Starting phenix.real_space_refine on Thu Jul 2 02:11:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtw_24691/07_2026/7rtw_24691.cif" } resolution = 3.23 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 Ca 2 9.91 5 S 24 5.16 5 C 3625 2.51 5 N 931 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s 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: 5644 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3027 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2418 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.34, per 1000 atoms: 0.24 Number of scatterers: 5644 At special positions: 0 Unit cell: (68.22, 92.097, 131.892, 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) Ca 2 19.99 S 24 16.00 O 1062 8.00 N 931 7.00 C 3625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 366 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 601 " - " ASN A 144 " " NAG C 1 " - " ASN A 126 " " NAG D 1 " - " ASN A 351 " " NAG E 1 " - " ASN B 126 " " NAG F 1 " - " ASN B 144 " " NAG G 1 " - " ASN B 351 " Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 217.3 milliseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 4.122A pdb=" N LEU A 15 " --> pdb=" O TRP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.674A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.687A pdb=" N ALA A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 147 removed outlier: 3.621A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.722A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 233 removed outlier: 4.295A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 273 removed outlier: 4.467A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 4.001A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 306 through 329 removed outlier: 4.157A pdb=" N LYS A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 4.300A pdb=" N GLU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 4.146A pdb=" N LEU A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 409 removed outlier: 4.471A pdb=" N LEU A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 147 Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.721A pdb=" N GLN B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 183 removed outlier: 4.147A pdb=" N ARG B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 234 Processing helix chain 'B' and resid 243 through 270 removed outlier: 4.492A pdb=" N VAL B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 4.051A pdb=" N PHE B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 307 through 323 removed outlier: 3.631A pdb=" N SER B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.698A pdb=" N ARG B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 364 removed outlier: 4.121A pdb=" N GLU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 removed outlier: 4.324A pdb=" N LEU B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 removed outlier: 4.011A pdb=" N TYR B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.649A pdb=" N ALA B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1790 1.34 - 1.46: 1317 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 5759 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 5754 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 7559 1.47 - 2.93: 223 2.93 - 4.40: 47 4.40 - 5.86: 21 5.86 - 7.33: 13 Bond angle restraints: 7863 Sorted by residual: angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 111.30 106.71 4.59 1.43e+00 4.89e-01 1.03e+01 angle pdb=" C ARG A 145 " pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta sigma weight residual 122.79 117.90 4.89 1.78e+00 3.16e-01 7.55e+00 angle pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " pdb=" CG ARG A 156 " ideal model delta sigma weight residual 114.10 119.13 -5.03 2.00e+00 2.50e-01 6.33e+00 angle pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" C VAL A 332 " ideal model delta sigma weight residual 108.88 113.95 -5.07 2.16e+00 2.14e-01 5.51e+00 angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.91 109.96 1.95 8.90e-01 1.26e+00 4.80e+00 ... (remaining 7858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 2865 16.17 - 32.35: 311 32.35 - 48.52: 69 48.52 - 64.70: 12 64.70 - 80.87: 9 Dihedral angle restraints: 3266 sinusoidal: 1240 harmonic: 2026 Sorted by residual: dihedral pdb=" CB CYS B 271 " pdb=" SG CYS B 271 " pdb=" SG CYS B 381 " pdb=" CB CYS B 381 " ideal model delta sinusoidal sigma weight residual 93.00 146.25 -53.25 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 381 " pdb=" CB CYS A 381 " ideal model delta sinusoidal sigma weight residual 93.00 143.40 -50.40 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CA GLU A 155 " pdb=" C GLU