Starting phenix.real_space_refine on Fri Aug 22 16:47:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zke_60190/08_2025/8zke_60190_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zke_60190/08_2025/8zke_60190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zke_60190/08_2025/8zke_60190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zke_60190/08_2025/8zke_60190.map" model { file = "/net/cci-nas-00/data/ceres_data/8zke_60190/08_2025/8zke_60190_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zke_60190/08_2025/8zke_60190_trim.cif" } resolution = 3.72 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= 0.011 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 S 20 5.16 5 C 1988 2.51 5 N 474 2.21 5 O 505 1.98 5 H 3070 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6057 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 6024 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 11, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'2YP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.93, per 1000 atoms: 0.15 Number of scatterers: 6057 At special positions: 0 Unit cell: (75.472, 74.624, 73.776, 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 20 16.00 O 505 8.00 N 474 7.00 C 1988 6.00 H 3070 1.00 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: 0.31 Conformation dependent library (CDL) restraints added in 141.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 696 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 4.357A pdb=" N LEU A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 42 removed outlier: 3.936A pdb=" N GLU A 42 " --> pdb=" O TRP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.996A pdb=" N GLY A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.749A pdb=" N GLY A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ALA A 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.697A pdb=" N MET A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 70' Processing helix chain 'A' and resid 82 through 101 removed outlier: 3.709A pdb=" N THR A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 4.061A pdb=" N ALA A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 131 removed outlier: 3.873A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 159 removed outlier: 4.450A pdb=" N SER A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.830A pdb=" N ALA A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N MET A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 183 removed outlier: 4.188A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 removed outlier: 4.137A pdb=" N CYS A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.411A pdb=" N VAL A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 212 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 removed outlier: 3.929A pdb=" N ARG A 216 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 235 removed outlier: 3.531A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 241 removed outlier: 3.628A pdb=" N PHE A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.660A pdb=" N ILE A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 266 through 285 removed outlier: 3.997A pdb=" N VAL A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 4.236A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.584A pdb=" N ASN A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TYR A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 345 removed outlier: 3.524A pdb=" N PHE A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N CYS A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 379 removed outlier: 3.505A pdb=" N PHE A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N GLY A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix removed outlier: 3.609A pdb=" N PHE A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 378 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.518A pdb=" N PHE A 387 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.762A pdb=" N LEU A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.828A pdb=" N TYR A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' 139 hydrogen bonds defined for protein. 