Starting phenix.real_space_refine on Fri Aug 22 15:56:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gei_29971/08_2025/8gei_29971.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gei_29971/08_2025/8gei_29971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gei_29971/08_2025/8gei_29971.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gei_29971/08_2025/8gei_29971.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gei_29971/08_2025/8gei_29971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gei_29971/08_2025/8gei_29971.map" } resolution = 4.1 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= -0.001 sd= 0.020 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 2 5.16 5 C 3449 2.51 5 N 1003 2.21 5 O 998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5452 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1591 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 203} Link IDs: {'PTRANS': 4, 'TRANS': 272} Chain breaks: 9 Unresolved non-hydrogen bonds: 738 Unresolved non-hydrogen angles: 921 Unresolved non-hydrogen dihedrals: 589 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 15, 'ARG:plan': 24, 'ASN:plan1': 16, 'GLU:plan': 22, 'ASP:plan': 17, 'HIS:plan': 2, 'PHE:plan': 4, 'TYR:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 445 Chain: "B" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 1907 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 5, 'TRANS': 322} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 791 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'ARG:plan': 15, 'GLN:plan1': 11, 'GLU:plan': 7, 'ASN:plan1': 14, 'ASP:plan': 29, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 327 Chain: "G" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 281 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "R" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 1658 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 271} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 600 Unresolved non-hydrogen angles: 770 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 94 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 9, 'ASN:plan1': 10, 'GLU:plan': 8, 'ARG:plan': 10, 'GLN:plan1': 8, 'ASP:plan': 5, 'TYR:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 248 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.29 Number of scatterers: 5452 At special positions: 0 Unit cell: (66.78, 96.46, 129.32, 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 2 16.00 O 998 8.00 N 1003 7.00 C 3449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.48 Conformation dependent library (CDL) restraints added in 261.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 49.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.856A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.768A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 91 No H-bonds generated for 'chain 'A' and resid 90 through 91' Processing helix chain 'A' and resid 93 through 93 No H-bonds generated for 'chain 'A' and resid 93 through 93' Processing helix chain 'A' and resid 94 through 106 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 157 through 166 removed outlier: 3.509A pdb=" N ALA A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 264 through 278 removed outlier: 4.166A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.793A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.981A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.510A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 4.540A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 8 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 22 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'G' and resid 44 through 46 No H-bonds generated for 'chain 'G' and resid 44 through 46' Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.581A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 85 Processing helix chain 'R' and resid 85 through 96 removed outlier: 3.874A pdb=" N PHE R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.569A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 170 removed outlier: 3.505A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 182 through 187 removed outlier: 3.787A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.526A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.209A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.662A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.531A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY R 315 " --> pdb=" O LEU R 311 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.787A pdb=" N GLU R 338 " --> pdb=" O ILE R 334 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.012A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 290 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.603A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 51 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.894A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.691A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.601A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.817A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.689A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 removed outlier: 5.943A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 353 hydrogen bonds defined for protein. 