Starting phenix.real_space_refine on Thu Jul 2 07:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.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/7zth_14960/07_2026/7zth_14960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.map" model { file = "/net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zth_14960/07_2026/7zth_14960.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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 18 5.16 5 C 4622 2.51 5 N 1325 2.21 5 O 1571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7620 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2962 Classifications: {'peptide': 360} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2977 Classifications: {'peptide': 362} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 345} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 834 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Time building chain proxies: 1.71, per 1000 atoms: 0.22 Number of scatterers: 7620 At special positions: 0 Unit cell: (82.677, 90.678, 132.461, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 84 15.00 O 1571 8.00 N 1325 7.00 C 4622 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: 0.38 Conformation dependent library (CDL) restraints added in 233.6 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 37.4% alpha, 8.6% beta 12 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.545A pdb=" N ARG A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 190 removed outlier: 4.151A pdb=" N GLN A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.695A pdb=" N LEU A 209 " --> pdb=" O MET A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.554A pdb=" N LYS A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN A 260 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 267 " --> pdb=" O HIS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.130A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.971A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.537A pdb=" N GLN A 346 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.879A pdb=" N ALA A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 removed outlier: 4.161A pdb=" N LYS A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 3.895A pdb=" N GLU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 463 removed outlier: 4.186A pdb=" N ALA A 456 " --> pdb=" O GLU A 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.361A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET B 132 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 156 removed outlier: 3.715A pdb=" N ILE B 155 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 207 through 211 removed outlier: 3.788A pdb=" N HIS B 211 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.682A pdb=" N ILE B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.852A pdb=" N HIS B 263 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.588A pdb=" N MET B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 291 through 296' Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.843A pdb=" N HIS B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.566A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 380 removed outlier: 3.518A pdb=" N TYR B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 383 No H-bonds generated for 'chain 'B' and resid 381 through 383' Processing helix chain 'B' and resid 407 through 415 removed outlier: 3.951A pdb=" N LEU B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.663A pdb=" N ALA B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 219 removed outlier: 3.532A pdb=" N ILE A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.544A pdb=" N ILE A 390 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.914A pdb=" N ILE B 273 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU B 304 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLU B 275 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ALA B 306 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY B 305 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AA6, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.971A pdb=" N VAL B 399 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B 439 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 134 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 0.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1671 1.33 - 1.45: 2151 1.45 - 1.57: 3955 1.57 - 1.69: 164 1.69 - 1.81: 32 Bond restraints: 7973 Sorted by residual: bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.536 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.540 0.186 2.00e-02 2.50e+03 8.67e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.437 -0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" C4 LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.464 1.618 -0.154 2.00e-02 2.50e+03 5.89e+01 ... (remaining 7968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 10445 2.16 - 4.32: 620 4.32 - 6.48: 63 6.48 - 8.64: 14 8.64 - 10.80: 10 Bond angle restraints: 11152 Sorted by residual: angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 109.01 100.06 8.95 1.13e+00 7.83e-01 6.28e+01 angle pdb=" O4' DA D 16 " pdb=" C4' DA D 16 " pdb=" C3' DA D 16 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.82e+01 angle pdb=" C ASP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.62e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.92 -3.02 6.00e-01 2.78e+00 2.53e+01 angle pdb=" O4' DG D 38 " pdb=" C4' DG D 38 " pdb=" C3' DG D 38 " ideal model delta sigma weight residual 106.00 102.99 3.01 6.00e-01 2.78e+00 2.52e+01 ... (remaining 11147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.96: 3953 29.96 - 59.91: 576 59.91 - 89.87: 27 