Starting phenix.real_space_refine on Fri Sep 11 04:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zth_14960/09_2026/7zth_14960.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zth_14960/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7zth_14960/09_2026/7zth_14960.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zth_14960/09_2026/7zth_14960.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zth_14960/09_2026/7zth_14960.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zth_14960/09_2026/7zth_14960.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zth_14960/09_2026/7zth_14960.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zth_14960/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 1.65, 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: 0.52 Conformation dependent library (CDL) restraints added in 282.9 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: 0.70 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: 0.64 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: 10443 2.16 - 4.32: 621 4.32 - 6.48: 64 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: 1.510 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.730 Find NCS groups from input model: 0.100 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.750 ------------------------------------------------------------------------------- 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= 0.571 Angle : 1.123 10.797 11152 Z= 0.761 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 1.12325 / 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 : 0.253 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: 0.0996 time to fit residues: 11.8229 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 : 0.250 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.168331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.132054 restraints weight = 14397.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133360 restraints weight = 11857.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134739 restraints weight = 8531.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.134797 restraints weight = 6681.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.135421 restraints weight = 6036.167| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7973 Z= 0.154 Angle : 0.728 8.994 11152 Z= 0.404 Chirality : 0.050 0.365 1221 Planarity : 0.006 0.065 1133 Dihedral : 24.869 146.118 1748 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.64 % Allowed : 20.03 % Favored : 77.33 % 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: -2.13 (0.49), residues: 106 loop : -2.88 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 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 0.00302 / 0.15 ( 7973) covalent geometry : angle 0.72806 / 0.40 (11152) hydrogen bonds : bond 0.05708 / 3.81 ( 161) hydrogen bonds : angle 6.11181 / 4.09 ( 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 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.169 Fit side-chains REVERT: A 122 GLU cc_start: 0.7709 (mp0) cc_final: 0.6662 (pm20) REVERT: A 138 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7404 (mtp180) REVERT: A 434 ILE cc_start: 0.7697 (pt) cc_final: 0.7427 (pt) REVERT: B 370 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7334 (ttm110) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.0622 time to fit residues: 7.7739 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 : 0.254 ------------------------------------------------------------------------------- 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: 4.9990 chunk 73 optimal weight: 30.0000 chunk 75 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN A 184 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.165012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128319 restraints weight = 14321.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.129307 restraints weight = 11822.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130743 restraints weight = 8718.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130784 restraints weight = 6714.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.131318 restraints weight = 6167.620| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7973 Z= 0.204 Angle : 0.723 8.834 11152 Z= 0.399 Chirality : 0.050 0.342 1221 Planarity : 0.006 0.059 1133 Dihedral : 24.851 146.327 1748 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 5.28 % Allowed : 20.96 % Favored : 73.76 % 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: -4.06 (0.28), residues: 712 helix: -2.83 (0.30), residues: 231 sheet: -2.10 (0.48), residues: 108 loop : -2.80 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.035 0.002 TYR B 303 PHE 0.013 0.002 PHE A 358 TRP 0.011 0.001 TRP A 124 HIS 0.008 0.002 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 ( 7973) covalent geometry : angle 0.72319 / 0.40 (11152) hydrogen bonds : bond 0.05349 / 3.47 ( 161) hydrogen bonds : angle 5.87981 / 3.92 ( 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: 34 poor density : 59 time to evaluate : 0.179 Fit side-chains REVERT: A 122 GLU cc_start: 0.7767 (mp0) cc_final: 0.6659 (pm20) REVERT: A 138 ARG cc_start: 0.7822 (mtt-85) cc_final: 0.7351 (mtp180) REVERT: B 281 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6985 (pm20) REVERT: B 365 MET cc_start: 0.7870 (mmm) cc_final: 0.7662 (mtp) outliers start: 34 outliers final: 20 residues processed: 86 average time/residue: 0.0598 time to fit residues: 7.7573 Evaluate side-chains 78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 281 GLU 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: 0.8980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 40.0000 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 HIS B 145 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.168117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.131763 restraints weight = 14600.