1035 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: 0.59 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1923 1.34 - 1.46: 1362 1.46 - 1.58: 2263 1.58 - 1.69: 1 1.69 - 1.81: 2 Bond restraints: 5551 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.600 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" CAF G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.519 1.573 -0.054 2.00e-02 2.50e+03 7.16e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.450 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.440 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.485 -0.034 2.00e-02 2.50e+03 2.82e+00 ... (remaining 5546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 7368 1.18 - 2.36: 266 2.36 - 3.55: 40 3.55 - 4.73: 7 4.73 - 5.91: 7 Bond angle restraints: 7688 Sorted by residual: angle pdb=" C VAL R 86 " pdb=" N VAL R 87 " pdb=" CA VAL R 87 " ideal model delta sigma weight residual 120.33 122.70 -2.37 8.00e-01 1.56e+00 8.79e+00 angle pdb=" C PHE R 321 " pdb=" N ASN R 322 " pdb=" CA ASN R 322 " ideal model delta sigma weight residual 120.09 123.58 -3.49 1.25e+00 6.40e-01 7.81e+00 angle pdb=" C VAL R 87 " pdb=" CA VAL R 87 " pdb=" CB VAL R 87 " ideal model delta sigma weight residual 114.00 110.43 3.57 1.31e+00 5.83e-01 7.45e+00 angle pdb=" C VAL R 210 " pdb=" CA VAL R 210 " pdb=" CB VAL R 210 " ideal model delta sigma weight residual 114.00 110.89 3.11 1.31e+00 5.83e-01 5.64e+00 angle pdb=" N ASN R 69 " pdb=" CA ASN R 69 " pdb=" C ASN R 69 " ideal model delta sigma weight residual 113.72 110.58 3.14 1.52e+00 4.33e-01 4.27e+00 ... (remaining 7683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.95: 3028 19.95 - 39.91: 60 39.91 - 59.86: 13 59.86 - 79.82: 1 79.82 - 99.77: 3 Dihedral angle restraints: 3105 sinusoidal: 386 harmonic: 2719 Sorted by residual: dihedral pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sinusoidal sigma weight residual -66.05 33.72 -99.77 1 3.00e+01 1.11e-03 1.25e+01 dihedral pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sinusoidal sigma weight residual 47.24 -51.60 98.84 1 3.00e+01 1.11e-03 1.23e+01 dihedral pdb=" CA TYR A 360 " pdb=" C TYR A 360 " pdb=" N PRO A 361 " pdb=" CA PRO A 361 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 3102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 595 0.028 - 0.057: 219 0.057 - 0.085: 75 0.085 - 0.114: 48 0.114 - 0.142: 6 Chirality restraints: 943 Sorted by residual: chirality pdb=" CG LEU B 51 " pdb=" CB LEU B 51 " pdb=" CD1 LEU B 51 " pdb=" CD2 LEU B 51 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 940 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 332 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 151 " -0.008 2.00e-02 2.50e+03 7.37e-03 9.52e-01 pdb=" CG PHE B 151 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE B 151 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 151 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 151 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 151 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 151 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.014 5.00e-02 4.00e+02 2.15e-02 7.42e-01 pdb=" N PRO B 236 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.012 5.00e-02 4.00e+02 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1016 2.76 - 3.30: 5365 3.30 - 3.83: 8575 3.83 - 4.37: 8541 4.37 - 4.90: 14877 Nonbonded interactions: 38374 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.226 3.040 nonbonded pdb=" O CYS A 237 " pdb=" OH TYR B 59 " model vdw 2.327 3.040 nonbonded pdb=" O ASN B 155 " pdb=" N ILE B 171 " model vdw 2.347 3.120 nonbonded pdb=" O HIS G 44 " pdb=" ND1 HIS G 44 " model vdw 2.353 3.120 nonbonded pdb=" OG SER B 331 " pdb=" O PHE B 335 " model vdw 2.374 3.040 ... (remaining 38369 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 group one per residue 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.280 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 0.077 5551 Z= 0.149 Angle : 0.543 5.909 7688 Z= 0.333 Chirality : 0.039 0.142 943 Planarity : 0.002 0.027 1037 Dihedral : 10.593 99.771 1327 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.29), residues: 902 helix: 2.48 (0.27), residues: 378 sheet: 0.29 (0.47), residues: 135 loop : -1.04 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 22 TYR 0.007 0.001 TYR A 253 PHE 0.017 0.001 PHE B 151 TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5551) covalent geometry : angle 0.54293 ( 7688) hydrogen bonds : bond 0.26033 ( 353) hydrogen bonds : angle 7.38436 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.0352 time to fit residues: 2.8182 Evaluate side-chains 42 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 1.9990 overall best weight: 1.2156 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.072234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.063714 restraints weight = 31048.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.064714 restraints weight = 20452.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065391 restraints weight = 15044.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.065898 restraints weight = 12042.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.066405 restraints weight = 10134.597| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5551 Z= 0.131 Angle : 0.470 9.368 7688 Z= 0.263 Chirality : 0.042 0.165 943 Planarity : 0.003 0.028 1037 Dihedral : 4.949 45.618 965 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.56 % Allowed : 6.67 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.29), residues: 902 helix: 2.47 (0.25), residues: 413 sheet: -0.33 (0.43), residues: 152 loop : -1.13 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.011 0.001 TYR R 199 PHE 0.020 0.002 PHE B 151 TRP 0.010 0.001 TRP R 313 HIS 0.002 0.001 HIS R 296 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5551) covalent geometry : angle 0.47048 ( 7688) hydrogen bonds : bond 0.04313 ( 353) hydrogen bonds : angle 4.78005 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.207 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 46 average time/residue: 0.0321 time to fit residues: 2.5810 Evaluate side-chains 42 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 75 optimal weight: 0.1980 chunk 43 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 8 optimal weight: 20.0000 chunk 57 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 12 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.074234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065696 restraints weight = 30245.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066785 restraints weight = 19740.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.067565 restraints weight = 14285.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.068067 restraints weight = 11215.