396 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3065 1.04 - 1.23: 65 1.23 - 1.43: 1213 1.43 - 1.62: 1754 1.62 - 1.82: 35 Bond restraints: 6132 Sorted by residual: bond pdb=" CA5 2YP A 501 " pdb=" OA5 2YP A 501 " ideal model delta sigma weight residual 1.421 1.225 0.196 2.00e-02 2.50e+03 9.63e+01 bond pdb=" C5 2YP A 501 " pdb=" O5 2YP A 501 " ideal model delta sigma weight residual 1.412 1.538 -0.126 2.00e-02 2.50e+03 3.94e+01 bond pdb=" CAE 2YP A 501 " pdb=" NAD 2YP A 501 " ideal model delta sigma weight residual 1.345 1.465 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA1 2YP A 501 " pdb=" OA5 2YP A 501 " ideal model delta sigma weight residual 1.400 1.285 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C2 2YP A 501 " pdb=" N2 2YP A 501 " ideal model delta sigma weight residual 1.437 1.544 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 6127 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.84: 11090 8.84 - 17.67: 10 17.67 - 26.51: 1 26.51 - 35.34: 0 35.34 - 44.18: 1 Bond angle restraints: 11102 Sorted by residual: angle pdb=" CA VAL A 338 " pdb=" CB VAL A 338 " pdb=" HB VAL A 338 " ideal model delta sigma weight residual 109.00 64.82 44.18 3.00e+00 1.11e-01 2.17e+02 angle pdb=" N THR A 191 " pdb=" CA THR A 191 " pdb=" C THR A 191 " ideal model delta sigma weight residual 112.90 102.55 10.35 1.31e+00 5.83e-01 6.25e+01 angle pdb=" N PHE A 255 " pdb=" CA PHE A 255 " pdb=" C PHE A 255 " ideal model delta sigma weight residual 111.07 102.94 8.13 1.07e+00 8.73e-01 5.77e+01 angle pdb=" CA LEU A 179 " pdb=" C LEU A 179 " pdb=" O LEU A 179 " ideal model delta sigma weight residual 120.55 112.94 7.61 1.06e+00 8.90e-01 5.15e+01 angle pdb=" N GLU A 326 " pdb=" CA GLU A 326 " pdb=" C GLU A 326 " ideal model delta sigma weight residual 111.14 104.03 7.11 1.08e+00 8.57e-01 4.34e+01 ... (remaining 11097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 2514 19.80 - 39.59: 268 39.59 - 59.39: 106 59.39 - 79.19: 5 79.19 - 98.99: 9 Dihedral angle restraints: 2902 sinusoidal: 1563 harmonic: 1339 Sorted by residual: dihedral pdb=" CA ARG A 221 " pdb=" C ARG A 221 " pdb=" N ASN A 222 " pdb=" CA ASN A 222 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C ARG A 153 " pdb=" N ARG A 153 " pdb=" CA ARG A 153 " pdb=" CB ARG A 153 " ideal model delta harmonic sigma weight residual -122.60 -112.83 -9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" CA ASN A 222 " pdb=" C ASN A 222 " pdb=" N ASN A 223 " pdb=" CA ASN A 223 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 2899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 341 0.057 - 0.114: 79 0.114 - 0.171: 58 0.171 - 0.228: 17 0.228 - 0.285: 5 Chirality restraints: 500 Sorted by residual: chirality pdb=" CA ARG A 153 " pdb=" N ARG A 153 " pdb=" C ARG A 153 " pdb=" CB ARG A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA5 2YP A 501 " pdb=" CA4 2YP A 501 " pdb=" CA6 2YP A 501 " pdb=" OA5 2YP A 501 " both_signs ideal model delta sigma weight residual False -2.67 -2.41 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 188 " pdb=" N ILE A 188 " pdb=" C ILE A 188 " pdb=" CB ILE A 188 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 497 not shown) Planarity restraints: 871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 124 " -0.237 2.00e-02 2.50e+03 3.30e-01 1.63e+03 pdb=" CD GLN A 124 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN A 124 " 0.235 2.00e-02 2.50e+03 pdb=" NE2 GLN A 124 " -0.006 2.00e-02 2.50e+03 pdb="HE21 GLN A 124 " 0.515 2.00e-02 2.50e+03 pdb="HE22 GLN A 124 " -0.525 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 251 " 0.284 9.50e-02 1.11e+02 2.67e-01 1.41e+03 pdb=" NE ARG A 251 " 0.207 2.00e-02 2.50e+03 pdb=" CZ ARG A 251 " 0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 251 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 251 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG A 251 " -0.528 2.00e-02 2.50e+03 pdb="HH12 ARG A 251 " 0.465 2.00e-02 2.50e+03 pdb="HH21 ARG A 251 " -0.126 2.00e-02 2.50e+03 pdb="HH22 ARG A 251 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 79 " 0.228 9.50e-02 1.11e+02 2.43e-01 1.21e+03 pdb=" NE ARG A 79 " 0.133 2.00e-02 2.50e+03 pdb=" CZ ARG A 79 " 0.028 2.00e-02 2.50e+03 pdb=" NH1 ARG A 79 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 79 " -0.056 2.00e-02 2.50e+03 pdb="HH11 ARG A 79 " 0.473 2.00e-02 2.50e+03 pdb="HH12 ARG A 79 " -0.451 2.00e-02 2.50e+03 pdb="HH21 ARG A 79 " -0.176 2.00e-02 2.50e+03 pdb="HH22 ARG A 79 " 0.026 2.00e-02 2.50e+03 ... (remaining 868 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1054 2.26 - 2.85: 13849 2.85 - 3.43: 16040 3.43 - 4.02: 20533 4.02 - 4.60: 30793 Nonbonded interactions: 82269 Sorted by model distance: nonbonded pdb=" O PHE A 349 " pdb=" HG SER A 350 " model vdw 1.679 2.450 nonbonded pdb=" H GLU A 140 " pdb=" HG3 GLU A 140 " model vdw 1.727 2.270 nonbonded pdb=" HD1 PHE A 375 " pdb=" HB2 PHE A 384 " model vdw 1.731 2.270 nonbonded pdb=" H ILE A 49 " pdb="HG13 ILE A 49 " model vdw 1.734 2.270 nonbonded pdb=" HA VAL A 338 " pdb=" HB VAL A 338 " model vdw 1.748 1.952 ... (remaining 82264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.590 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 