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.133568 restraints weight = 11896.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134483 restraints weight = 8310.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134696 restraints weight = 6801.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135343 restraints weight = 5910.488| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7973 Z= 0.144 Angle : 0.645 10.080 11152 Z= 0.356 Chirality : 0.047 0.344 1221 Planarity : 0.005 0.056 1133 Dihedral : 24.726 146.338 1748 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.90 % Allowed : 21.12 % Favored : 72.98 % 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: -3.71 (0.28), residues: 712 helix: -2.56 (0.31), residues: 231 sheet: -1.80 (0.50), residues: 104 loop : -2.61 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.019 0.002 TYR B 303 PHE 0.009 0.001 PHE B 358 TRP 0.012 0.001 TRP A 124 HIS 0.007 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 7973) covalent geometry : angle 0.64509 / 0.36 (11152) hydrogen bonds : bond 0.04351 / 2.94 ( 161) hydrogen bonds : angle 5.46469 / 3.62 ( 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 106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.157 Fit side-chains REVERT: A 122 GLU cc_start: 0.7752 (mp0) cc_final: 0.6620 (pm20) REVERT: A 138 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7383 (mtp180) REVERT: B 281 GLU cc_start: 0.7167 (pm20) cc_final: 0.6937 (pm20) REVERT: B 370 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7330 (ttp-110) outliers start: 38 outliers final: 26 residues processed: 97 average time/residue: 0.0586 time to fit residues: 8.4243 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 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 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 312 ILE Chi-restraints excluded: chain B residue 383 TYR 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=3.50 ------------------------------------------------------------------------------- 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: 7.9990 chunk 77 optimal weight: 30.0000 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 29 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4309 r_free = 0.4309 target = 0.167801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.131464 restraints weight = 14525.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133019 restraints weight = 11702.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134065 restraints weight = 8259.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.134226 restraints weight = 6804.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.134891 restraints weight = 5950.983| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7973 Z= 0.147 Angle : 0.652 10.230 11152 Z= 0.354 Chirality : 0.047 0.344 1221 Planarity : 0.005 0.053 1133 Dihedral : 24.648 147.374 1748 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 5.90 % Allowed : 21.43 % Favored : 72.67 % 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: -3.45 (0.29), residues: 712 helix: -2.28 (0.32), residues: 230 sheet: -1.65 (0.50), residues: 106 loop : -2.51 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.021 0.002 TYR B 284 PHE 0.012 0.001 PHE A 334 TRP 0.012 0.001 TRP A 124 HIS 0.006 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 7973) covalent geometry : angle 0.65177 / 0.35 (11152) hydrogen bonds : bond 0.04210 / 2.76 ( 161) hydrogen bonds : angle 5.32265 / 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 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.260 Fit side-chains REVERT: A 122 GLU cc_start: 0.7632 (mp0) cc_final: 0.6633 (pm20) REVERT: A 138 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7357 (mtp180) REVERT: A 434 ILE cc_start: 0.7438 (pt) cc_final: 0.7185 (pt) outliers start: 38 outliers final: 34 residues processed: 89 average time/residue: 0.0584 time to fit residues: 7.7396 Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 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 B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL 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 251 SER 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 348 VAL Chi-restraints excluded: chain B residue 383 TYR 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: 0.9980 chunk 77 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.166972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.130908 restraints weight = 14503.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131142 restraints weight = 13670.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.132635 restraints weight = 9918.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.133157 restraints weight = 7279.