89.87 - 119.83: 0 119.83 - 149.78: 3 Dihedral angle restraints: 4559 sinusoidal: 2427 harmonic: 2132 Sorted by residual: dihedral pdb=" CA GLY B 286 " pdb=" C GLY B 286 " pdb=" N LYS B 287 " pdb=" CA LYS B 287 " ideal model delta harmonic sigma weight residual 180.00 -136.34 -43.66 0 5.00e+00 4.00e-02 7.63e+01 dihedral pdb=" CA GLY B 177 " pdb=" C GLY B 177 " pdb=" N VAL B 178 " pdb=" CA VAL B 178 " ideal model delta harmonic sigma weight residual 180.00 151.51 28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASN B 136 " pdb=" C ASN B 136 " pdb=" N HIS B 137 " pdb=" CA HIS B 137 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 4556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1010 0.081 - 0.161: 199 0.161 - 0.241: 10 0.241 - 0.322: 1 0.322 - 0.402: 1 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CB ILE A 446 " pdb=" CA ILE A 446 " pdb=" CG1 ILE A 446 " pdb=" CG2 ILE A 446 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' DA D 33 " pdb=" C4' DA D 33 " pdb=" O3' DA D 33 " pdb=" C2' DA D 33 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1218 not shown) Planarity restraints: 1133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.157 2.00e-02 2.50e+03 2.82e-01 7.96e+02 pdb=" NZ LLP A 309 " -0.384 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.132 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " -0.297 2.00e-02 2.50e+03 2.77e-01 7.65e+02 pdb=" NZ LLP B 309 " 0.311 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " -0.253 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " 0.240 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 289 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO A 290 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 290 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 290 " 0.040 5.00e-02 4.00e+02 ... (remaining 1130 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1636 2.78 - 3.31: 6210 3.31 - 3.84: 12588 3.84 - 4.37: 13923 4.37 - 4.90: 22293 Nonbonded interactions: 56650 Sorted by model distance: nonbonded pdb=" OH TYR A 240 " pdb=" OD2 ASP A 276 " model vdw 2.244 3.040 nonbonded pdb=" O SER A 314 " pdb=" OG SER A 314 " model vdw 2.261 3.040 nonbonded pdb=" OE1 GLN A 184 " pdb=" OH TYR A 330 " model vdw 2.268 3.040 nonbonded pdb=" O GLU B 453 " pdb=" OG1 THR B 457 " model vdw 2.290 3.040 nonbonded pdb=" O GLY B 177 " pdb=" OG SER B 318 " model vdw 2.294 3.040 ... (remaining 56645 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 105 through 464) } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.009 0.190 7973 Z= 0.570 Angle : 1.120 10.797 11152 Z= 0.756 Chirality : 0.062 0.402 1221 Planarity : 0.014 0.282 1133 Dihedral : 23.039 149.781 3191 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.24 % Allowed : 15.06 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -5.31 (0.24), residues: 712 helix: -4.33 (0.17), residues: 232 sheet: -3.13 (0.41), residues: 112 loop : -3.09 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 316 TYR 0.028 0.003 TYR B 202 PHE 0.025 0.004 PHE A 307 TRP 0.026 0.003 TRP A 124 HIS 0.015 0.002 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00950 / 0.57 ( 7973) covalent geometry : angle 1.12005 / 0.76 (11152) hydrogen bonds : bond 0.23684 / 15.23 ( 161) hydrogen bonds : angle 8.19228 / 5.67 ( 435) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.242 Fit side-chains REVERT: A 122 GLU cc_start: 0.7870 (mp0) cc_final: 0.6731 (pm20) REVERT: A 138 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7291 (mtp180) REVERT: A 353 MET cc_start: 0.7643 (mtm) cc_final: 0.7435 (mtm) outliers start: 8 outliers final: 3 residues processed: 91 average time/residue: 0.0866 time to fit residues: 10.2632 Evaluate side-chains 58 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN A 146 GLN A 211 HIS B 211 HIS B 246 HIS B 328 HIS B 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.168173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.132338 restraints weight = 14397.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.133730 restraints weight = 10628.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.134735 restraints weight = 7744.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134996 restraints weight = 6260.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.135099 restraints weight = 5458.420| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7973 Z= 0.151 Angle : 0.719 8.724 11152 Z= 0.401 Chirality : 0.050 0.358 1221 Planarity : 0.006 0.063 1133 Dihedral : 24.903 146.852 1748 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.48 % Allowed : 20.34 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -4.36 (0.27), residues: 712 helix: -3.28 (0.27), residues: 232 sheet: -2.11 (0.49), residues: 106 loop : -2.89 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 316 TYR 0.021 0.002 TYR A 157 PHE 0.009 0.001 PHE B 247 TRP 0.014 0.001 TRP A 124 HIS 0.012 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 ( 7973) covalent geometry : angle 0.71872 / 0.40 (11152) hydrogen bonds : bond 0.05715 / 3.81 ( 161) hydrogen bonds : angle 6.12786 / 4.10 ( 435) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.148 Fit side-chains REVERT: A 122 GLU cc_start: 0.7698 (mp0) cc_final: 0.6661 (pm20) REVERT: A 138 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7410 (mtp180) REVERT: A 434 ILE cc_start: 0.7509 (pt) cc_final: 0.7247 (pt) REVERT: B 370 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7318 (ttm110) outliers start: 16 outliers final: 13 residues processed: 82 average time/residue: 0.0516 time to fit residues: 6.2616 Evaluate side-chains 75 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 30.0000 chunk 74 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 75 optimal weight: 40.0000 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN A 211 HIS A 214 ASN B 123 GLN ** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.164966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.128164 restraints weight = 14309.