Starting phenix.real_space_refine on Sun May 11 19:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d0a_46448/05_2025/9d0a_46448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d0a_46448/05_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_46448/05_2025/9d0a_46448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d0a_46448/05_2025/9d0a_46448.map" model { file = "/net/cci-nas-00/data/ceres_data/9d0a_46448/05_2025/9d0a_46448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d0a_46448/05_2025/9d0a_46448.cif" } resolution = 3.1 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= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 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: 5.13, per 1000 atoms: 0.61 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: 2.23 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.13 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: 2.38 Time building geometry restraints manager: 2.59 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: 0.980 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.010 Find NCS groups from input model: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- 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 : 7.74 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 (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: -0.63 (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 TRP 0.011 0.001 TRP R 141 HIS 0.008 0.001 HIS B 91 PHE 0.023 0.001 PHE E 212 TYR 0.011 0.001 TYR B 145 ARG 0.009 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.23619 ( 383) hydrogen bonds : angle 9.06118 ( 1068) SS BOND : bond 0.00558 ( 3) SS BOND : angle 0.95647 ( 6) covalent geometry : bond 0.00273 ( 8608) covalent geometry : angle 0.53181 (11684) *********************** 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 : 0.835 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: 0.2116 time to fit residues: 56.0962 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 : 0.924 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 R 310 HIS A 349 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.150621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132550 restraints weight = 13672.964| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.68 r_work: 0.3704 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1634 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= 0.172 Angle : 0.648 8.160 11690 Z= 0.343 Chirality : 0.046 0.184 1328 Planarity : 0.005 0.065 1470 Dihedral : 5.080 20.146 1172 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.33 % Allowed : 15.95 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.28 (0.26), residues: 1063 helix: 0.81 (0.29), residues: 318 sheet: -0.37 (0.29), residues: 293 loop : -0.65 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.007 0.001 HIS B 91 PHE 0.021 0.002 PHE E 212 TYR 0.019 0.002 TYR R 296 ARG 0.007 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 383) hydrogen bonds : angle 5.87285 ( 1068) SS BOND : bond 0.00797 ( 3) SS BOND : angle 1.31681 ( 6) covalent geometry : bond 0.00389 ( 8608) covalent geometry : angle 0.64740 (11684) *********************** 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 219 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7937 (m100) cc_final: 0.7736 (m100) REVERT: B 76 ASP cc_start: 0.7595 (t0) cc_final: 0.7366 (t0) REVERT: B 212 ASP cc_start: 0.7185 (t0) cc_final: 0.6758 (t0) REVERT: B 219 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.8011 (mmm-85) REVERT: B 241 PHE cc_start: 0.7479 (p90) cc_final: 0.7250 (p90) REVERT: B 292 PHE cc_start: 0.7990 (m-10) cc_final: 0.7639 (m-10) REVERT: B 294 CYS cc_start: 0.8286 (m) cc_final: 0.8068 (m) REVERT: B 313 ASN cc_start: 0.8272 (t0) cc_final: 0.7957 (t0) REVERT: B 338 ILE cc_start: 0.8363 (mm) cc_final: 0.8128 (mm) REVERT: E 173 TYR cc_start: 0.8139 (m-80) cc_final: 0.7831 (m-80) REVERT: E 176 TRP cc_start: 0.6800 (m100) cc_final: 0.6587 (m100) REVERT: R 174 TYR cc_start: 0.7540 (t80) cc_final: 0.7285 (t80) REVERT: R 290 VAL cc_start: 0.8460 (t) cc_final: 0.8258 (p) REVERT: A 52 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7880 (mtpt) REVERT: A 252 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6357 (ttp80) outliers start: 21 outliers final: 13 residues processed: 211 average time/residue: 0.2027 time to fit residues: 58.5278 Evaluate side-chains 198 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 184 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 252 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.151731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133891 restraints weight = 13930.023| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 2.68 r_work: 0.3721 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8611 Z= 0.149 Angle : 0.598 9.840 11690 Z= 0.318 Chirality : 