A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 3263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 923 0.083 - 0.165: 51 0.165 - 0.248: 1 0.248 - 0.331: 6 0.331 - 0.413: 1 Chirality restraints: 982 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 351 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 126 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 979 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 341 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO B 342 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 346 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C VAL B 346 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 346 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 347 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 347 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C GLN B 347 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN B 347 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 348 " -0.010 2.00e-02 2.50e+03 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 776 2.75 - 3.29: 5852 3.29 - 3.83: 9409 3.83 - 4.36: 9783 4.36 - 4.90: 17338 Nonbonded interactions: 43158 Sorted by model distance: nonbonded pdb=" OH TYR A 39 " pdb=" OD2 ASP A 269 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN B 126 " pdb=" N2 NAG E 1 " model vdw 2.316 3.120 nonbonded pdb=" OD2 ASP A 113 " pdb="CA CA A 603 " model vdw 2.346 2.510 nonbonded pdb=" O3 NAG C 1 " pdb=" O5 NAG C 2 " model vdw 2.353 3.040 nonbonded pdb=" OE2 GLU A 110 " pdb="CA CA A 602 " model vdw 2.355 2.510 ... (remaining 43153 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 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 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 : 0.004 0.076 5778 Z= 0.186 Angle : 0.702 7.329 7916 Z= 0.326 Chirality : 0.046 0.413 982 Planarity : 0.004 0.075 963 Dihedral : 14.675 80.870 1950 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.34), residues: 693 helix: 1.98 (0.23), residues: 546 sheet: None (None), residues: 0 loop : -1.19 (0.53), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.019 0.001 TYR A 296 PHE 0.015 0.001 PHE A 402 TRP 0.008 0.001 TRP A 88 HIS 0.008 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 ( 5759) covalent geometry : angle 0.67649 / 0.32 ( 7863) SS BOND : bond 0.00265 / 0.13 ( 4) SS BOND : angle 1.81908 / 1.08 ( 8) hydrogen bonds : bond 0.14995 / 9.65 ( 441) hydrogen bonds : angle 5.85006 / 4.45 ( 1317) link_BETA1-4 : bond 0.00467 / 0.23 ( 9) link_BETA1-4 : angle 2.24020 / 1.37 ( 27) link_NAG-ASN : bond 0.00765 / 0.38 ( 6) link_NAG-ASN : angle 2.78048 / 1.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.201 Fit side-chains REVERT: A 405 ILE cc_start: 0.8137 (mp) cc_final: 0.7908 (mp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.0773 time to fit residues: 8.1872 Evaluate side-chains 60 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4382 r_free = 0.4382 target = 0.162136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.144027 restraints weight = 11011.947| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 2.62 r_work: 0.4080 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5778 Z= 0.156 Angle : 0.661 6.722 7916 Z= 0.318 Chirality : 0.042 0.287 982 Planarity : 0.004 0.059 963 Dihedral : 4.194 23.984 759 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.70 % Allowed : 10.71 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.33), residues: 693 helix: 2.12 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -1.46 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 334 TYR 0.011 0.001 TYR A 373 PHE 0.023 0.002 PHE A 380 TRP 0.010 0.001 TRP A 11 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 ( 5759) covalent geometry : angle 0.63938 / 0.31 ( 7863) SS BOND : bond 0.00240 / 0.12 ( 4) SS BOND : angle 1.14615 / 0.71 ( 8) hydrogen bonds : bond 0.05524 / 3.60 ( 441) hydrogen bonds : angle 4.61057 / 3.38 ( 1317) link_BETA1-4 : bond 0.00495 / 0.24 ( 9) link_BETA1-4 : angle 2.17396 / 1.31 ( 27) link_NAG-ASN : bond 0.00678 / 0.34 ( 6) link_NAG-ASN : angle 2.44510 / 1.