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068187 restraints weight = 9373.399| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5551 Z= 0.088 Angle : 0.406 5.289 7688 Z= 0.227 Chirality : 0.040 0.143 943 Planarity : 0.002 0.022 1037 Dihedral : 3.764 31.317 965 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.29), residues: 902 helix: 2.77 (0.25), residues: 410 sheet: -0.24 (0.44), residues: 151 loop : -0.98 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.007 0.001 TYR R 199 PHE 0.016 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00161 ( 5551) covalent geometry : angle 0.40553 ( 7688) hydrogen bonds : bond 0.03421 ( 353) hydrogen bonds : angle 3.99617 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.174 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0303 time to fit residues: 2.6460 Evaluate side-chains 44 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 20.0000 chunk 60 optimal weight: 0.0470 chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.5882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.072364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063824 restraints weight = 30616.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.064837 restraints weight = 20312.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.065545 restraints weight = 14923.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.066008 restraints weight = 11810.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066135 restraints weight = 9968.697| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5551 Z= 0.138 Angle : 0.437 5.329 7688 Z= 0.249 Chirality : 0.041 0.161 943 Planarity : 0.002 0.022 1037 Dihedral : 3.857 34.876 965 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.56 % Allowed : 3.33 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.29), residues: 902 helix: 2.98 (0.26), residues: 405 sheet: -0.31 (0.44), residues: 144 loop : -1.13 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.010 0.001 TYR A 360 PHE 0.021 0.002 PHE B 151 TRP 0.009 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5551) covalent geometry : angle 0.43738 ( 7688) hydrogen bonds : bond 0.03343 ( 353) hydrogen bonds : angle 3.99050 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.161 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.0286 time to fit residues: 2.3624 Evaluate side-chains 42 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3217 r_free = 0.3217 target = 0.070047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.061665 restraints weight = 32074.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.062620 restraints weight = 21180.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063263 restraints weight = 15430.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063516 restraints weight = 12352.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.063913 restraints weight = 10856.511| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5551 Z= 0.210 Angle : 0.502 5.489 7688 Z= 0.292 Chirality : 0.042 0.199 943 Planarity : 0.003 0.025 1037 Dihedral : 4.472 40.527 965 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.07 (0.29), residues: 902 helix: 2.81 (0.26), residues: 402 sheet: -0.28 (0.48), residues: 128 loop : -1.39 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.023 0.002 TYR R 141 PHE 0.029 0.002 PHE B 151 TRP 0.009 0.002 TRP R 105 HIS 0.005 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 5551) covalent geometry : angle 0.50206 ( 7688) hydrogen bonds : bond 0.03827 ( 353) hydrogen bonds : angle 4.27791 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0353 time to fit residues: 2.6659 Evaluate side-chains 37 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 84 optimal weight: 0.0670 chunk 0 optimal weight: 10.0000 overall best weight: 1.9522 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.070949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.062549 restraints weight = 31640.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.063628 restraints weight = 20930.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.064229 restraints weight = 15325.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064763 restraints weight = 11990.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.064993 restraints weight = 9873.309| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5551 Z= 0.154 Angle : 0.459 5.391 7688 Z= 0.264 Chirality : 0.041 0.154 943 Planarity : 0.003 0.024 1037 Dihedral : 4.240 38.530 965 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.13 (0.29), residues: 902 helix: 2.91 (0.26), residues: 404 sheet: -0.42 (0.48), residues: 128 loop : -1.37 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 22 TYR 0.014 0.001 TYR R 199 PHE 0.027 0.002 PHE A 273 TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 5551) covalent geometry : angle 0.45908 ( 7688) hydrogen bonds : bond 0.03418 ( 353) hydrogen bonds : angle 4.02142 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.0331 time to fit residues: 2.7146 Evaluate side-chains 39 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 0.0030 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.072917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064478 restraints weight = 31363.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065502 restraints weight = 20601.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.066035 restraints weight = 15000.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.066689 restraints weight = 12229.