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 : 0.012 0.196 3062 Z= 0.763 Angle : 1.575 11.761 4171 Z= 1.114 Chirality : 0.075 0.285 500 Planarity : 0.009 0.062 498 Dihedral : 17.440 98.986 1092 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.99 % Allowed : 23.18 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.39), residues: 382 helix: -2.03 (0.32), residues: 205 sheet: None (None), residues: 0 loop : -2.09 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 251 TYR 0.009 0.001 TYR A 72 PHE 0.014 0.001 PHE A 52 TRP 0.050 0.003 TRP A 307 HIS 0.004 0.002 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.01185 ( 3062) covalent geometry : angle 1.57453 ( 4171) hydrogen bonds : bond 0.31897 ( 139) hydrogen bonds : angle 10.44046 ( 396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 VAL cc_start: 0.8404 (m) cc_final: 0.8196 (m) REVERT: A 110 MET cc_start: 0.3780 (mtt) cc_final: 0.3332 (mtt) REVERT: A 129 ASP cc_start: 0.6320 (t70) cc_final: 0.6094 (t0) REVERT: A 231 ILE cc_start: 0.8765 (tp) cc_final: 0.8503 (mt) REVERT: A 301 VAL cc_start: 0.8088 (m) cc_final: 0.7866 (t) REVERT: A 341 LEU cc_start: 0.8225 (tt) cc_final: 0.8025 (tt) REVERT: A 407 GLU cc_start: 0.4972 (mt-10) cc_final: 0.4520 (pt0) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.1358 time to fit residues: 15.8057 Evaluate side-chains 71 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.215763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.202992 restraints weight = 14664.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.208037 restraints weight = 6888.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.210842 restraints weight = 3579.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.212555 restraints weight = 2041.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.213691 restraints weight = 1259.756| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3062 Z= 0.179 Angle : 0.756 5.900 4171 Z= 0.388 Chirality : 0.037 0.114 500 Planarity : 0.005 0.046 498 Dihedral : 9.492 39.460 470 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.38 % Favored : 91.36 % Rotamer: Outliers : 2.32 % Allowed : 22.19 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.38), residues: 382 helix: -1.44 (0.31), residues: 235 sheet: None (None), residues: 0 loop : -2.39 (0.43), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 365 TYR 0.009 0.002 TYR A 367 PHE 0.014 0.002 PHE A 289 TRP 0.013 0.001 TRP A 307 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3062) covalent geometry : angle 0.75557 ( 4171) hydrogen bonds : bond 0.06097 ( 139) hydrogen bonds : angle 6.19772 ( 396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7275 (t60) cc_final: 0.6838 (t60) REVERT: A 70 ASP cc_start: 0.4938 (p0) cc_final: 0.4712 (p0) REVERT: A 71 ARG cc_start: 0.7020 (ttt180) cc_final: 0.6714 (ttm110) REVERT: A 110 MET cc_start: 0.4178 (mtt) cc_final: 0.3767 (mtt) REVERT: A 129 ASP cc_start: 0.7326 (t70) cc_final: 0.6947 (t0) REVERT: A 177 TYR cc_start: 0.7582 (m-80) cc_final: 0.7069 (m-80) REVERT: A 332 MET cc_start: 0.8475 (mtt) cc_final: 0.7921 (mtt) outliers start: 7 outliers final: 2 residues processed: 77 average time/residue: 0.1172 time to fit residues: 11.2486 Evaluate side-chains 70 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.212533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.199446 restraints weight = 14594.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.204634 restraints weight = 6941.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.207420 restraints weight = 3657.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.209180 restraints weight = 2112.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.210335 restraints weight = 1302.984| |-----------------------------------------------------------------------------| r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3062 Z= 0.151 Angle : 0.636 5.413 4171 Z= 0.328 Chirality : 0.036 0.144 500 Planarity : 0.005 0.058 498 Dihedral : 8.643 49.026 470 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.59 % Favored : 92.15 % Rotamer: Outliers : 2.65 % Allowed : 21.52 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.40), residues: 382 helix: -0.99 (0.31), residues: 243 sheet: None (None), residues: 0 loop : -2.12 (0.48), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.005 0.001 TYR A 234 PHE 0.016 0.001 PHE A 63 TRP 0.012 0.001 TRP A 83 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 3062) covalent geometry : angle 0.63588 ( 4171) hydrogen bonds : bond 0.05420 ( 139) hydrogen bonds : angle 5.48953 ( 396) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.4317 (mtt) cc_final: 0.3902 (mtt) REVERT: A 129 ASP cc_start: 0.7343 (t70) cc_final: 0.6970 (t0) REVERT: A 332 MET cc_start: 0.8467 (mtt) cc_final: 0.7815 (mtt) outliers start: 8 outliers final: 5 residues processed: 77 average time/residue: 0.1135 time to fit residues: 10.7662 Evaluate side-chains 74 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.208954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195583 restraints weight = 14466.