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133421 restraints weight = 6749.956| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7973 Z= 0.164 Angle : 0.653 9.387 11152 Z= 0.355 Chirality : 0.047 0.348 1221 Planarity : 0.005 0.054 1133 Dihedral : 24.607 148.037 1748 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 6.52 % Allowed : 21.43 % Favored : 72.05 % 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: -3.31 (0.29), residues: 712 helix: -2.14 (0.32), residues: 230 sheet: -1.46 (0.51), residues: 104 loop : -2.47 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.016 0.002 TYR B 303 PHE 0.011 0.002 PHE A 307 TRP 0.014 0.001 TRP A 124 HIS 0.009 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 7973) covalent geometry : angle 0.65319 / 0.35 (11152) hydrogen bonds : bond 0.04190 / 2.72 ( 161) hydrogen bonds : angle 5.27615 / 3.50 ( 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 104 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 62 time to evaluate : 0.182 Fit side-chains REVERT: A 122 GLU cc_start: 0.7639 (mp0) cc_final: 0.6647 (pm20) REVERT: A 138 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7356 (mtp180) outliers start: 42 outliers final: 33 residues processed: 96 average time/residue: 0.0570 time to fit residues: 8.3588 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL 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 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 383 TYR 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: 4.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 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: 9.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.0470 overall best weight: 3.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 404 ASN B 438 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.165505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.128961 restraints weight = 14527.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.130261 restraints weight = 12521.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131643 restraints weight = 8585.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.131706 restraints weight = 6636.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132205 restraints weight = 6257.775| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7973 Z= 0.201 Angle : 0.710 12.502 11152 Z= 0.377 Chirality : 0.049 0.351 1221 Planarity : 0.005 0.053 1133 Dihedral : 24.635 148.438 1748 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 5.75 % Allowed : 22.36 % Favored : 71.89 % 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: -3.38 (0.29), residues: 712 helix: -2.22 (0.32), residues: 234 sheet: -1.62 (0.51), residues: 106 loop : -2.45 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 370 TYR 0.016 0.002 TYR A 157 PHE 0.015 0.002 PHE A 334 TRP 0.015 0.001 TRP A 124 HIS 0.008 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 ( 7973) covalent geometry : angle 0.71008 / 0.38 (11152) hydrogen bonds : bond 0.04388 / 2.78 ( 161) hydrogen bonds : angle 5.55090 / 3.74 ( 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 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 0.156 Fit side-chains REVERT: A 122 GLU cc_start: 0.7615 (mp0) cc_final: 0.6695 (pm20) REVERT: A 138 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7348 (mtp180) outliers start: 37 outliers final: 32 residues processed: 91 average time/residue: 0.0557 time to fit residues: 7.5139 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 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 B residue 141 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 172 VAL 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 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 383 TYR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 0.0010 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.5304 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.170130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134128 restraints weight = 14481.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.135539 restraints weight = 11505.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.136493 restraints weight = 8373.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136807 restraints weight = 6850.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137395 restraints weight = 5960.202| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2675 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= 0.123 Angle : 0.633 10.667 11152 Z= 0.340 Chirality : 0.045 0.356 1221 Planarity : 0.005 0.055 1133 Dihedral : 24.499 149.302 1748 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.19 % Allowed : 24.07 % Favored : 71.74 % 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: -2.97 (0.29), residues: 712 helix: -2.01 (0.32), residues: 237 sheet: -1.36 (0.48), residues: 105 loop : -2.11 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 370 TYR 0.017 0.001 TYR B 303 PHE 0.008 0.001 PHE B 121 TRP 0.019 0.002 TRP A 124 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 7973) covalent geometry : angle 0.63302 / 0.34 (11152) hydrogen bonds : bond 0.03830 / 2.53 ( 161) hydrogen bonds : angle 5.11010 / 3.44 ( 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 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.271 Fit side-chains REVERT: A 122 GLU cc_start: 0.7536 (mp0) cc_final: 0.6639 (pm20) REVERT: A 138 ARG cc_start: 0.7733 (mtt-85) cc_final: 0.7355 (mtp180) REVERT: A 434 ILE cc_start: 0.7516 (pt) cc_final: 0.7254 (pt) REVERT: B 281 GLU cc_start: 0.7029 (pm20) cc_final: 0.6775 (pm20) outliers start: 27 outliers final: 25 residues processed: 87 average time/residue: 0.0584 time to fit residues: 7.5560 Evaluate side-chains 85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 202 TYR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain A residue 289 ILE 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 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 247 PHE 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 383 TYR 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: 0.0670 chunk 28 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 40.0000 chunk 44 optimal weight: 5.9990 chunk 73 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 = 0.4337 r_free = 0.4337 target = 0.170361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.134438 restraints weight = 14411.