.066 1470 Dihedral : 5.103 20.128 1172 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.33 % Allowed : 15.84 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1063 helix: 0.69 (0.29), residues: 324 sheet: -0.35 (0.30), residues: 292 loop : -0.63 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.017 0.002 TYR R 296 PHE 0.021 0.002 PHE E 212 TRP 0.023 0.002 TRP B 169 HIS 0.007 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 8608) covalent geometry : angle 0.65146 (11684) SS BOND : bond 0.00817 ( 3) SS BOND : angle 1.37877 ( 6) hydrogen bonds : bond 0.04663 ( 383) hydrogen bonds : angle 5.95256 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 76 ASP cc_start: 0.7582 (t0) cc_final: 0.7354 (t0) REVERT: B 212 ASP cc_start: 0.7188 (t0) cc_final: 0.6782 (t0) REVERT: B 219 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.8021 (mmm-85) REVERT: B 241 PHE cc_start: 0.7487 (p90) cc_final: 0.7245 (p90) REVERT: B 292 PHE cc_start: 0.8002 (m-10) cc_final: 0.7717 (m-10) REVERT: B 313 ASN cc_start: 0.8266 (t0) cc_final: 0.7964 (t0) REVERT: B 325 MET cc_start: 0.7975 (ttm) cc_final: 0.7715 (ttm) REVERT: B 338 ILE cc_start: 0.8365 (mm) cc_final: 0.8136 (mm) REVERT: E 173 TYR cc_start: 0.8133 (m-80) cc_final: 0.7814 (m-80) REVERT: E 176 TRP cc_start: 0.6813 (m100) cc_final: 0.6602 (m100) REVERT: R 174 TYR cc_start: 0.7554 (t80) cc_final: 0.7260 (t80) REVERT: A 52 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7829 (mtpt) REVERT: A 361 ARG cc_start: 0.7867 (ptp90) cc_final: 0.7635 (ptt-90) outliers start: 21 outliers final: 14 residues processed: 209 average time/residue: 0.0940 time to fit residues: 26.9915 Evaluate side-chains 202 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 321 HIS Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 34 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 230 ASN A 239 GLN A 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.133709 restraints weight = 13674.427| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.66 r_work: 0.3729 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8611 Z= 0.143 Angle : 0.589 7.462 11690 Z= 0.314 Chirality : 0.044 0.172 1328 Planarity : 0.005 0.061 1470 Dihedral : 4.828 19.738 1172 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.21 % Allowed : 18.05 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.26), residues: 1063 helix: 0.93 (0.29), residues: 325 sheet: -0.24 (0.30), residues: 293 loop : -0.54 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.015 0.001 TYR B 145 PHE 0.028 0.001 PHE B 235 TRP 0.018 0.002 TRP B 169 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8608) covalent geometry : angle 0.58802 (11684) SS BOND : bond 0.00695 ( 3) SS BOND : angle 1.44241 ( 6) hydrogen bonds : bond 0.03955 ( 383) hydrogen bonds : angle 5.43277 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 152 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.4846 (tp) REVERT: B 219 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7948 (mmm-85) REVERT: B 234 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: B 241 PHE cc_start: 0.7455 (p90) cc_final: 0.7232 (p90) REVERT: B 338 ILE cc_start: 0.8373 (mm) cc_final: 0.8140 (mm) REVERT: E 173 TYR cc_start: 0.8053 (m-80) cc_final: 0.7469 (m-80) REVERT: R 142 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.8028 (tp) REVERT: R 315 LYS cc_start: 0.8460 (tptt) cc_final: 0.8165 (tptt) REVERT: R 337 SER cc_start: 0.8388 (p) cc_final: 0.8161 (p) REVERT: A 52 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7730 (mtpt) REVERT: A 55 PHE cc_start: 0.6708 (p90) cc_final: 0.6402 (p90) REVERT: A 319 ASP cc_start: 0.7800 (t0) cc_final: 0.7566 (m-30) outliers start: 29 outliers final: 20 residues processed: 210 average time/residue: 0.0984 time to fit residues: 28.3001 Evaluate side-chains 209 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.151554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133427 restraints weight = 13970.899| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.68 r_work: 0.3718 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8611 Z= 0.156 Angle : 0.601 8.951 11690 Z= 0.316 Chirality : 0.045 0.175 1328 Planarity : 0.005 0.061 1470 Dihedral : 4.809 20.356 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.21 % Allowed : 18.49 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1063 helix: 0.97 (0.29), residues: 323 sheet: -0.32 (0.30), residues: 301 loop : -0.51 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.015 0.001 TYR R 296 PHE 0.031 0.002 PHE B 235 TRP 0.028 0.002 TRP E 176 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8608) covalent geometry : angle 0.60008 (11684) SS BOND : bond 0.00575 ( 3) SS BOND : angle 1.50195 ( 6) hydrogen bonds : bond 0.03852 ( 383) hydrogen bonds : angle 5.30680 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6698 (m-80) cc_final: 0.6470 (m-80) REVERT: B 61 MET