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.200948 restraints weight = 6854.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.203844 restraints weight = 3604.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.205633 restraints weight = 2061.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.206713 restraints weight = 1256.622| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3062 Z= 0.148 Angle : 0.625 4.875 4171 Z= 0.324 Chirality : 0.035 0.123 500 Planarity : 0.004 0.052 498 Dihedral : 7.865 37.702 470 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.90 % Favored : 90.84 % Rotamer: Outliers : 2.65 % Allowed : 21.85 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.41), residues: 382 helix: -0.53 (0.34), residues: 238 sheet: None (None), residues: 0 loop : -2.14 (0.46), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.007 0.001 TYR A 72 PHE 0.011 0.001 PHE A 255 TRP 0.016 0.001 TRP A 83 HIS 0.001 0.001 HIS A 379 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3062) covalent geometry : angle 0.62475 ( 4171) hydrogen bonds : bond 0.04528 ( 139) hydrogen bonds : angle 5.06302 ( 396) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.4293 (mtt) cc_final: 0.3906 (mtt) REVERT: A 129 ASP cc_start: 0.7305 (t70) cc_final: 0.6989 (t0) REVERT: A 332 MET cc_start: 0.8438 (mtt) cc_final: 0.7924 (mtt) REVERT: A 379 HIS cc_start: 0.6079 (OUTLIER) cc_final: 0.5357 (t-170) outliers start: 8 outliers final: 6 residues processed: 78 average time/residue: 0.1313 time to fit residues: 12.4213 Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.210161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.197145 restraints weight = 14495.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.202385 restraints weight = 6853.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.205279 restraints weight = 3610.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.207062 restraints weight = 2042.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.208141 restraints weight = 1225.888| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3062 Z= 0.119 Angle : 0.583 4.570 4171 Z= 0.299 Chirality : 0.034 0.143 500 Planarity : 0.004 0.064 498 Dihedral : 7.587 40.442 470 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.38 % Favored : 91.36 % Rotamer: Outliers : 2.32 % Allowed : 23.51 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.42), residues: 382 helix: -0.39 (0.34), residues: 241 sheet: None (None), residues: 0 loop : -2.00 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.005 0.001 TYR A 152 PHE 0.010 0.001 PHE A 255 TRP 0.007 0.001 TRP A 307 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3062) covalent geometry : angle 0.58257 ( 4171) hydrogen bonds : bond 0.04005 ( 139) hydrogen bonds : angle 4.77421 ( 396) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.4307 (mtt) cc_final: 0.3927 (mtt) REVERT: A 129 ASP cc_start: 0.7254 (t70) cc_final: 0.6952 (t0) REVERT: A 332 MET cc_start: 0.8427 (mtt) cc_final: 0.7926 (mtt) REVERT: A 379 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5483 (t-170) outliers start: 7 outliers final: 5 residues processed: 76 average time/residue: 0.1214 time to fit residues: 11.3370 Evaluate side-chains 75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 69 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.209318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.196513 restraints weight = 14607.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.201637 restraints weight = 6945.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.204474 restraints weight = 3685.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.206217 restraints weight = 2120.