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.135740 restraints weight = 12170.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.137126 restraints weight = 8463.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137307 restraints weight = 6508.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.137595 restraints weight = 6179.711| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7973 Z= 0.122 Angle : 0.622 10.352 11152 Z= 0.332 Chirality : 0.045 0.355 1221 Planarity : 0.005 0.055 1133 Dihedral : 24.448 150.813 1748 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.73 % Allowed : 24.53 % Favored : 71.74 % 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: -2.78 (0.30), residues: 712 helix: -1.78 (0.32), residues: 237 sheet: -1.23 (0.48), residues: 105 loop : -2.06 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 370 TYR 0.017 0.001 TYR B 303 PHE 0.009 0.001 PHE A 334 TRP 0.018 0.002 TRP A 124 HIS 0.006 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 ( 7973) covalent geometry : angle 0.62220 / 0.33 (11152) hydrogen bonds : bond 0.03743 / 2.43 ( 161) hydrogen bonds : angle 5.03778 / 3.38 ( 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 91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.164 Fit side-chains REVERT: A 122 GLU cc_start: 0.7532 (mp0) cc_final: 0.6715 (pm20) REVERT: A 138 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7394 (mtp180) REVERT: A 434 ILE cc_start: 0.7441 (pt) cc_final: 0.7192 (pt) outliers start: 24 outliers final: 20 residues processed: 84 average time/residue: 0.0668 time to fit residues: 8.0226 Evaluate side-chains 81 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 202 TYR 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 312 ILE Chi-restraints excluded: chain B residue 383 TYR 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: 4.9990 chunk 33 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.165415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.128805 restraints weight = 14430.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.130150 restraints weight = 12385.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.131341 restraints weight = 8579.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.131525 restraints weight = 6779.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.132178 restraints weight = 6195.496| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7973 Z= 0.225 Angle : 0.729 9.965 11152 Z= 0.387 Chirality : 0.050 0.355 1221 Planarity : 0.006 0.055 1133 Dihedral : 24.561 151.140 1748 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.19 % Allowed : 24.53 % Favored : 71.27 % 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: -2.99 (0.30), residues: 712 helix: -2.00 (0.32), residues: 242 sheet: -1.32 (0.51), residues: 103 loop : -2.15 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 343 TYR 0.016 0.002 TYR A 157 PHE 0.018 0.002 PHE A 334 TRP 0.014 0.002 TRP A 124 HIS 0.008 0.002 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.22 ( 7973) covalent geometry : angle 0.72911 / 0.39 (11152) hydrogen bonds : bond 0.04400 / 2.74 ( 161) hydrogen bonds : angle 5.44788 / 3.65 ( 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 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.265 Fit side-chains REVERT: A 122 GLU cc_start: 0.7599 (mp0) cc_final: 0.6723 (pm20) REVERT: A 138 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7452 (mtp180) outliers start: 27 outliers final: 25 residues processed: 81 average time/residue: 0.0624 time to fit residues: 7.6140 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 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 234 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 312 ILE Chi-restraints excluded: chain B residue 383 TYR Chi-restraints excluded: chain B residue 396 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.0670 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 16 optimal weight: 0.0070 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.170556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.134576 restraints weight = 14465.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.135926 restraints weight = 12042.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.137217 restraints weight = 8362.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137389 restraints weight = 6549.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137882 restraints weight = 5996.447| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7973 Z= 0.125 Angle : 0.651 11.942 11152 Z= 0.345 Chirality : 0.045 0.361 1221 Planarity : 0.005 0.057 1133 Dihedral : 24.449 151.120 1748 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.26 % Allowed : 26.09 % Favored : 70.65 % 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: -2.68 (0.30), residues: 712 helix: -1.74 (0.32), residues: 246 sheet: -1.20 (0.48), residues: 105 loop : -1.94 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 370 TYR 0.018 0.001 TYR A 157 PHE 0.010 0.001 PHE B 121 TRP 0.042 0.003 TRP A 124 HIS 0.008 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 7973) covalent geometry : angle 0.65122 / 0.35 (11152) hydrogen bonds : bond 0.03794 / 2.47 ( 161) hydrogen bonds : angle 5.01357 / 3.37 ( 435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1009.47 seconds wall clock time: 18 minutes 11.47 seconds (1091.47 seconds total)