Starting phenix.real_space_refine on Fri Aug 22 16:40:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8geh_29970/08_2025/8geh_29970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8geh_29970/08_2025/8geh_29970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8geh_29970/08_2025/8geh_29970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8geh_29970/08_2025/8geh_29970.map" model { file = "/net/cci-nas-00/data/ceres_data/8geh_29970/08_2025/8geh_29970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8geh_29970/08_2025/8geh_29970.cif" } resolution = 4.0 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= 0.021 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 11 5.16 5 C 3853 2.51 5 N 1069 2.21 5 O 1062 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: 5995 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 1812 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 8, 'TRANS': 292} Chain breaks: 8 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 714 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 578 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 15, 'ARG:plan': 20, 'ASN:plan1': 15, 'GLU:plan': 23, 'ASP:plan': 19, 'PHE:plan': 5, 'TYR:plan': 7, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 438 Chain: "B" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2133 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 309 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'ARG:plan': 12, 'GLN:plan1': 10, 'GLU:plan': 7, 'ASN:plan1': 12, 'ASP:plan': 24, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 244 Chain: "G" Number of atoms: 312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 312 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "R" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 1723 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 160} Link IDs: {'PTRANS': 7, 'TRANS': 270} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 664 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 5, 'ASN:plan1': 9, 'GLU:plan': 10, 'ARG:plan': 9, 'GLN:plan1': 9, 'TYR:plan': 3, 'ASP:plan': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 236 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: 1.95, per 1000 atoms: 0.33 Number of scatterers: 5995 At special positions: 0 Unit cell: (68.9, 98.58, 128.26, 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 11 16.00 O 1062 8.00 N 1069 7.00 C 3853 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: 0.60 Conformation dependent library (CDL) restraints added in 509.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 8 sheets defined 50.1% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.551A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 removed outlier: 4.009A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 114 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.850A pdb=" N CYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 238' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.907A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.429A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.757A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 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 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.591A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.634A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 86 removed outlier: 4.158A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER R 74 " --> pdb=" O TYR R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.654A pdb=" N VAL R 117 " --> pdb=" O ASP R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 163 Processing helix chain 'R' and resid 165 through 172 removed outlier: 3.892A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 removed outlier: 3.963A pdb=" N TYR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA R 186 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.597A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 236 removed outlier: 3.615A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 293 removed outlier: 3.523A pdb=" N ILE R 277 " --> pdb=" O LYS R 273 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 294 through 299 removed outlier: 4.271A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 326 removed outlier: 3.631A pdb=" N ILE R 309 " --> pdb=" O LYS R 305 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.768A 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 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 212 removed outlier: 5.744A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.808A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.776A 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: 6.350A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.821A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.657A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.336A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.312A 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 278 removed outlier: 5.692A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1089 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: 0.94 Time building geometry restraints manager: 0.76 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: 2024 1.34 - 1.46: 1381 1.46 - 1.57: 2692 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 6111 Sorted by residual: 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 6.