Starting phenix.real_space_refine on Fri Jul 3 12:03:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1h_13159/07_2026/7p1h_13159_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1h_13159/07_2026/7p1h_13159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p1h_13159/07_2026/7p1h_13159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1h_13159/07_2026/7p1h_13159.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1h_13159/07_2026/7p1h_13159_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1h_13159/07_2026/7p1h_13159_trim.cif" } resolution = 3.9 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= 0.000 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 34 5.16 5 C 4454 2.51 5 N 1171 2.21 5 O 1377 1.98 5 H 6926 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 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: 13966 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6173 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain: "B" Number of atoms: 5679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5679 Classifications: {'peptide': 365} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2082 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 2.47, per 1000 atoms: 0.18 Number of scatterers: 13966 At special positions: 0 Unit cell: (119, 108.8, 82.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 34 16.00 P 3 15.00 O 1377 8.00 N 1171 7.00 C 4454 6.00 H 6926 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: 1.16 Conformation dependent library (CDL) restraints added in 433.9 milliseconds 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 48.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 19 through 36 Proline residue: A 25 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.854A pdb=" N ILE A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 252 through 260 removed outlier: 4.196A pdb=" N GLU A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.687A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.643A pdb=" N ASP A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.579A pdb=" N PHE A 316 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.674A pdb=" N PHE A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 329 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.305A pdb=" N ASN A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 383 " --> pdb=" O TRP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.701A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 285 through 288 removed outlier: 5.712A pdb=" N ASP B 288 " --> pdb=" O CYS B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 285 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 349 removed outlier: 4.420A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 4.046A pdb=" N MET B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.555A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 12 Processing helix chain 'P' and resid 38 through 42 Processing helix chain 'P' and resid 43 through 51 removed outlier: 3.514A pdb=" N VAL P 47 " --> pdb=" O THR P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 62 removed outlier: 3.961A pdb=" N VAL P 60 " --> pdb=" O SER P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 137 removed outlier: 3.810A pdb=" N ILE P 123 " --> pdb=" O HIS P 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 353 removed outlier: 5.027A pdb=" N THR A 218 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 221 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132 removed outlier: 5.039A pdb=" N ILE A 190 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR A 171 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.377A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.861A pdb=" N ILE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.638A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.280A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'P' and resid 29 through 33 removed outlier: 5.404A pdb=" N VAL P 30 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY P 23 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN P 99 " --> pdb=" O GLY P 114 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER P 84 " --> pdb=" O ASP P 75 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP P 75 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP P 86 " --> pdb=" O ILE P 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU P 63 " --> pdb=" O CYS P 70 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 936 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: 3.04 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6910 1.03 - 1.22: 19 1.22 - 1.42: 2972 1.42 - 1.61: 4151 1.61 - 1.81: 60 Bond restraints: 14112 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" HE1 HIC B 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" CA HIC B 73 " pdb=" HA HIC B 73 " ideal model delta sigma