0.044 0.177 1328 Planarity : 0.005 0.062 1470 Dihedral : 4.848 19.868 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 : 3.32 % Allowed : 17.94 % 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 (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: -0.11 (0.26), residues: 1063 helix: 0.92 (0.29), residues: 326 sheet: -0.29 (0.29), residues: 298 loop : -0.54 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.029 0.001 PHE B 235 TYR 0.016 0.001 TYR R 296 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 383) hydrogen bonds : angle 5.41054 ( 1068) SS BOND : bond 0.00720 ( 3) SS BOND : angle 1.48290 ( 6) covalent geometry : bond 0.00335 ( 8608) covalent geometry : angle 0.59717 (11684) *********************** 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 221 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6931 (m-80) cc_final: 0.6665 (m-80) REVERT: B 152 LEU cc_start: 0.6000 (OUTLIER) cc_final: 0.4905 (tp) REVERT: B 219 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7948 (mmm-85) REVERT: B 234 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: B 241 PHE cc_start: 0.7415 (p90) cc_final: 0.7195 (p90) REVERT: B 294 CYS cc_start: 0.8280 (m) cc_final: 0.8073 (m) REVERT: B 313 ASN cc_start: 0.8306 (t0) cc_final: 0.8075 (t0) REVERT: B 338 ILE cc_start: 0.8360 (mm) cc_final: 0.8120 (mm) REVERT: E 173 TYR cc_start: 0.8078 (m-80) cc_final: 0.7486 (m-80) REVERT: R 174 TYR cc_start: 0.7490 (t80) cc_final: 0.7288 (t80) REVERT: R 290 VAL cc_start: 0.8469 (t) cc_final: 0.8260 (p) REVERT: R 315 LYS cc_start: 0.8445 (tptt) cc_final: 0.8132 (tptt) REVERT: A 52 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7696 (mtpt) REVERT: A 55 PHE cc_start: 0.6718 (p90) cc_final: 0.6414 (p90) REVERT: A 252 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6341 (ttp80) REVERT: A 319 ASP cc_start: 0.7811 (t0) cc_final: 0.7586 (m-30) REVERT: A 361 ARG cc_start: 0.7845 (ptp90) cc_final: 0.7590 (ptt-90) outliers start: 30 outliers final: 19 residues processed: 206 average time/residue: 0.2056 time to fit residues: 57.3475 Evaluate side-chains 206 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 316 SER 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 57 THR 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 196 LEU 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 73 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.150305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.132243 restraints weight = 13753.894| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.65 r_work: 0.3704 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8611 Z= 0.186 Angle : 0.626 9.941 11690 Z= 0.328 Chirality : 0.046 0.179 1328 Planarity : 0.005 0.067 1470 Dihedral : 4.914 20.800 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.99 % Allowed : 18.83 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.16 (0.26), residues: 1063 helix: 0.91 (0.29), residues: 324 sheet: -0.36 (0.30), residues: 301 loop : -0.56 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 176 HIS 0.003 0.001 HIS E 167 PHE 0.031 0.002 PHE B 235 TYR 0.018 0.002 TYR R 296 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 383) hydrogen bonds : angle 5.40452 ( 1068) SS BOND : bond 0.00679 ( 3) SS BOND : angle 1.64695 ( 6) covalent geometry : bond 0.00423 ( 8608) covalent geometry : angle 0.62472 (11684) *********************** 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 216 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6982 (m-80) cc_final: 0.6721 (m-80) REVERT: B 61 MET cc_start: 0.7935 (ppp) cc_final: 0.7465 (ppp) REVERT: B 76 ASP cc_start: 0.7718 (t0) cc_final: 0.7414 (t0) REVERT: B 152 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5039 (tp) REVERT: B 234 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: E 173 TYR cc_start: 0.7990 (m-80) cc_final: 0.7510 (m-80) REVERT: R 174 TYR cc_start: 0.7580 (t80) cc_final: 0.7307 (t80) REVERT: R 223 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6904 (pp) REVERT: R 315 LYS cc_start: 0.8465 (tptt) cc_final: 0.8164 (tptt) REVERT: A 52 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7658 (mtpt) REVERT: A 55 PHE cc_start: 0.6826 (p90) cc_final: 0.6537 (p90) REVERT: A 205 ASP cc_start: 0.7828 (t0) cc_final: 0.7593 (t0) REVERT: A 252 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.6339 (ttp80) REVERT: A 319 ASP cc_start: 0.7851 (t0) cc_final: 0.7581 (m-30) outliers start: 36 outliers final: 22 residues processed: 202 average time/residue: 0.1993 time to fit residues: 54.8707 Evaluate side-chains 207 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 130 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 288 LEU 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 Chi-restraints excluded: chain A residue 252 ARG 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 83 