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.572 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.564 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.487 -0.036 2.00e-02 2.50e+03 3.30e+00 ... (remaining 6106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 8216 1.09 - 2.17: 175 2.17 - 3.26: 28 3.26 - 4.34: 10 4.34 - 5.43: 7 Bond angle restraints: 8436 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.44 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" N GLY B 202 " pdb=" CA GLY B 202 " pdb=" C GLY B 202 " ideal model delta sigma weight residual 111.46 114.89 -3.43 1.75e+00 3.27e-01 3.83e+00 angle pdb=" C VAL A 214 " pdb=" N ASP A 215 " pdb=" CA ASP A 215 " ideal model delta sigma weight residual 121.54 125.12 -3.58 1.91e+00 2.74e-01 3.51e+00 angle pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sigma weight residual 110.89 116.32 -5.43 3.00e+00 1.11e-01 3.27e+00 angle pdb=" CA ILE B 270 " pdb=" C ILE B 270 " pdb=" N CYS B 271 " ideal model delta sigma weight residual 118.71 116.64 2.07 1.15e+00 7.56e-01 3.24e+00 ... (remaining 8431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.91: 3159 10.91 - 21.82: 157 21.82 - 32.74: 77 32.74 - 43.65: 36 43.65 - 54.56: 9 Dihedral angle restraints: 3438 sinusoidal: 644 harmonic: 2794 Sorted by residual: dihedral pdb=" CA HIS B 183 " pdb=" C HIS B 183 " pdb=" N THR B 184 " pdb=" CA THR B 184 " ideal model delta harmonic sigma weight residual 180.00 -164.10 -15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ARG A 380 " pdb=" CB ARG A 380 " pdb=" CG ARG A 380 " pdb=" CD ARG A 380 " ideal model delta sinusoidal sigma weight residual -60.00 -109.66 49.66 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG B 49 " pdb=" CB ARG B 49 " pdb=" CG ARG B 49 " pdb=" CD ARG B 49 " ideal model delta sinusoidal sigma weight residual 180.00 132.13 47.87 3 1.50e+01 4.44e-03 8.56e+00 ... (remaining 3435 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 730 0.034 - 0.068: 233 0.068 - 0.102: 68 0.102 - 0.136: 18 0.136 - 0.171: 2 Chirality restraints: 1051 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 7.27e-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 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE B 157 " pdb=" N ILE B 157 " pdb=" C ILE B 157 " pdb=" CB ILE B 157 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 1048 not shown) Planarity restraints: 1096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO R 168 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.05e+00 pdb=" N PRO B 236 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.005 2.00e-02 2.50e+03 1.00e-02 1.00e+00 pdb=" C THR B 87 " -0.017 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.006 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.006 2.00e-02 2.50e+03 ... (remaining 1093 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1650 2.80 - 3.33: 5824 3.33 - 3.85: 9406 3.85 - 4.38: 9766 4.38 - 4.90: 17270 Nonbonded interactions: 43916 Sorted by model distance: nonbonded pdb=" O LEU A 282 " pdb=" NE2 HIS A 357 " model vdw 2.276 3.120 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.289 3.040 nonbonded pdb=" ND1 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.331 3.120 nonbonded pdb=" NE1 TRP A 277 " pdb=" O SER A 349 " model vdw 2.352 3.120 nonbonded pdb=" NH2 ARG B 49 " pdb=" O PHE G 61 " model vdw 2.357 3.120 ... (remaining 43911 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: 1.950 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 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 0.053 6111 Z= 0.136 Angle : 0.433 5.428 8436 Z= 0.241 Chirality : 0.039 0.171 1051 Planarity : 0.002 0.032 1096 Dihedral : 10.847 54.562 1612 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 1.54 (0.28), residues: 930 helix: 2.42 (0.24), residues: 415 sheet: 0.67 (0.44), residues: 163 loop : -0.52 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.014 0.001 TYR R 141 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6111) covalent geometry : angle 0.43294 ( 8436) hydrogen bonds : bond 0.25326 ( 373) hydrogen bonds : angle 7.08136 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.211 Fit side-chains REVERT: A 380 ARG cc_start: 0.8813 (tmm-80) cc_final: 0.8369 (ttm170) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0583 time to fit residues: 4.9916 Evaluate side-chains 44 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3368 r_free = 0.3368 target = 0.085310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.074036 restraints weight = 22144.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075482 restraints weight = 13237.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076655 restraints weight = 9198.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077292 restraints weight = 6941.