cc_start: 0.8013 (ppp) cc_final: 0.7412 (ppp) REVERT: B 76 ASP cc_start: 0.7380 (t0) cc_final: 0.6971 (t0) REVERT: B 152 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.4875 (tp) REVERT: B 234 PHE cc_start: 0.8260 (OUTLIER) cc_final: 0.7649 (m-80) REVERT: B 241 PHE cc_start: 0.7346 (p90) cc_final: 0.7141 (p90) REVERT: B 325 MET cc_start: 0.7910 (ttm) cc_final: 0.7643 (ttp) REVERT: E 173 TYR cc_start: 0.7983 (m-80) cc_final: 0.7502 (m-80) REVERT: R 142 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7965 (tp) REVERT: R 315 LYS cc_start: 0.8467 (tptt) cc_final: 0.8162 (tptt) REVERT: A 52 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7639 (mtpt) REVERT: A 55 PHE cc_start: 0.6724 (p90) cc_final: 0.6448 (p90) REVERT: A 205 ASP cc_start: 0.7832 (t0) cc_final: 0.7593 (t0) REVERT: A 319 ASP cc_start: 0.7832 (t0) cc_final: 0.7571 (m-30) outliers start: 38 outliers final: 26 residues processed: 206 average time/residue: 0.0981 time to fit residues: 27.6739 Evaluate side-chains 211 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 321 HIS Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 354 HIS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 91 optimal weight: 0.0060 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** R 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.152192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.134259 restraints weight = 13802.252| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.66 r_work: 0.3731 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8611 Z= 0.143 Angle : 0.590 9.620 11690 Z= 0.307 Chirality : 0.044 0.153 1328 Planarity : 0.005 0.059 1470 Dihedral : 4.729 20.461 1172 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.65 % Allowed : 19.82 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.27), residues: 1063 helix: 1.14 (0.30), residues: 326 sheet: -0.22 (0.30), residues: 301 loop : -0.53 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.022 0.002 TYR E 59 PHE 0.030 0.001 PHE B 235 TRP 0.027 0.002 TRP E 176 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8608) covalent geometry : angle 0.58905 (11684) SS BOND : bond 0.00634 ( 3) SS BOND : angle 1.38819 ( 6) hydrogen bonds : bond 0.03637 ( 383) hydrogen bonds : angle 5.13568 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6772 (m-80) cc_final: 0.6526 (m-80) REVERT: B 61 MET cc_start: 0.7989 (ppp) cc_final: 0.7396 (ppp) REVERT: B 76 ASP cc_start: 0.7373 (t0) cc_final: 0.6987 (t0) REVERT: B 152 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5409 (mt) REVERT: B 234 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: B 315 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8359 (m) REVERT: B 338 ILE cc_start: 0.8355 (mm) cc_final: 0.8115 (mm) REVERT: E 173 TYR cc_start: 0.7893 (m-80) cc_final: 0.7290 (m-80) REVERT: A 52 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7667 (mtpt) REVERT: A 55 PHE cc_start: 0.6686 (p90) cc_final: 0.6455 (p90) REVERT: A 205 ASP cc_start: 0.7813 (t0) cc_final: 0.7529 (t0) outliers start: 33 outliers final: 24 residues processed: 206 average time/residue: 0.0958 time to fit residues: 27.2873 Evaluate side-chains 208 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 130 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 339 ILE Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 354 HIS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 45 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.152448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134681 restraints weight = 13704.609| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.63 r_work: 0.3729 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8611 Z= 0.140 Angle : 0.588 10.318 11690 Z= 0.304 Chirality : 0.044 0.152 1328 Planarity : 0.005 0.058 1470 Dihedral : 4.685 21.389 1172 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.21 % Allowed : 20.04 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.27), residues: 1063 helix: 1.20 (0.29), residues: 326 sheet: -0.10 (0.31), residues: 292 loop : -0.56 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.016 0.001 TYR E 59 PHE 0.033 0.001 PHE B 235 TRP 0.028 0.002 TRP E 176 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8608) covalent geometry : angle 0.58762 (11684) SS BOND : bond 0.00581 ( 3) SS BOND : angle 1.31612 ( 6) hydrogen bonds : bond 0.03570 ( 383) hydrogen bonds : angle 5.06008 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6808 (m-80) cc_final: 0.6554 (m-80) REVERT: B 61 MET cc_start: 0.7970 (ppp) cc_final: 0.7363 (ppp) REVERT: B 76 ASP cc_start: 0.7391 (t0) cc_final: 0.7044 (t0) REVERT: B 152 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5487 (mt) REVERT: B 169 TRP cc_start: 0.8527 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: B 234 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: E 83 MET cc_start: 0.5470 (mmm) cc_final: 0.5069 (tpp) REVERT: E 