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.207312 restraints weight = 1281.667| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3062 Z= 0.120 Angle : 0.577 5.261 4171 Z= 0.297 Chirality : 0.035 0.143 500 Planarity : 0.004 0.062 498 Dihedral : 7.439 43.242 470 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.64 % Favored : 91.10 % Rotamer: Outliers : 3.64 % Allowed : 23.18 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.43), residues: 382 helix: -0.17 (0.35), residues: 235 sheet: None (None), residues: 0 loop : -1.83 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.006 0.001 TYR A 367 PHE 0.011 0.001 PHE A 255 TRP 0.008 0.001 TRP A 307 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 3062) covalent geometry : angle 0.57742 ( 4171) hydrogen bonds : bond 0.03805 ( 139) hydrogen bonds : angle 4.62074 ( 396) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7514 (t60) cc_final: 0.7185 (t60) REVERT: A 110 MET cc_start: 0.4069 (mtt) cc_final: 0.3642 (mtt) REVERT: A 129 ASP cc_start: 0.7270 (t70) cc_final: 0.6958 (t0) REVERT: A 332 MET cc_start: 0.8446 (mtt) cc_final: 0.7947 (mtt) REVERT: A 379 HIS cc_start: 0.6246 (OUTLIER) cc_final: 0.5493 (t-170) outliers start: 11 outliers final: 6 residues processed: 78 average time/residue: 0.1267 time to fit residues: 11.9982 Evaluate side-chains 75 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.192608 restraints weight = 14550.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.197816 restraints weight = 6862.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.200666 restraints weight = 3604.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.202395 restraints weight = 2055.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.203479 restraints weight = 1252.744| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3062 Z= 0.148 Angle : 0.610 5.633 4171 Z= 0.315 Chirality : 0.036 0.146 500 Planarity : 0.005 0.064 498 Dihedral : 7.541 49.187 470 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.90 % Favored : 90.84 % Rotamer: Outliers : 3.31 % Allowed : 24.17 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.43), residues: 382 helix: -0.16 (0.35), residues: 235 sheet: None (None), residues: 0 loop : -1.90 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 221 TYR 0.007 0.001 TYR A 72 PHE 0.013 0.001 PHE A 325 TRP 0.008 0.001 TRP A 307 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3062) covalent geometry : angle 0.61030 ( 4171) hydrogen bonds : bond 0.03955 ( 139) hydrogen bonds : angle 4.63012 ( 396) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7653 (t60) cc_final: 0.7311 (t60) REVERT: A 110 MET cc_start: 0.4251 (mtt) cc_final: 0.3816 (mtt) REVERT: A 129 ASP cc_start: 0.7330 (t70) cc_final: 0.7038 (t0) REVERT: A 379 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5576 (t-170) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.1003 time to fit residues: 9.6304 Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.206035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.193407 restraints weight = 14744.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.198464 restraints weight = 7059.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.201213 restraints weight = 3751.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.202902 restraints weight = 2170.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.204056 restraints weight = 1340.789| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3062 Z= 0.125 Angle : 0.603 6.879 4171 Z= 0.309 Chirality : 0.035 0.144 500 Planarity : 0.005 0.067 498 Dihedral : 7.513 53.983 470 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.38 % Favored : 91.36 % Rotamer: Outliers : 2.98 % Allowed : 24.17 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.43), residues: 382 helix: -0.06 (0.35), residues: 235 sheet: None (None), residues: 0 loop : -1.90 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.005 0.001 TYR A 152 PHE 0.011 0.001 PHE A 255 TRP 0.006 0.001 TRP A 38 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3062) covalent geometry : angle 0.60344 ( 4171) hydrogen bonds : bond 0.03748 ( 139) hydrogen bonds : angle 4.49434 ( 396) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7568 (t60) cc_final: 0.7270 (t60) REVERT: A 110 MET cc_start: 0.4245 (mtt) cc_final: 0.3803 (mtt) REVERT: A 123 SER cc_start: 0.8285 (m) cc_final: 0.7628 (t) REVERT: A 129 ASP cc_start: 0.7319 (t0) cc_final: 0.7023 (t0) REVERT: A 332 MET cc_start: 0.8425 (mtt) cc_final: 0.7873 (mtt) REVERT: A 379 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.5741 (t-170) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 0.1065 time to fit residues: 9.8146 Evaluate side-chains 77 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.205917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.193281 restraints weight = 14412.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.198363 restraints weight = 6878.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.201177 restraints weight = 3629.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.202926 restraints weight = 2058.