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 243 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133713 restraints weight = 13652.613| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.67 r_work: 0.3725 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8611 Z= 0.145 Angle : 0.589 10.206 11690 Z= 0.308 Chirality : 0.044 0.153 1328 Planarity : 0.005 0.063 1470 Dihedral : 4.786 21.600 1172 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.88 % Allowed : 19.27 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.11 (0.26), residues: 1063 helix: 0.98 (0.29), residues: 327 sheet: -0.32 (0.30), residues: 301 loop : -0.59 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 176 HIS 0.003 0.001 HIS B 54 PHE 0.031 0.001 PHE B 235 TYR 0.013 0.001 TYR R 296 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 383) hydrogen bonds : angle 5.21373 ( 1068) SS BOND : bond 0.00656 ( 3) SS BOND : angle 1.43503 ( 6) covalent geometry : bond 0.00329 ( 8608) covalent geometry : angle 0.58780 (11684) *********************** 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 218 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6955 (m-80) cc_final: 0.6666 (m-80) REVERT: B 61 MET cc_start: 0.7901 (ppp) cc_final: 0.7400 (ppp) REVERT: B 76 ASP cc_start: 0.7725 (t0) cc_final: 0.7433 (t0) REVERT: B 152 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5356 (mt) REVERT: B 234 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: E 173 TYR cc_start: 0.7964 (m-80) cc_final: 0.7369 (m-80) REVERT: R 174 TYR cc_start: 0.7586 (t80) cc_final: 0.7344 (t80) REVERT: R 223 ILE cc_start: 0.7191 (OUTLIER) cc_final: 0.6896 (pp) REVERT: A 52 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7883 (mtpt) REVERT: A 205 ASP cc_start: 0.7812 (t0) cc_final: 0.7562 (t0) REVERT: A 252 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6391 (ttp80) REVERT: A 319 ASP cc_start: 0.7809 (t0) cc_final: 0.7559 (m-30) outliers start: 35 outliers final: 23 residues processed: 202 average time/residue: 0.2084 time to fit residues: 57.1551 Evaluate side-chains 204 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 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 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 196 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 223 ILE 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 26 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.0970 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ** 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 = 0.4049 r_free = 0.4049 target = 0.149189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.131110 restraints weight = 13645.180| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.70 r_work: 0.3685 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8611 Z= 0.220 Angle : 0.646 10.413 11690 Z= 0.338 Chirality : 0.047 0.178 1328 Planarity : 0.005 0.067 1470 Dihedral : 5.057 23.375 1172 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.10 % Allowed : 20.71 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.25 (0.26), residues: 1063 helix: 0.84 (0.29), residues: 327 sheet: -0.37 (0.30), residues: 303 loop : -0.67 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 176 HIS 0.004 0.001 HIS E 167 PHE 0.033 0.002 PHE B 235 TYR 0.025 0.002 TYR E 59 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 383) hydrogen bonds : angle 5.37320 ( 1068) SS BOND : bond 0.00927 ( 3) SS BOND : angle 1.76673 ( 6) covalent geometry : bond 0.00504 ( 8608) covalent geometry : angle 0.64510 (11684) *********************** 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: 37 poor density : 186 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7176 (mtmm) REVERT: B 59 TYR cc_start: 0.7051 (m-80) cc_final: 0.6689 (m-80) REVERT: B 76 ASP cc_start: 0.7837 (t0) cc_final: 0.7465 (t0) REVERT: B 152 LEU cc_start: 0.6029 (OUTLIER) cc_final: 0.5006 (tp) REVERT: B 169 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.8301 (m-10) REVERT: B 234 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7857 (m-80) REVERT: R 174 TYR cc_start: 0.7664 (t80) cc_final: 0.7296 (t80) REVERT: R 223 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6920 (pp) REVERT: R 315 LYS cc_start: 0.8530 (tptt) cc_final: 0.8205 (tptt) REVERT: A 52 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7861 (mtpt) REVERT: A 205 ASP cc_start: 0.7773 (t0) cc_final: 0.7569 (t0) outliers start: 37 outliers final: 26 residues processed: 204 average time/residue: 0.2105 time to fit residues: 58.3130 Evaluate side-chains 214 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 223 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 0.0370 chunk 72 optimal weight: 0.0980 chunk 77 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.153069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.135346 restraints weight = 