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129200 restraints weight = 11737.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130610 restraints weight = 8664.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130681 restraints weight = 6622.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.130838 restraints weight = 6132.035| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7973 Z= 0.206 Angle : 0.722 8.697 11152 Z= 0.400 Chirality : 0.050 0.322 1221 Planarity : 0.006 0.057 1133 Dihedral : 24.898 147.015 1748 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 4.97 % Allowed : 20.96 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 are not related in a simple way. whole: -4.08 (0.28), residues: 712 helix: -2.85 (0.30), residues: 231 sheet: -2.09 (0.48), residues: 108 loop : -2.82 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 163 TYR 0.032 0.002 TYR B 303 PHE 0.013 0.002 PHE A 358 TRP 0.012 0.002 TRP A 124 HIS 0.010 0.002 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 ( 7973) covalent geometry : angle 0.72174 / 0.40 (11152) hydrogen bonds : bond 0.05334 / 3.48 ( 161) hydrogen bonds : angle 5.94417 / 3.96 ( 435) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 61 time to evaluate : 0.149 Fit side-chains REVERT: A 122 GLU cc_start: 0.7756 (mp0) cc_final: 0.6652 (pm20) REVERT: A 138 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7349 (mtp180) REVERT: B 275 GLU cc_start: 0.8353 (pp20) cc_final: 0.7818 (pp20) outliers start: 32 outliers final: 21 residues processed: 86 average time/residue: 0.0580 time to fit residues: 7.4427 Evaluate side-chains 76 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 chunk 75 optimal weight: 40.0000 chunk 32 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 65 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN B 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.170393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.134860 restraints weight = 14461.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136408 restraints weight = 11638.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137572 restraints weight = 8164.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137681 restraints weight = 6644.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.138326 restraints weight = 5836.756| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7973 Z= 0.128 Angle : 0.633 10.255 11152 Z= 0.348 Chirality : 0.046 0.314 1221 Planarity : 0.005 0.055 1133 Dihedral : 24.714 147.220 1748 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.81 % Allowed : 21.27 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -3.66 (0.28), residues: 712 helix: -2.62 (0.30), residues: 233 sheet: -1.60 (0.50), residues: 104 loop : -2.56 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.021 0.001 TYR B 303 PHE 0.012 0.001 PHE B 358 TRP 0.010 0.001 TRP A 124 HIS 0.006 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 7973) covalent geometry : angle 0.63272 / 0.35 (11152) hydrogen bonds : bond 0.04183 / 2.87 ( 161) hydrogen bonds : angle 5.29316 / 3.51 ( 435) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.165 Fit side-chains REVERT: A 122 GLU cc_start: 0.7670 (mp0) cc_final: 0.6559 (pm20) REVERT: A 138 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7428 (mtp180) REVERT: B 179 GLU cc_start: 0.8367 (mp0) cc_final: 0.8073 (mp0) REVERT: B 370 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7243 (ttp-110) outliers start: 31 outliers final: 17 residues processed: 93 average time/residue: 0.0562 time to fit residues: 7.8398 Evaluate side-chains 77 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 30.0000 chunk 59 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 chunk 29 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.167876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132032 restraints weight = 14483.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.132557 restraints weight = 12691.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.133929 restraints weight = 9135.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.134259 restraints weight = 6935.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134699 restraints weight = 6226.228| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7973 Z= 0.154 Angle : 0.648 9.913 11152 Z= 0.353 Chirality : 0.046 0.314 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.660 148.541 1748 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.12 % Allowed : 22.05 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -3.43 (0.29), residues: 712 helix: -2.30 (0.32), residues: 232 sheet: -1.53 (0.50), residues: 106 loop : -2.50 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.020 0.002 TYR B 284 PHE 0.015 0.002 PHE A 334 TRP 0.007 0.001 TRP B 264 HIS 0.006 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 7973) covalent geometry : angle 0.64821 / 0.35 (11152) hydrogen bonds : bond 0.04166 / 2.74 ( 161) hydrogen bonds : angle 5.29973 / 3.54 ( 435) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.174 Fit side-chains REVERT: A 122 GLU cc_start: 0.7616 (mp0) cc_final: 0.6615 (pm20) REVERT: A 138 ARG cc_start: 0.7755 (mtt-85) cc_final: 0.7360 (mtp180) REVERT: A 434 ILE cc_start: 0.7493 (pt) cc_final: 0.7248 (pt) REVERT: B 281 GLU cc_start: 0.7235 (pm20) cc_final: 0.6946 (pm20) outliers start: 33 outliers final: 27 residues processed: 84 average time/residue: 0.0540 time to fit residues: 6.8380 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 40.0000 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.168544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.132611 restraints weight = 14401.