weight residual 0.970 1.131 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" CD2 HIC B 73 " pdb=" HD2 HIC B 73 " ideal model delta sigma weight residual 0.930 1.087 -0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" CB HIC B 73 " pdb=" HB2 HIC B 73 " ideal model delta sigma weight residual 0.970 1.124 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" CZ HIC B 73 " pdb=" HZ1 HIC B 73 " ideal model delta sigma weight residual 0.970 1.123 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 14107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 25462 3.97 - 7.94: 61 7.94 - 11.91: 3 11.91 - 15.88: 2 15.88 - 19.85: 1 Bond angle restraints: 25529 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 120.02 19.85 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 122.53 14.30 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N3 ATP B 402 " ideal model delta sigma weight residual 126.80 119.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" N3 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N9 ATP B 402 " ideal model delta sigma weight residual 127.04 134.55 -7.51 1.15e+00 7.59e-01 4.28e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 110.80 97.76 13.04 2.13e+00 2.20e-01 3.75e+01 ... (remaining 25524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5825 17.47 - 34.93: 528 34.93 - 52.40: 181 52.40 - 69.86: 123 69.86 - 87.33: 17 Dihedral angle restraints: 6674 sinusoidal: 3653 harmonic: 3021 Sorted by residual: dihedral pdb=" CA LEU A 217 " pdb=" C LEU A 217 " pdb=" N THR A 218 " pdb=" CA THR A 218 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA SER A 127 " pdb=" C SER A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta harmonic sigma weight residual 180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASP A 129 " pdb=" C ASP A 129 " pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 6671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 642 0.037 - 0.075: 282 0.075 - 0.112: 115 0.112 - 0.149: 37 0.149 - 0.186: 6 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CA LYS A 402 " pdb=" N LYS A 402 " pdb=" C LYS A 402 " pdb=" CB LYS A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CG LEU A 399 " pdb=" CB LEU A 399 " pdb=" CD1 LEU A 399 " pdb=" CD2 LEU A 399 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA VAL A 179 " pdb=" N VAL A 179 " pdb=" C VAL A 179 " pdb=" CB VAL A 179 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1079 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 265 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C ASN A 265 " 0.084 2.00e-02 2.50e+03 pdb=" O ASN A 265 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS A 266 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 106 " 0.090 9.50e-02 1.11e+02 3.90e-02 1.47e+01 pdb=" NE ARG A 106 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 106 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 106 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG A 106 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 106 " 0.014 2.00e-02 2.50e+03 pdb="HH12 ARG A 106 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 106 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 106 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " 0.069 9.50e-02 1.11e+02 3.37e-02 1.41e+01 pdb=" NE ARG A 278 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 278 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG A 278 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG A 278 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 278 " 0.013 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 456 2.09 - 2.71: 24523 2.71 - 3.34: 41366 3.34 - 3.97: 51840 3.97 - 4.60: 81313 Nonbonded interactions: 199498 Sorted by model distance: nonbonded pdb=" H THR B 201 " pdb=" OE1 GLU B 205 " model vdw 1.457 2.450 nonbonded pdb=" HZ1 LYS A 176 " pdb=" OD2 ASP A 183 " model vdw 1.524 2.450 nonbonded pdb=" O SER B 344 " pdb=" HG SER B 348 " model vdw 1.526 2.450 nonbonded pdb=" O ALA A 103 " pdb=" HG SER A 104 " model vdw 1.537 2.450 nonbonded pdb=" OD2 ASP B 288 " pdb=" HZ1 LYS P 69 " model vdw 1.537 2.450 ... (remaining 199493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.310 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 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 : 0.005 0.076 7186 Z= 0.288 Angle : 1.010 19.849 9739 Z= 0.630 Chirality : 0.051 0.186 1082 Planarity : 0.007 0.051 1253 Dihedral : 14.378 87.170 2681 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.60 (0.25), residues: 887 helix: -1.09 (0.24), residues: 327 sheet: -0.25 (0.39), residues: 154 loop : -1.25 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.008 ARG A 278 TYR 0.037 0.005 TYR A 144 PHE 0.029 0.003 PHE A 321 TRP 0.027 0.006 TRP B 86 HIS 0.008 0.002 HIS B 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.29 ( 7186) covalent geometry : angle 