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.077902 restraints weight = 5730.072| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6111 Z= 0.125 Angle : 0.435 4.771 8436 Z= 0.251 Chirality : 0.040 0.139 1051 Planarity : 0.003 0.030 1096 Dihedral : 3.644 14.331 1000 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.31 % Allowed : 9.43 % Favored : 90.25 % 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: 1.98 (0.28), residues: 930 helix: 2.86 (0.24), residues: 429 sheet: 0.64 (0.42), residues: 173 loop : -0.44 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.014 0.001 TYR R 199 PHE 0.008 0.001 PHE B 199 TRP 0.018 0.001 TRP B 297 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6111) covalent geometry : angle 0.43457 ( 8436) hydrogen bonds : bond 0.04543 ( 373) hydrogen bonds : angle 4.74510 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.224 Fit side-chains REVERT: A 380 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8317 (ttm170) REVERT: B 17 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8446 (tm-30) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.0503 time to fit residues: 3.8340 Evaluate side-chains 43 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3351 r_free = 0.3351 target = 0.084650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.073245 restraints weight = 22100.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074683 restraints weight = 13469.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075670 restraints weight = 9394.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076268 restraints weight = 7265.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076998 restraints weight = 6101.199| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6111 Z= 0.124 Angle : 0.413 5.112 8436 Z= 0.234 Chirality : 0.039 0.147 1051 Planarity : 0.003 0.030 1096 Dihedral : 3.667 18.081 1000 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.94 % Allowed : 14.78 % Favored : 84.28 % 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: 2.11 (0.28), residues: 930 helix: 3.08 (0.24), residues: 429 sheet: 0.47 (0.41), residues: 180 loop : -0.42 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 380 TYR 0.015 0.001 TYR R 199 PHE 0.008 0.001 PHE B 199 TRP 0.021 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6111) covalent geometry : angle 0.41288 ( 8436) hydrogen bonds : bond 0.03593 ( 373) hydrogen bonds : angle 4.15327 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.235 Fit side-chains REVERT: A 380 ARG cc_start: 0.8733 (tmm-80) cc_final: 0.8511 (tmm-80) REVERT: A 385 ARG cc_start: 0.8445 (mtt90) cc_final: 0.7875 (mtt90) REVERT: B 17 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 3 outliers final: 1 residues processed: 49 average time/residue: 0.0652 time to fit residues: 4.7687 Evaluate side-chains 44 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3346 r_free = 0.3346 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.073018 restraints weight = 22237.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.074501 restraints weight = 13524.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.075429 restraints weight = 9357.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076278 restraints weight = 7229.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.076682 restraints weight = 5889.747| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6111 Z= 0.118 Angle : 0.405 5.106 8436 Z= 0.230 Chirality : 0.039 0.144 1051 Planarity : 0.003 0.030 1096 Dihedral : 3.610 16.979 1000 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.57 % Allowed : 17.61 % Favored : 80.82 % 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: 2.23 (0.29), residues: 930 helix: 3.18 (0.24), residues: 431 sheet: 0.51 (0.41), residues: 178 loop : -0.36 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 22 TYR 0.019 0.001 TYR R 199 PHE 0.010 0.001 PHE B 199 TRP 0.031 0.001 TRP B 297 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6111) covalent geometry : angle 0.40452 ( 8436) hydrogen bonds : bond 0.03131 ( 373) hydrogen bonds : angle 3.91759 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.226 Fit side-chains REVERT: A 380 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8208 (ttt90) REVERT: A 385 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7858 (mtt90) REVERT: B 297 TRP cc_start: 0.8176 (OUTLIER) cc_final: 0.7957 (m-10) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.0610 time to fit residues: 4.4293 Evaluate side-chains 46 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 19 optimal weight: 0.0370 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3364 r_free = 0.3364 target = 0.085342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073856 restraints weight = 22273.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.075353 restraints weight = 13494.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.076408 restraints weight = 9343.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077228 restraints weight = 7133.