173 TYR cc_start: 0.7895 (m-80) cc_final: 0.7618 (m-10) REVERT: R 213 LYS cc_start: 0.7392 (tppt) cc_final: 0.7192 (tppt) REVERT: A 52 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7960 (mtpt) outliers start: 38 outliers final: 25 residues processed: 208 average time/residue: 0.0936 time to fit residues: 26.4954 Evaluate side-chains 207 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 338 CYS Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.152414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.134570 restraints weight = 13845.782| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.67 r_work: 0.3734 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8611 Z= 0.140 Angle : 0.592 10.592 11690 Z= 0.306 Chirality : 0.044 0.153 1328 Planarity : 0.005 0.059 1470 Dihedral : 4.670 21.519 1172 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.43 % Allowed : 21.82 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.27), residues: 1063 helix: 1.32 (0.29), residues: 322 sheet: -0.15 (0.31), residues: 292 loop : -0.43 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 252 TYR 0.015 0.002 TYR E 190 PHE 0.033 0.001 PHE B 235 TRP 0.029 0.002 TRP E 176 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8608) covalent geometry : angle 0.59128 (11684) SS BOND : bond 0.00619 ( 3) SS BOND : angle 1.34099 ( 6) hydrogen bonds : bond 0.03526 ( 383) hydrogen bonds : angle 5.01361 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ARG cc_start: 0.8298 (mmt-90) cc_final: 0.8010 (mmt-90) REVERT: B 59 TYR cc_start: 0.6821 (m-80) cc_final: 0.6531 (m-80) REVERT: B 76 ASP cc_start: 0.7550 (t0) cc_final: 0.7089 (t0) REVERT: B 152 LEU cc_start: 0.5904 (OUTLIER) cc_final: 0.5471 (mt) REVERT: B 169 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: B 234 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: E 173 TYR cc_start: 0.7889 (m-80) cc_final: 0.7584 (m-10) REVERT: R 114 MET cc_start: 0.7544 (mtt) cc_final: 0.7338 (mtm) REVERT: A 52 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7985 (mtpt) outliers start: 31 outliers final: 24 residues processed: 204 average time/residue: 0.1021 time to fit residues: 28.2259 Evaluate side-chains 212 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 313 LEU Chi-restraints excluded: chain R residue 338 CYS Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 354 HIS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN A 329 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.152358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.134512 restraints weight = 13654.374| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.66 r_work: 0.3735 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8611 Z= 0.145 Angle : 0.607 10.648 11690 Z= 0.312 Chirality : 0.045 0.186 1328 Planarity : 0.005 0.061 1470 Dihedral : 4.675 26.672 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.54 % Allowed : 22.15 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.27), residues: 1063 helix: 1.37 (0.30), residues: 322 sheet: -0.16 (0.31), residues: 289 loop : -0.42 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.016 0.002 TYR R 326 PHE 0.030 0.001 PHE B 235 TRP 0.033 0.002 TRP E 176 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8608) covalent geometry : angle 0.60596 (11684) SS BOND : bond 0.00632 ( 3) SS BOND : angle 1.42252 ( 6) hydrogen bonds : bond 0.03527 ( 383) hydrogen bonds : angle 5.02378 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.8033 (mmt-90) REVERT: B 59 TYR cc_start: 0.6819 (m-80) cc_final: 0.6599 (m-80) REVERT: B 61 MET cc_start: 0.7726 (ppp) cc_final: 0.7426 (ppp) REVERT: B 76 ASP cc_start: 0.7567 (t0) cc_final: 0.7198 (t0) REVERT: B 152 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5408 (mt) REVERT: B 169 TRP cc_start: 0.8546 (OUTLIER) cc_final: 0.8229 (m-10) REVERT: B 234 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: G 38 MET cc_start: 0.7262 (mtt) cc_final: 0.6929 (mtt) REVERT: E 173 TYR cc_start: 0.7821 (m-80) cc_final: 0.7500 (m-10) REVERT: A 52 LYS cc_start: 0.8297 (mtpt) cc_final: 0.7952 (mtpt) REVERT: A 191 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6483 (mt-10) REVERT: A 205 ASP cc_start: 0.7815 (t0) cc_final: 0.7589 (t0) outliers start: 32 outliers final: 26 residues processed: 210 average time/residue: 0.1023 time to fit residues: 29.2892 Evaluate side-chains 221 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 295 MET Chi-restraints excluded: chain R residue 338 CYS Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 354 HIS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.149713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131763 restraints weight = 13629.471| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.63 r_work: 0.3698 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8611 Z= 0.217 Angle : 0.675 10.716 11690 Z= 0.346 Chirality : 0.047 0.214 1328 Planarity : 0.005 0.065 1470 Dihedral : 5.024 25.651 1172 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.43 % Allowed : 22.70 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.27), residues: 1063 helix: 1.12 (0.29), residues: 322 sheet: -0.25 (0.31), residues: 296 loop : -0.58 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.024 0.002 TYR R 296 PHE 0.029 0.002 PHE B 235 TRP 0.037 0.002 TRP E 176 HIS 0.004 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 8608) covalent geometry : angle 0.67380 (11684) SS BOND : bond 0.00948 ( 3) SS BOND : angle 1.88235 ( 6) hydrogen bonds : bond 0.04135 ( 383) hydrogen bonds : angle 5.32266 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ARG cc_start: 0.8328 (mmt-90) cc_final: 0.8057 (mmt-90) REVERT: B 57 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7846 (mtmm) REVERT: B 61 MET cc_start: 0.7866 (ppp) cc_final: 0.7523 (ppp) REVERT: B 76 ASP cc_start: 0.7733 (t0) cc_final: 0.7279 (t0) REVERT: B 152 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.4938 (tp) REVERT: B 234 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7871 (m-80) REVERT: G 38 MET cc_start: 0.7271 (mtt) cc_final: 0.6919 (mtt) REVERT: R 315 LYS cc_start: 0.8494 (tptt) cc_final: 0.8197 (tptt) REVERT: A 39 GLU cc_start: 0.6485 (pm20) cc_final: 0.5968 (pm20) REVERT: A 52 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7931 (mtpt) REVERT: A 191 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6680 (mt-10) outliers start: 31 outliers final: 24 residues processed: 210 average time/residue: 0.0974 time to fit residues: 27.9835 Evaluate side-chains 215 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 338 CYS Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain R residue 354 HIS Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 51 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.152682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134801 restraints weight = 13758.580| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.64 r_work: 0.3743 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8611 Z= 0.133 Angle : 0.626 10.511 11690 Z= 0.319 Chirality : 0.044 0.164 1328 Planarity : 0.005 0.060 1470 Dihedral : 4.750 30.588 1172 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.55 % Allowed : 23.70 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.27), residues: 1063 helix: 1.39 (0.30), residues: 321 sheet: -0.15 (0.31), residues: 294 loop : -0.61 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.024 0.002 TYR R 326 PHE 0.028 0.001 PHE B 235 TRP 0.045 0.002 TRP E 176 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8608) covalent geometry : angle 0.62584 (11684) SS BOND : bond 0.00611 ( 3) SS BOND : angle 1.39118 ( 6) hydrogen bonds : bond 0.03459 ( 383) hydrogen bonds : angle 5.05104 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 ARG cc_start: 0.8288 (mmt-90) cc_final: 0.8029 (mmt-90) REVERT: B 59 TYR cc_start: 0.6912 (m-80) cc_final: 0.6601 (m-80) REVERT: B 61 MET cc_start: 0.7618 (ppp) cc_final: 0.7402 (ptm) REVERT: G 38 MET cc_start: 0.7204 (mtt) cc_final: 0.6860 (mtt) REVERT: R 174 TYR cc_start: 0.7671 (t80) cc_final: 0.7358 (t80) REVERT: A 39 GLU cc_start: 0.6542 (pm20) cc_final: 0.6014 (pm20) REVERT: A 52 LYS cc_start: 0.8287 (mtpt) cc_final: 0.8007 (mtpt) REVERT: A 205 ASP cc_start: 0.7784 (t0) cc_final: 0.7562 (t0) REVERT: A 248 ILE cc_start: 0.7539 (mm) cc_final: 0.7295 (mt) outliers start: 23 outliers final: 20 residues processed: 205 average time/residue: 0.0974 time to fit residues: 27.3832 Evaluate side-chains 208 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 LEU Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 343 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 0.0770 chunk 94 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.151257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133176 restraints weight = 13788.963| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.65 r_work: 0.3718 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8611 Z= 0.175 Angle : 0.654 10.572 11690 Z= 0.336 Chirality : 0.046 0.192 1328 Planarity : 0.005 0.063 1470 Dihedral : 4.866 29.333 1172 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.33 % Allowed : 24.58 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.27), residues: 1063 helix: 1.31 (0.30), residues: 321 sheet: -0.12 (0.31), residues: 300 loop : -0.65 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 134 TYR 0.027 0.002 TYR R 326 PHE 0.033 0.002 PHE E 29 TRP 0.043 0.002 TRP E 176 HIS 0.003 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8608) covalent geometry : angle 0.65296 (11684) SS BOND : bond 0.00807 ( 3) SS BOND : angle 1.72243 ( 6) hydrogen bonds : bond 0.03785 ( 383) hydrogen bonds : angle 5.13211 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2059.62 seconds wall clock time: 36 minutes 15.69 seconds (2175.69 seconds total)