13822.510| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.67 r_work: 0.3751 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8611 Z= 0.123 Angle : 0.575 9.924 11690 Z= 0.300 Chirality : 0.044 0.154 1328 Planarity : 0.005 0.063 1470 Dihedral : 4.672 24.063 1172 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.65 % Allowed : 21.37 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.06 (0.27), residues: 1063 helix: 1.18 (0.29), residues: 322 sheet: -0.16 (0.30), residues: 299 loop : -0.56 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 176 HIS 0.004 0.001 HIS B 54 PHE 0.030 0.001 PHE B 235 TYR 0.015 0.001 TYR E 59 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 383) hydrogen bonds : angle 5.07182 ( 1068) SS BOND : bond 0.00583 ( 3) SS BOND : angle 1.23103 ( 6) covalent geometry : bond 0.00275 ( 8608) covalent geometry : angle 0.57398 (11684) *********************** 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 222 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6925 (m-80) cc_final: 0.6622 (m-80) REVERT: B 76 ASP cc_start: 0.7677 (t0) cc_final: 0.7461 (t0) REVERT: B 152 LEU cc_start: 0.5724 (OUTLIER) cc_final: 0.5486 (mt) REVERT: B 169 TRP cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (m-10) REVERT: B 234 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: E 52 SER cc_start: 0.7858 (t) cc_final: 0.7583 (p) REVERT: E 173 TYR cc_start: 0.7787 (m-80) cc_final: 0.7331 (m-80) REVERT: R 130 LEU cc_start: 0.8257 (tp) cc_final: 0.8027 (tt) REVERT: R 315 LYS cc_start: 0.8492 (tptt) cc_final: 0.8138 (tptt) REVERT: A 52 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7915 (mtpt) REVERT: A 205 ASP cc_start: 0.7797 (t0) cc_final: 0.7510 (t0) outliers start: 33 outliers final: 24 residues processed: 207 average time/residue: 0.2060 time to fit residues: 57.9021 Evaluate side-chains 209 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 103 CYS 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 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 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 288 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 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 90 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.149463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.131388 restraints weight = 13824.140| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.66 r_work: 0.3691 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8611 Z= 0.217 Angle : 0.658 10.341 11690 Z= 0.343 Chirality : 0.047 0.165 1328 Planarity : 0.005 0.067 1470 Dihedral : 4.988 23.624 1172 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.77 % Allowed : 22.48 % 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 (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: -0.09 (0.27), residues: 1063 helix: 0.96 (0.29), residues: 321 sheet: -0.27 (0.31), residues: 296 loop : -0.54 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 176 HIS 0.004 0.001 HIS E 167 PHE 0.033 0.002 PHE B 235 TYR 0.027 0.002 TYR R 296 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 383) hydrogen bonds : angle 5.31129 ( 1068) SS BOND : bond 0.00916 ( 3) SS BOND : angle 1.83474 ( 6) covalent geometry : bond 0.00498 ( 8608) covalent geometry : angle 0.65666 (11684) *********************** 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 230 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7243 (mtmm) REVERT: B 59 TYR cc_start: 0.7052 (m-80) cc_final: 0.6677 (m-80) REVERT: B 76 ASP cc_start: 0.7827 (t0) cc_final: 0.7514 (t0) REVERT: B 152 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.4941 (tp) REVERT: B 169 TRP cc_start: 0.8575 (OUTLIER) cc_final: 0.8365 (m-10) REVERT: B 338 ILE cc_start: 0.8384 (mm) cc_final: 0.8149 (mm) REVERT: G 38 MET cc_start: 0.7283 (mtt) cc_final: 0.6939 (mtt) REVERT: E 173 TYR cc_start: 0.7842 (m-80) cc_final: 0.7596 (m-10) REVERT: R 174 TYR cc_start: 0.7669 (t80) cc_final: 0.7338 (t80) REVERT: R 315 LYS cc_start: 0.8511 (tptt) cc_final: 0.8161 (tppp) REVERT: A 52 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7882 (mtpt) REVERT: A 191 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6637 (mt-10) REVERT: A 205 ASP cc_start: 0.7762 (t0) cc_final: 0.7553 (t0) outliers start: 34 outliers final: 28 residues processed: 211 average time/residue: 0.2065 time to fit residues: 58.7387 Evaluate side-chains 225 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 103 CYS 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 169 TRP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE 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 189 ILE Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 34 optimal weight: 0.0070 chunk 92 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.135300 restraints weight = 13820.998| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.67 