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132836 restraints weight = 13711.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134370 restraints weight = 9794.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.134849 restraints weight = 7196.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135139 restraints weight = 6669.015| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7973 Z= 0.144 Angle : 0.627 9.439 11152 Z= 0.341 Chirality : 0.046 0.319 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.586 148.801 1748 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 5.75 % Allowed : 22.05 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -3.23 (0.29), residues: 712 helix: -2.14 (0.32), residues: 236 sheet: -1.33 (0.50), residues: 104 loop : -2.40 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.023 0.002 TYR A 157 PHE 0.014 0.002 PHE A 334 TRP 0.012 0.001 TRP B 264 HIS 0.006 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7973) covalent geometry : angle 0.62656 / 0.34 (11152) hydrogen bonds : bond 0.03958 / 2.61 ( 161) hydrogen bonds : angle 5.16211 / 3.42 ( 435) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.181 Fit side-chains REVERT: A 122 GLU cc_start: 0.7576 (mp0) cc_final: 0.6625 (pm20) REVERT: A 138 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7395 (mtp180) REVERT: A 434 ILE cc_start: 0.7440 (pt) cc_final: 0.7218 (pt) REVERT: B 281 GLU cc_start: 0.6997 (pm20) cc_final: 0.6711 (pm20) outliers start: 37 outliers final: 31 residues processed: 91 average time/residue: 0.0593 time to fit residues: 8.1316 Evaluate side-chains 88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 57 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Chi-restraints excluded: chain B residue 458 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 78 optimal weight: 30.0000 chunk 51 optimal weight: 0.0010 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 110 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 = 0.4327 r_free = 0.4327 target = 0.169408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.133362 restraints weight = 14342.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134195 restraints weight = 12248.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.135330 restraints weight = 8954.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.135697 restraints weight = 6963.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.136342 restraints weight = 6268.166| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7973 Z= 0.132 Angle : 0.614 9.477 11152 Z= 0.334 Chirality : 0.045 0.322 1221 Planarity : 0.005 0.053 1133 Dihedral : 24.527 149.753 1748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.28 % Allowed : 22.36 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -3.10 (0.29), residues: 712 helix: -2.05 (0.31), residues: 240 sheet: -1.34 (0.49), residues: 108 loop : -2.27 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 125 TYR 0.020 0.001 TYR A 157 PHE 0.012 0.001 PHE A 334 TRP 0.019 0.002 TRP A 124 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 7973) covalent geometry : angle 0.61369 / 0.33 (11152) hydrogen bonds : bond 0.03811 / 2.50 ( 161) hydrogen bonds : angle 5.09993 / 3.37 ( 435) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.149 Fit side-chains REVERT: A 122 GLU cc_start: 0.7577 (mp0) cc_final: 0.6658 (pm20) REVERT: A 138 ARG cc_start: 0.7738 (mtt-85) cc_final: 0.7387 (mtp180) REVERT: B 148 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6648 (tp30) outliers start: 34 outliers final: 31 residues processed: 88 average time/residue: 0.0560 time to fit residues: 7.3956 Evaluate side-chains 89 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 110 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 = 0.4342 r_free = 0.4342 target = 0.170629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.134463 restraints weight = 14442.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.135988 restraints weight = 12201.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137259 restraints weight = 8345.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137360 restraints weight = 6591.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137951 restraints weight = 6095.609| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7973 Z= 0.122 Angle : 0.609 11.679 11152 Z= 0.329 Chirality : 0.044 0.324 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.454 150.899 1748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.28 % Allowed : 22.52 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -2.83 (0.30), residues: 712 helix: -1.84 (0.32), residues: 242 sheet: -1.04 (0.50), residues: 106 loop : -2.14 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.020 0.001 TYR A 157 PHE 0.010 0.001 PHE A 334 TRP 0.019 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 7973) covalent geometry : angle 0.60886 / 0.33 (11152) hydrogen bonds : bond 0.03653 / 2.39 ( 161) hydrogen bonds : angle 4.95831 / 3.28 ( 435) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 69 time to evaluate : 0.226 Fit side-chains REVERT: A 122 GLU cc_start: 0.7595 (mp0) cc_final: 0.6704 (pm20) REVERT: A 138 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7372 (mtp180) REVERT: A 343 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7597 (ttt180) REVERT: B 148 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6713 (tp30) outliers start: 34 outliers final: 27 residues processed: 94 average time/residue: 0.0593 time to fit residues: 8.1247 Evaluate side-chains 86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 59 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 452 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 28 optimal weight: 0.0670 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 HIS ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.170343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134291 restraints weight = 14394.