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.143 Fit side-chains REVERT: A 53 CYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8674 (t) REVERT: A 348 GLU cc_start: 0.7900 (tp30) cc_final: 0.7648 (tp30) REVERT: A 405 ILE cc_start: 0.8085 (mp) cc_final: 0.7865 (mt) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.0772 time to fit residues: 7.3117 Evaluate side-chains 72 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.163284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144423 restraints weight = 10765.329| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.64 r_work: 0.4060 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5778 Z= 0.142 Angle : 0.614 7.112 7916 Z= 0.295 Chirality : 0.040 0.272 982 Planarity : 0.004 0.039 963 Dihedral : 4.104 23.658 759 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.21 % Allowed : 13.95 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.33), residues: 693 helix: 2.13 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -1.68 (0.52), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 156 TYR 0.011 0.001 TYR A 373 PHE 0.025 0.002 PHE A 402 TRP 0.008 0.001 TRP A 11 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 5759) covalent geometry : angle 0.59261 / 0.29 ( 7863) SS BOND : bond 0.00244 / 0.12 ( 4) SS BOND : angle 0.96490 / 0.59 ( 8) hydrogen bonds : bond 0.05268 / 3.46 ( 441) hydrogen bonds : angle 4.32733 / 3.16 ( 1317) link_BETA1-4 : bond 0.00467 / 0.23 ( 9) link_BETA1-4 : angle 2.12005 / 1.29 ( 27) link_NAG-ASN : bond 0.00608 / 0.30 ( 6) link_NAG-ASN : angle 2.31693 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.158 Fit side-chains REVERT: A 53 CYS cc_start: 0.8998 (m) cc_final: 0.8741 (t) REVERT: A 348 GLU cc_start: 0.7929 (tp30) cc_final: 0.7668 (tp30) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.0654 time to fit residues: 6.3941 Evaluate side-chains 74 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.162510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.144806 restraints weight = 10943.201| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.57 r_work: 0.4103 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5778 Z= 0.133 Angle : 0.597 6.590 7916 Z= 0.285 Chirality : 0.039 0.256 982 Planarity : 0.003 0.036 963 Dihedral : 4.039 23.693 759 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.21 % Allowed : 15.99 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.33), residues: 693 helix: 2.21 (0.22), residues: 557 sheet: None (None), residues: 0 loop : -1.73 (0.51), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.011 0.001 TYR A 373 PHE 0.018 0.001 PHE A 60 TRP 0.007 0.001 TRP A 11 HIS 0.002 0.000 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 5759) covalent geometry : angle 0.57647 / 0.28 ( 7863) SS BOND : bond 0.00247 / 0.12 ( 4) SS BOND : angle 0.87026 / 0.54 ( 8) hydrogen bonds : bond 0.04996 / 3.29 ( 441) hydrogen bonds : angle 4.22272 / 3.09 ( 1317) link_BETA1-4 : bond 0.00470 / 0.23 ( 9) link_BETA1-4 : angle 2.06510 / 1.26 ( 27) link_NAG-ASN : bond 0.00598 / 0.30 ( 6) link_NAG-ASN : angle 2.23476 / 1.30 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.167 Fit side-chains REVERT: A 53 CYS cc_start: 0.8849 (m) cc_final: 0.8620 (t) REVERT: A 348 GLU cc_start: 0.7882 (tp30) cc_final: 0.7619 (tp30) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.0705 time to fit residues: 6.8566 Evaluate side-chains 72 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4401 r_free = 0.4401 target = 0.162418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.144631 restraints weight = 11220.971| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.58 r_work: 0.4137 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5778 Z= 0.129 Angle : 0.589 7.190 7916 Z= 0.281 Chirality : 0.039 0.252 982 Planarity : 0.003 0.032 963 Dihedral : 4.000 24.113 759 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.55 % Allowed : 17.69 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.33), residues: 693 helix: 2.26 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -1.73 (0.52), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.012 0.001 TYR A 373 PHE 0.010 0.001 PHE A 380 TRP 0.007 0.001 TRP A 11 HIS 0.002 0.001 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 5759) covalent geometry : angle 0.56904 / 0.28 ( 7863) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 0.83064 / 0.51 ( 8) hydrogen bonds : bond 0.04848 / 3.19 ( 441) hydrogen bonds : angle 4.14369 / 3.03 ( 1317) link_BETA1-4 : bond 0.00474 / 0.23 ( 9) link_BETA1-4 : angle 2.02327 / 1.23 ( 27) link_NAG-ASN : bond 0.00566 / 0.28 ( 6) link_NAG-ASN : angle 2.19030 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.197 Fit side-chains REVERT: A 53 CYS cc_start: 0.8853 (m) cc_final: 0.8603 (t) REVERT: A 348 GLU cc_start: 0.7860 (tp30) cc_final: 0.7588 (tp30) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.0770 time to fit residues: 7.1592 Evaluate side-chains 73 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 14 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4291 r_free = 0.4291 target = 0.158736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.140576 restraints weight = 11230.131| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 2.51 r_work: 0.3995 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5778 Z= 0.132 Angle : 0.591 7.126 7916 Z= 0.281 Chirality : 0.039 0.254 982 Planarity : 0.003 0.031 963 Dihedral : 3.988 24.890 759 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.06 % Allowed : 17.86 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.33), residues: 693 helix: 2.31 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -1.69 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.011 0.001 TYR A 373 PHE 0.020 0.001 PHE A 60 TRP 0.007 0.001 TRP A 11 HIS 0.002 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 5759) covalent geometry : angle 0.57124 / 0.28 ( 7863) SS BOND : bond 0.00251 / 0.12 ( 4) SS BOND : angle 0.83335 / 0.51 ( 8) hydrogen bonds : bond 0.04872 / 3.21 ( 441) hydrogen bonds : angle 4.11745 / 3.01 ( 1317) link_BETA1-4 : bond 0.00451 / 0.22 ( 9) link_BETA1-4 : angle 2.01343 / 1.22 ( 27) link_NAG-ASN : bond 0.00564 / 0.28 ( 6) link_NAG-ASN : angle 2.17991 / 1.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.206 Fit side-chains REVERT: A 53 CYS cc_start: 0.8866 (m) cc_final: 0.8610 (t) REVERT: A 348 GLU cc_start: 0.7809 (tp30) cc_final: 0.7563 (tp30) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.0726 time to fit residues: 7.5425 Evaluate side-chains 75 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 325 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4242 r_free = 0.4242 target = 0.154051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.135491 restraints weight = 11439.975| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 2.55 r_work: 0.3951 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5778 Z= 0.181 Angle : 0.676 7.765 7916 Z= 0.323 Chirality : 0.043 0.303 982 Planarity : 0.004 0.031 963 Dihedral : 4.245 29.394 759 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.74 % Allowed : 18.37 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.33), residues: 693 helix: 2.08 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -1.84 (0.51), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.012 0.001 TYR A 373 PHE 0.017 0.002 PHE B 277 TRP 0.008 0.001 TRP B 210 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 5759) covalent geometry : angle 0.65488 / 0.32 ( 7863) SS BOND : bond 0.00328 / 0.16 ( 4) SS BOND : angle 1.17961 / 0.69 ( 8) hydrogen bonds : bond 0.05747 / 3.79 ( 441) hydrogen bonds : angle 4.32961 / 3.16 ( 1317) link_BETA1-4 : bond 0.00368 / 0.18 ( 9) link_BETA1-4 : angle 2.15727 / 1.30 ( 27) link_NAG-ASN : bond 0.00528 / 0.26 ( 6) link_NAG-ASN : angle 2.42096 / 1.40 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.125 Fit side-chains REVERT: A 53 CYS cc_start: 0.8851 (m) cc_final: 0.8622 (t) REVERT: A 348 GLU cc_start: 0.7807 (tp30) cc_final: 0.7580 (tp30) REVERT: B 226 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7619 (mp) outliers start: 22 outliers final: 15 residues processed: 82 average time/residue: 0.0683 time to fit residues: 7.3594 Evaluate side-chains 81 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 206 ASP Chi-restraints excluded: chain B residue 226 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.0020 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4271 r_free = 0.4271 target = 0.157129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.138933 restraints weight = 11100.794| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.51 r_work: 0.3991 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5778 Z= 0.134 Angle : 0.612 7.204 7916 Z= 0.293 Chirality : 0.040 0.266 982 Planarity : 0.003 0.029 963 Dihedral : 4.110 26.512 759 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.38 % Allowed : 20.92 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.33), residues: 693 helix: 2.28 (0.22), residues: 555 sheet: None (None), residues: 0 loop : -1.72 (0.50), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 345 TYR 0.010 0.001 TYR A 373 PHE 0.009 0.001 PHE A 380 TRP 0.008 0.001 TRP A 11 HIS 0.002 0.000 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 5759) covalent geometry : angle 0.59103 / 0.29 ( 7863) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 0.93770 / 0.58 ( 8) hydrogen bonds : bond 0.05076 / 3.35 ( 441) hydrogen bonds : angle 4.13935 / 3.04 ( 1317) link_BETA1-4 : bond 0.00526 / 0.26 ( 9) link_BETA1-4 : angle 2.04594 / 1.24 ( 27) link_NAG-ASN : bond 0.00577 / 0.29 ( 6) link_NAG-ASN : angle 2.28632 / 1.