r_work: 0.3754 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8611 Z= 0.122 Angle : 0.597 10.200 11690 Z= 0.309 Chirality : 0.044 0.153 1328 Planarity : 0.005 0.063 1470 Dihedral : 4.641 26.505 1172 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.99 % Allowed : 23.03 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.00 (0.27), residues: 1063 helix: 1.17 (0.29), residues: 325 sheet: -0.31 (0.30), residues: 301 loop : -0.55 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 176 HIS 0.003 0.001 HIS B 62 PHE 0.028 0.001 PHE B 235 TYR 0.016 0.001 TYR E 190 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03330 ( 383) hydrogen bonds : angle 4.98819 ( 1068) SS BOND : bond 0.00574 ( 3) SS BOND : angle 1.33325 ( 6) covalent geometry : bond 0.00276 ( 8608) covalent geometry : angle 0.59607 (11684) *********************** 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 223 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.6956 (m-80) cc_final: 0.6686 (m-80) REVERT: B 76 ASP cc_start: 0.7682 (t0) cc_final: 0.7450 (t0) REVERT: G 38 MET cc_start: 0.7186 (mtt) cc_final: 0.6859 (mtt) REVERT: E 52 SER cc_start: 0.7807 (t) cc_final: 0.7552 (p) REVERT: A 39 GLU cc_start: 0.6501 (pm20) cc_final: 0.6012 (pm20) REVERT: A 52 LYS cc_start: 0.8277 (mtpt) cc_final: 0.7925 (mtpt) outliers start: 27 outliers final: 22 residues processed: 207 average time/residue: 0.1974 time to fit residues: 55.9356 Evaluate side-chains 215 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 232 ILE 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 189 ILE Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 288 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 104 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.152074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.134069 restraints weight = 13622.917| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.63 r_work: 0.3735 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8611 Z= 0.159 Angle : 0.621 10.015 11690 Z= 0.321 Chirality : 0.045 0.163 1328 Planarity : 0.005 0.064 1470 Dihedral : 4.698 23.753 1172 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.66 % Allowed : 24.03 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.27), residues: 1063 helix: 1.09 (0.29), residues: 324 sheet: -0.37 (0.30), residues: 304 loop : -0.52 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 176 HIS 0.002 0.001 HIS E 167 PHE 0.033 0.002 PHE E 29 TYR 0.022 0.002 TYR R 296 ARG 0.007 0.000 ARG A 252 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 383) hydrogen bonds : angle 5.06255 ( 1068) SS BOND : bond 0.00735 ( 3) SS BOND : angle 1.66851 ( 6) covalent geometry : bond 0.00365 ( 8608) covalent geometry : angle 0.62045 (11684) ********************** 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 224 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7039 (m-80) cc_final: 0.6757 (m-80) REVERT: B 76 ASP cc_start: 0.7784 (t0) cc_final: 0.7492 (t0) REVERT: G 38 MET cc_start: 0.7216 (mtt) cc_final: 0.6879 (mtt) REVERT: R 315 LYS cc_start: 0.8469 (tptt) cc_final: 0.8139 (tppp) REVERT: A 39 GLU cc_start: 0.6501 (pm20) cc_final: 0.5979 (pm20) REVERT: A 52 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7955 (mtpt) REVERT: A 361 ARG cc_start: 0.7934 (ptt-90) cc_final: 0.7662 (ptp90) outliers start: 24 outliers final: 21 residues processed: 210 average time/residue: 0.2013 time to fit residues: 57.6266 Evaluate side-chains 216 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 103 CYS 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 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 204 LEU Chi-restraints excluded: chain R residue 288 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.152116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133952 restraints weight = 13863.791| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.65 r_work: 0.3731 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8611 Z= 0.160 Angle : 0.631 10.456 11690 Z= 0.325 Chirality : 0.045 0.189 1328 Planarity : 0.005 0.063 1470 Dihedral : 4.754 26.794 1172 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.99 % Allowed : 24.25 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.04 (0.27), residues: 1063 helix: 1.07 (0.29), residues: 324 sheet: -0.33 (0.30), residues: 294 loop : -0.51 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP E 176 HIS 0.003 0.001 HIS E 167 PHE 0.033 0.002 PHE E 29 TYR 0.022 0.002 TYR R 296 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 383) hydrogen bonds : angle 5.05961 ( 1068) SS BOND : bond 0.00735 ( 3) SS BOND : angle 1.63740 ( 6) covalent geometry : bond 0.00368 ( 8608) covalent geometry : angle 0.63016 (11684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4000.75 seconds wall clock time: 70 minutes 20.42 seconds (4220.42 seconds total)