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077572 restraints weight = 5757.238| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6111 Z= 0.094 Angle : 0.392 5.042 8436 Z= 0.221 Chirality : 0.038 0.138 1051 Planarity : 0.002 0.030 1096 Dihedral : 3.431 16.418 1000 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.52 % Allowed : 18.87 % Favored : 78.62 % 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: 2.32 (0.29), residues: 930 helix: 3.26 (0.25), residues: 431 sheet: 0.65 (0.41), residues: 174 loop : -0.38 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 385 TYR 0.019 0.001 TYR R 141 PHE 0.008 0.001 PHE B 199 TRP 0.024 0.001 TRP B 297 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 6111) covalent geometry : angle 0.39173 ( 8436) hydrogen bonds : bond 0.02872 ( 373) hydrogen bonds : angle 3.77662 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.232 Fit side-chains REVERT: A 380 ARG cc_start: 0.8714 (tmm-80) cc_final: 0.8179 (ttt90) REVERT: A 385 ARG cc_start: 0.8436 (mtt90) cc_final: 0.7821 (mtt90) REVERT: B 273 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8539 (mp) REVERT: R 141 TYR cc_start: 0.7196 (t80) cc_final: 0.6993 (t80) outliers start: 8 outliers final: 4 residues processed: 53 average time/residue: 0.0594 time to fit residues: 4.7613 Evaluate side-chains 48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 47 optimal weight: 0.0040 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3339 r_free = 0.3339 target = 0.084293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.072868 restraints weight = 22030.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074300 restraints weight = 13419.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.075396 restraints weight = 9373.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075878 restraints weight = 7112.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076491 restraints weight = 6051.966| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6111 Z= 0.135 Angle : 0.416 5.121 8436 Z= 0.236 Chirality : 0.039 0.143 1051 Planarity : 0.003 0.028 1096 Dihedral : 3.620 16.916 1000 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.46 % Allowed : 18.87 % Favored : 77.67 % 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: 2.23 (0.29), residues: 930 helix: 3.24 (0.25), residues: 433 sheet: 0.36 (0.40), residues: 178 loop : -0.39 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.019 0.001 TYR R 141 PHE 0.010 0.001 PHE B 199 TRP 0.039 0.002 TRP B 297 HIS 0.002 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6111) covalent geometry : angle 0.41631 ( 8436) hydrogen bonds : bond 0.03033 ( 373) hydrogen bonds : angle 3.85676 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.286 Fit side-chains REVERT: A 380 ARG cc_start: 0.8739 (tmm-80) cc_final: 0.8244 (ttt90) REVERT: A 385 ARG cc_start: 0.8517 (mtt90) cc_final: 0.7954 (mtt90) REVERT: B 273 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 11 outliers final: 5 residues processed: 54 average time/residue: 0.0591 time to fit residues: 4.8178 Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 0.0030 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3361 r_free = 0.3361 target = 0.085221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.073735 restraints weight = 22061.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075201 restraints weight = 13402.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076325 restraints weight = 9245.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077001 restraints weight = 7031.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077602 restraints weight = 5797.727| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6111 Z= 0.095 Angle : 0.433 9.985 8436 Z= 0.230 Chirality : 0.039 0.137 1051 Planarity : 0.002 0.029 1096 Dihedral : 3.475 17.035 1000 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.52 % Allowed : 20.13 % Favored : 77.36 % 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: 2.30 (0.29), residues: 930 helix: 3.31 (0.25), residues: 431 sheet: 0.48 (0.40), residues: 174 loop : -0.39 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.021 0.001 TYR R 141 PHE 0.009 0.001 PHE B 199 TRP 0.034 0.001 TRP B 297 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 6111) covalent geometry : angle 0.43321 ( 8436) hydrogen bonds : bond 0.02796 ( 373) hydrogen bonds : angle 3.74111 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.226 Fit side-chains REVERT: A 380 ARG cc_start: 0.8723 (tmm-80) cc_final: 0.8220 (ttt90) REVERT: A 385 ARG cc_start: 0.8486 (mtt90) cc_final: 0.7844 (mtt90) REVERT: B 273 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8566 (mp) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 0.0550 time to fit residues: 4.3196 Evaluate side-chains 46 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3366 r_free = 0.3366 target = 0.085409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073941 restraints weight = 22029.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075428 restraints weight = 13427.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.076251 restraints weight = 9236.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077229 restraints weight = 7282.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077396 restraints weight = 5853.636| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6111 Z= 0.096 Angle : 0.423 9.661 8436 Z= 0.226 Chirality : 0.038 0.138 1051 Planarity : 0.002 0.028 1096 Dihedral : 3.430 15.394 1000 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.89 % Allowed : 21.70 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.29), residues: 930 helix: 3.36 (0.25), residues: 431 sheet: 0.44 (0.40), residues: 174 loop : -0.41 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.013 0.001 TYR R 199 PHE 0.008 0.001 PHE B 199 TRP 0.031 0.001 TRP B 297 HIS 0.002 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 6111) covalent geometry : angle 0.42290 ( 8436) hydrogen bonds : bond 0.02717 ( 373) hydrogen bonds : angle 3.70488 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.231 Fit side-chains REVERT: A 380 ARG cc_start: 0.8712 (tmm-80) cc_final: 0.8223 (ttt90) REVERT: A 385 ARG cc_start: 0.8485 (mtt90) cc_final: 0.7927 (mtt90) REVERT: B 273 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8563 (mp) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 0.0588 time to fit residues: 4.4543 Evaluate side-chains 47 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 90 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3356 r_free = 0.3356 target = 0.084910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073487 restraints weight = 22229.