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.145 Fit side-chains REVERT: A 53 CYS cc_start: 0.8883 (m) cc_final: 0.8632 (t) REVERT: B 161 ARG cc_start: 0.5558 (mtm180) cc_final: 0.5271 (mtp180) outliers start: 14 outliers final: 10 residues processed: 75 average time/residue: 0.0611 time to fit residues: 5.8684 Evaluate side-chains 72 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4278 r_free = 0.4278 target = 0.157430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.139273 restraints weight = 11389.686| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.54 r_work: 0.3993 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5778 Z= 0.135 Angle : 0.612 7.957 7916 Z= 0.292 Chirality : 0.040 0.260 982 Planarity : 0.004 0.033 963 Dihedral : 4.071 26.265 759 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.87 % Allowed : 21.43 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.33), residues: 693 helix: 2.28 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -1.79 (0.50), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 117 TYR 0.011 0.001 TYR A 373 PHE 0.020 0.001 PHE B 277 TRP 0.007 0.001 TRP A 11 HIS 0.003 0.000 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 5759) covalent geometry : angle 0.59206 / 0.29 ( 7863) SS BOND : bond 0.00221 / 0.11 ( 4) SS BOND : angle 0.94214 / 0.58 ( 8) hydrogen bonds : bond 0.04953 / 3.27 ( 441) hydrogen bonds : angle 4.08429 / 2.99 ( 1317) link_BETA1-4 : bond 0.00452 / 0.22 ( 9) link_BETA1-4 : angle 2.00578 / 1.21 ( 27) link_NAG-ASN : bond 0.00579 / 0.29 ( 6) link_NAG-ASN : angle 2.21256 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.236 Fit side-chains REVERT: A 53 CYS cc_start: 0.8853 (m) cc_final: 0.8604 (t) REVERT: A 321 MET cc_start: 0.7341 (mmm) cc_final: 0.6764 (mtt) REVERT: B 161 ARG cc_start: 0.5609 (mtm180) cc_final: 0.5312 (mtp180) REVERT: B 321 MET cc_start: 0.6826 (mmm) cc_final: 0.6375 (mtt) outliers start: 11 outliers final: 11 residues processed: 76 average time/residue: 0.0687 time to fit residues: 6.7728 Evaluate side-chains 75 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4245 r_free = 0.4245 target = 0.154294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.135744 restraints weight = 11483.315| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.58 r_work: 0.3952 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5778 Z= 0.176 Angle : 0.674 8.907 7916 Z= 0.323 Chirality : 0.043 0.298 982 Planarity : 0.004 0.036 963 Dihedral : 4.265 29.370 759 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.21 % Allowed : 21.09 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.33), residues: 693 helix: 2.11 (0.22), residues: 557 sheet: None (None), residues: 0 loop : -1.89 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.011 0.001 TYR A 373 PHE 0.020 0.002 PHE A 60 TRP 0.007 0.001 TRP B 210 HIS 0.002 0.001 HIS B 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 ( 5759) covalent geometry : angle 0.65350 / 0.32 ( 7863) SS BOND : bond 0.00305 / 0.15 ( 4) SS BOND : angle 1.24789 / 0.74 ( 8) hydrogen bonds : bond 0.05594 / 3.69 ( 441) hydrogen bonds : angle 4.23824 / 3.10 ( 1317) link_BETA1-4 : bond 0.00386 / 0.19 ( 9) link_BETA1-4 : angle 2.11393 / 1.27 ( 27) link_NAG-ASN : bond 0.00530 / 0.26 ( 6) link_NAG-ASN : angle 2.41143 / 1.38 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.211 Fit side-chains REVERT: A 53 CYS cc_start: 0.8885 (m) cc_final: 0.8640 (t) REVERT: B 321 MET cc_start: 0.7246 (mmm) cc_final: 0.6957 (mtt) REVERT: B 396 PHE cc_start: 0.6452 (m-80) cc_final: 0.6206 (m-10) outliers start: 13 outliers final: 11 residues processed: 76 average time/residue: 0.0793 time to fit residues: 7.9194 Evaluate side-chains 76 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 GLN ** 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 = 0.4273 r_free = 0.4273 target = 0.156904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.138931 restraints weight = 11131.937| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 2.49 r_work: 0.3987 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5778 Z= 0.138 Angle : 0.634 8.163 7916 Z= 0.303 Chirality : 0.040 0.238 982 Planarity : 0.004 0.030 963 Dihedral : 4.114 26.721 759 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.38 % Allowed : 20.92 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.33), residues: 693 helix: 2.30 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -1.86 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 117 TYR 0.010 0.001 TYR A 373 PHE 0.022 0.001 PHE A 60 TRP 0.008 0.001 TRP A 11 HIS 0.003 0.000 HIS B 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 5759) covalent geometry : angle 0.61505 / 0.30 ( 7863) SS BOND : bond 0.00224 / 0.11 ( 4) SS BOND : angle 0.94709 / 0.59 ( 8) hydrogen bonds : bond 0.05134 / 3.38 ( 441) hydrogen bonds : angle 4.13225 / 3.04 ( 1317) link_BETA1-4 : bond 0.00475 / 0.23 ( 9) link_BETA1-4 : angle 2.04486 / 1.24 ( 27) link_NAG-ASN : bond 0.00563 / 0.28 ( 6) link_NAG-ASN : angle 2.17373 / 1.27 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1175.99 seconds wall clock time: 20 minutes 53.85 seconds (1253.85 seconds total)