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135605 restraints weight = 12079.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.136692 restraints weight = 8393.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137314 restraints weight = 6468.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137520 restraints weight = 5857.038| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7973 Z= 0.128 Angle : 0.635 14.380 11152 Z= 0.339 Chirality : 0.045 0.324 1221 Planarity : 0.005 0.055 1133 Dihedral : 24.427 151.767 1748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 5.12 % Allowed : 23.76 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -2.63 (0.30), residues: 712 helix: -1.68 (0.32), residues: 241 sheet: -0.93 (0.51), residues: 106 loop : -2.03 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 370 TYR 0.020 0.001 TYR B 336 PHE 0.010 0.001 PHE A 334 TRP 0.018 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 7973) covalent geometry : angle 0.63450 / 0.34 (11152) hydrogen bonds : bond 0.03641 / 2.37 ( 161) hydrogen bonds : angle 4.99032 / 3.36 ( 435) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.222 Fit side-chains REVERT: A 122 GLU cc_start: 0.7519 (mp0) cc_final: 0.6723 (pm20) REVERT: A 138 ARG cc_start: 0.7712 (mtt-85) cc_final: 0.7324 (mtp180) REVERT: A 343 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7611 (ttt180) REVERT: B 148 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6702 (tp30) outliers start: 33 outliers final: 30 residues processed: 86 average time/residue: 0.0698 time to fit residues: 8.7911 Evaluate side-chains 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 40.0000 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 110 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 = 0.4350 r_free = 0.4350 target = 0.171189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.135173 restraints weight = 14224.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.136256 restraints weight = 11445.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137103 restraints weight = 8692.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.137510 restraints weight = 6757.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.137762 restraints weight = 6099.577| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7973 Z= 0.122 Angle : 0.614 12.176 11152 Z= 0.329 Chirality : 0.044 0.326 1221 Planarity : 0.005 0.058 1133 Dihedral : 24.379 152.578 1748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.66 % Allowed : 23.76 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -2.45 (0.30), residues: 712 helix: -1.52 (0.33), residues: 242 sheet: -0.82 (0.51), residues: 106 loop : -1.92 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 370 TYR 0.020 0.001 TYR B 336 PHE 0.008 0.001 PHE A 334 TRP 0.019 0.001 TRP A 124 HIS 0.005 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 7973) covalent geometry : angle 0.61414 / 0.33 (11152) hydrogen bonds : bond 0.03512 / 2.27 ( 161) hydrogen bonds : angle 4.90536 / 3.31 ( 435) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.230 Fit side-chains REVERT: A 122 GLU cc_start: 0.7554 (mp0) cc_final: 0.6738 (pm20) REVERT: A 138 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7331 (mtp180) REVERT: A 307 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7160 (t80) REVERT: A 343 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7603 (ttt180) REVERT: B 148 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6683 (tp30) outliers start: 30 outliers final: 29 residues processed: 88 average time/residue: 0.0582 time to fit residues: 7.7279 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.0570 chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 110 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 = 0.4362 r_free = 0.4362 target = 0.172237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.136665 restraints weight = 14320.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137845 restraints weight = 11637.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138791 restraints weight = 8480.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.139367 restraints weight = 6395.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.139501 restraints weight = 5800.548| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7973 Z= 0.116 Angle : 0.616 11.851 11152 Z= 0.328 Chirality : 0.044 0.326 1221 Planarity : 0.005 0.060 1133 Dihedral : 24.343 153.337 1748 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 4.19 % Allowed : 24.22 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 are not related in a simple way. whole: -2.35 (0.30), residues: 712 helix: -1.53 (0.33), residues: 242 sheet: -0.70 (0.52), residues: 106 loop : -1.81 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.020 0.001 TYR A 157 PHE 0.007 0.001 PHE A 334 TRP 0.016 0.001 TRP B 264 HIS 0.004 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 7973) covalent geometry : angle 0.61620 / 0.33 (11152) hydrogen bonds : bond 0.03423 / 2.20 ( 161) hydrogen bonds : angle 4.80794 / 3.24 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.59 seconds wall clock time: 17 minutes 39.28 seconds (1059.28 seconds total)