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.074841 restraints weight = 13356.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.076015 restraints weight = 9432.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.076738 restraints weight = 7120.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077305 restraints weight = 5815.716| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6111 Z= 0.110 Angle : 0.428 9.115 8436 Z= 0.230 Chirality : 0.039 0.140 1051 Planarity : 0.003 0.028 1096 Dihedral : 3.472 14.553 1000 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.94 % Allowed : 22.64 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.28 (0.29), residues: 930 helix: 3.34 (0.25), residues: 433 sheet: 0.29 (0.39), residues: 176 loop : -0.39 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.014 0.001 TYR R 199 PHE 0.009 0.001 PHE B 199 TRP 0.021 0.001 TRP B 297 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6111) covalent geometry : angle 0.42772 ( 8436) hydrogen bonds : bond 0.02784 ( 373) hydrogen bonds : angle 3.69884 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.243 Fit side-chains REVERT: A 380 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8236 (ttt90) REVERT: A 385 ARG cc_start: 0.8502 (mtt90) cc_final: 0.7953 (mtt90) REVERT: B 273 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8571 (mp) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.0562 time to fit residues: 4.0657 Evaluate side-chains 48 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3372 r_free = 0.3372 target = 0.085810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074397 restraints weight = 22081.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.075859 restraints weight = 13259.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077021 restraints weight = 9179.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077630 restraints weight = 6934.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.078269 restraints weight = 5767.725| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6111 Z= 0.088 Angle : 0.414 8.922 8436 Z= 0.221 Chirality : 0.038 0.138 1051 Planarity : 0.002 0.028 1096 Dihedral : 3.392 19.625 1000 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.94 % Allowed : 23.27 % Favored : 75.79 % 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: 2.31 (0.29), residues: 930 helix: 3.36 (0.25), residues: 433 sheet: 0.38 (0.39), residues: 174 loop : -0.42 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.011 0.001 TYR R 199 PHE 0.008 0.001 PHE B 199 TRP 0.019 0.001 TRP B 297 HIS 0.002 0.001 HIS R 93 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 6111) covalent geometry : angle 0.41386 ( 8436) hydrogen bonds : bond 0.02604 ( 373) hydrogen bonds : angle 3.60143 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1860 Ramachandran restraints generated. 930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.258 Fit side-chains REVERT: A 380 ARG cc_start: 0.8707 (tmm-80) cc_final: 0.8212 (ttt90) REVERT: A 385 ARG cc_start: 0.8525 (mtt90) cc_final: 0.7911 (mtt90) REVERT: B 273 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8549 (mp) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.0526 time to fit residues: 3.8450 Evaluate side-chains 46 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain R residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 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 = 0.3359 r_free = 0.3359 target = 0.085072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.073579 restraints weight = 22100.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.075058 restraints weight = 13455.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.076083 restraints weight = 9279.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.076890 restraints weight = 7111.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.077315 restraints weight = 5804.858| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6111 Z= 0.108 Angle : 0.424 8.682 8436 Z= 0.229 Chirality : 0.039 0.165 1051 Planarity : 0.003 0.028 1096 Dihedral : 3.459 18.001 1000 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.57 % Allowed : 22.96 % Favored : 75.47 % 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: 2.31 (0.29), residues: 930 helix: 3.38 (0.25), residues: 433 sheet: 0.24 (0.39), residues: 178 loop : -0.37 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 385 TYR 0.015 0.001 TYR B 111 PHE 0.009 0.001 PHE B 199 TRP 0.025 0.002 TRP A 277 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 6111) covalent geometry : angle 0.42431 ( 8436) hydrogen bonds : bond 0.02716 ( 373) hydrogen bonds : angle 3.64446 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 948.17 seconds wall clock time: 17 minutes 0.92 seconds (1020.92 seconds total)