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.204029 restraints weight = 1233.413| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3062 Z= 0.129 Angle : 0.605 7.142 4171 Z= 0.311 Chirality : 0.036 0.149 500 Planarity : 0.005 0.068 498 Dihedral : 7.487 55.182 470 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 2.32 % Allowed : 23.51 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.43), residues: 382 helix: -0.09 (0.35), residues: 235 sheet: None (None), residues: 0 loop : -1.86 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.011 0.001 TYR A 72 PHE 0.011 0.001 PHE A 61 TRP 0.009 0.001 TRP A 83 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3062) covalent geometry : angle 0.60497 ( 4171) hydrogen bonds : bond 0.03675 ( 139) hydrogen bonds : angle 4.47561 ( 396) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7608 (t60) cc_final: 0.7301 (t60) REVERT: A 110 MET cc_start: 0.4127 (mtt) cc_final: 0.3677 (mtt) REVERT: A 123 SER cc_start: 0.8276 (m) cc_final: 0.7623 (t) REVERT: A 129 ASP cc_start: 0.7344 (t0) cc_final: 0.7026 (t0) REVERT: A 332 MET cc_start: 0.8427 (mtt) cc_final: 0.7866 (mtt) REVERT: A 379 HIS cc_start: 0.6452 (OUTLIER) cc_final: 0.5824 (t-170) outliers start: 7 outliers final: 6 residues processed: 76 average time/residue: 0.1064 time to fit residues: 9.9538 Evaluate side-chains 76 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.202983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190658 restraints weight = 14516.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.195767 restraints weight = 6912.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.198593 restraints weight = 3609.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.200257 restraints weight = 2012.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.201269 restraints weight = 1180.993| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3062 Z= 0.143 Angle : 0.619 7.483 4171 Z= 0.319 Chirality : 0.036 0.159 500 Planarity : 0.005 0.066 498 Dihedral : 7.580 58.443 470 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 2.32 % Allowed : 24.50 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.43), residues: 382 helix: -0.07 (0.35), residues: 235 sheet: None (None), residues: 0 loop : -1.90 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 403 TYR 0.007 0.001 TYR A 72 PHE 0.014 0.001 PHE A 349 TRP 0.009 0.001 TRP A 307 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3062) covalent geometry : angle 0.61860 ( 4171) hydrogen bonds : bond 0.03913 ( 139) hydrogen bonds : angle 4.51913 ( 396) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 764 Ramachandran restraints generated. 382 Oldfield, 0 Emsley, 382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 TRP cc_start: 0.7699 (t60) cc_final: 0.7416 (t60) REVERT: A 123 SER cc_start: 0.8279 (m) cc_final: 0.7647 (t) REVERT: A 129 ASP cc_start: 0.7297 (t0) cc_final: 0.6979 (t0) REVERT: A 255 PHE cc_start: 0.6828 (t80) cc_final: 0.6274 (t80) REVERT: A 317 MET cc_start: 0.6355 (ppp) cc_final: 0.6073 (ppp) REVERT: A 332 MET cc_start: 0.8443 (mtt) cc_final: 0.7907 (mtt) REVERT: A 379 HIS cc_start: 0.6547 (OUTLIER) cc_final: 0.5981 (t-170) outliers start: 7 outliers final: 6 residues processed: 81 average time/residue: 0.1035 time to fit residues: 10.6436 Evaluate side-chains 79 residues out of total 302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 379 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.202735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.190183 restraints weight = 14341.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.195225 restraints weight = 6878.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.198114 restraints weight = 3650.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.199814 restraints weight = 2063.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.200862 restraints weight = 1225.548| |-----------------------------------------------------------------------------| r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3062 Z= 0.142 Angle : 0.622 7.475 4171 Z= 0.319 Chirality : 0.037 0.162 500 Planarity : 0.005 0.066 498 Dihedral : 7.630 59.249 470 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.12 % Favored : 91.62 % Rotamer: Outliers : 2.65 % Allowed : 25.17 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.43), residues: 382 helix: -0.09 (0.35), residues: 235 sheet: None (None), residues: 0 loop : -1.88 (0.48), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 251 TYR 0.009 0.001 TYR A 72 PHE 0.013 0.001 PHE A 349 TRP 0.009 0.001 TRP A 307 HIS 0.001 0.000 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3062) covalent geometry : angle 0.62178 ( 4171) hydrogen bonds : bond 0.03860 ( 139) hydrogen bonds : angle 4.50536 ( 396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.28 seconds wall clock time: 25 minutes 59.56 seconds (1559.56 seconds total)