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.067041 restraints weight = 10073.163| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5551 Z= 0.080 Angle : 0.405 5.264 7688 Z= 0.224 Chirality : 0.040 0.140 943 Planarity : 0.002 0.020 1037 Dihedral : 3.714 33.359 965 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.29), residues: 902 helix: 3.15 (0.25), residues: 405 sheet: -0.65 (0.44), residues: 141 loop : -1.21 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.021 0.001 TYR R 141 PHE 0.016 0.001 PHE B 151 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00153 ( 5551) covalent geometry : angle 0.40470 ( 7688) hydrogen bonds : bond 0.02746 ( 353) hydrogen bonds : angle 3.55154 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.207 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0290 time to fit residues: 2.5449 Evaluate side-chains 39 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 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 = 0.3191 r_free = 0.3191 target = 0.068963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060745 restraints weight = 31844.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.061448 restraints weight = 20734.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062180 restraints weight = 15897.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062732 restraints weight = 12739.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.062979 restraints weight = 10393.882| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5551 Z= 0.261 Angle : 0.563 5.856 7688 Z= 0.330 Chirality : 0.043 0.275 943 Planarity : 0.003 0.024 1037 Dihedral : 4.745 42.679 965 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.64 (0.29), residues: 902 helix: 2.56 (0.26), residues: 406 sheet: -0.89 (0.47), residues: 131 loop : -1.63 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.017 0.002 TYR A 360 PHE 0.036 0.003 PHE A 273 TRP 0.010 0.002 TRP R 105 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 5551) covalent geometry : angle 0.56288 ( 7688) hydrogen bonds : bond 0.04064 ( 353) hydrogen bonds : angle 4.50006 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0307 time to fit residues: 2.1913 Evaluate side-chains 34 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 59 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 296 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.072142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.063722 restraints weight = 31235.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.064715 restraints weight = 20710.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.065437 restraints weight = 15187.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.065951 restraints weight = 12038.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066245 restraints weight = 10004.031| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5551 Z= 0.093 Angle : 0.434 6.168 7688 Z= 0.241 Chirality : 0.041 0.207 943 Planarity : 0.002 0.022 1037 Dihedral : 4.017 37.396 965 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.29), residues: 902 helix: 2.86 (0.26), residues: 409 sheet: -1.02 (0.45), residues: 134 loop : -1.27 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.011 0.001 TYR R 141 PHE 0.026 0.002 PHE A 273 TRP 0.012 0.001 TRP R 313 HIS 0.008 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 5551) covalent geometry : angle 0.43359 ( 7688) hydrogen bonds : bond 0.02967 ( 353) hydrogen bonds : angle 3.73246 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0313 time to fit residues: 2.5444 Evaluate side-chains 37 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 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 = 0.3261 r_free = 0.3261 target = 0.072035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063565 restraints weight = 31411.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.064628 restraints weight = 20787.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065265 restraints weight = 15085.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065776 restraints weight = 12121.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.066092 restraints weight = 10126.047| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5551 Z= 0.103 Angle : 0.429 6.103 7688 Z= 0.238 Chirality : 0.041 0.198 943 Planarity : 0.002 0.022 1037 Dihedral : 3.840 35.360 965 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.29), residues: 902 helix: 3.07 (0.26), residues: 406 sheet: -1.09 (0.43), residues: 148 loop : -1.27 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.026 0.001 TYR R 141 PHE 0.019 0.001 PHE B 151 TRP 0.019 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5551) covalent geometry : angle 0.42854 ( 7688) hydrogen bonds : bond 0.02894 ( 353) hydrogen bonds : angle 3.63883 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.210 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0269 time to fit residues: 2.0666 Evaluate side-chains 37 residues out of total 811 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 12 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 8 optimal weight: 40.0000 chunk 72 optimal weight: 4.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 59 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 = 0.3182 r_free = 0.3182 target = 0.068860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.060650 restraints weight = 32003.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.061562 restraints weight = 21150.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062009 restraints weight = 15583.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062539 restraints weight = 12952.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.063044 restraints weight = 10854.919| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5551 Z= 0.268 Angle : 0.554 5.648 7688 Z= 0.327 Chirality : 0.043 0.250 943 Planarity : 0.003 0.024 1037 Dihedral : 4.811 41.347 965 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.57 (0.29), residues: 902 helix: 2.44 (0.26), residues: 414 sheet: -1.06 (0.46), residues: 138 loop : -1.63 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 22 TYR 0.028 0.002 TYR R 141 PHE 0.032 0.003 PHE B 151 TRP 0.016 0.002 TRP B 169 HIS 0.007 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 5551) covalent geometry : angle 0.55422 ( 7688) hydrogen bonds : bond 0.03985 ( 353) hydrogen bonds : angle 4.40273 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 792.77 seconds wall clock time: 14 minutes 10.99 seconds (850.99 seconds total)