1.01038 / 0.63 ( 9739) hydrogen bonds : bond 0.17052 / 11.25 ( 339) hydrogen bonds : angle 9.11292 / 6.36 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.378 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 PHE cc_start: 0.8119 (m-80) cc_final: 0.7417 (m-80) REVERT: B 153 MET cc_start: 0.8489 (tmm) cc_final: 0.8273 (tmm) REVERT: B 208 ILE cc_start: 0.9124 (mt) cc_final: 0.8734 (tp) REVERT: B 292 ASP cc_start: 0.8639 (m-30) cc_final: 0.8190 (t0) REVERT: P 125 LYS cc_start: 0.8703 (tttt) cc_final: 0.8354 (tmtt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1804 time to fit residues: 50.9160 Evaluate side-chains 135 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 368 ASN B 12 ASN B 59 GLN P 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.096870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.078915 restraints weight = 84427.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.082405 restraints weight = 43873.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.084591 restraints weight = 27373.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.086206 restraints weight = 19813.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.087258 restraints weight = 15504.193| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7186 Z= 0.184 Angle : 0.708 7.379 9739 Z= 0.388 Chirality : 0.044 0.178 1082 Planarity : 0.006 0.048 1253 Dihedral : 7.776 60.448 1000 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.70 % Allowed : 12.40 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -0.54 (0.28), residues: 887 helix: 0.41 (0.28), residues: 340 sheet: -0.61 (0.39), residues: 158 loop : -0.83 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 354 TYR 0.025 0.002 TYR A 214 PHE 0.012 0.002 PHE A 321 TRP 0.013 0.002 TRP A 238 HIS 0.013 0.002 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 7186) covalent geometry : angle 0.70821 / 0.39 ( 9739) hydrogen bonds : bond 0.04807 / 3.28 ( 339) hydrogen bonds : angle 6.86494 / 4.76 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.501 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8023 (tmm) cc_final: 0.7664 (tmm) REVERT: B 208 ILE cc_start: 0.9065 (mt) cc_final: 0.8717 (tp) REVERT: B 241 GLU cc_start: 0.8570 (pm20) cc_final: 0.8079 (pm20) REVERT: B 263 GLN cc_start: 0.8559 (mt0) cc_final: 0.8278 (mp10) REVERT: B 292 ASP cc_start: 0.8987 (m-30) cc_final: 0.8340 (t0) REVERT: P 18 ASP cc_start: 0.2089 (t0) cc_final: 0.1540 (t0) REVERT: P 39 PHE cc_start: 0.4985 (m-10) cc_final: 0.4249 (m-10) REVERT: P 125 LYS cc_start: 0.8349 (tttt) cc_final: 0.8117 (tmtt) outliers start: 13 outliers final: 11 residues processed: 144 average time/residue: 0.1507 time to fit residues: 31.0411 Evaluate side-chains 132 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.095874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.078193 restraints weight = 84939.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.081495 restraints weight = 45064.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.083794 restraints weight = 28299.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.085272 restraints weight = 20229.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.086100 restraints weight = 15969.217| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7186 Z= 0.157 Angle : 0.636 7.476 9739 Z= 0.348 Chirality : 0.042 0.149 1082 Planarity : 0.005 0.051 1253 Dihedral : 7.018 53.752 1000 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.44 % Allowed : 13.45 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.37 (0.28), residues: 887 helix: 0.63 (0.29), residues: 342 sheet: -0.81 (0.41), residues: 143 loop : -0.70 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.031 0.002 TYR A 214 PHE 0.017 0.002 PHE B 266 TRP 0.012 0.001 TRP A 238 HIS 0.008 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.16 ( 7186) covalent geometry : angle 0.63586 / 0.35 ( 9739) hydrogen bonds : bond 0.04069 / 2.79 ( 339) hydrogen bonds : angle 6.27505 / 4.34 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.369 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.8069 (tmm) cc_final: 0.7688 (tmm) REVERT: B 208 ILE cc_start: 0.9070 (mt) cc_final: 0.8739 (tp) REVERT: B 292 ASP cc_start: 0.9035 (m-30) cc_final: 0.8421 (t0) REVERT: B 369 ILE cc_start: 0.9005 (tt) cc_final: 0.8653 (tp) outliers start: 11 outliers final: 11 residues processed: 125 average time/residue: 0.1475 time to fit residues: 26.5980 Evaluate side-chains 121 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.091934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.074321 restraints weight = 84532.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.077597 restraints weight = 43823.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.079776 restraints weight = 27420.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.081227 restraints weight = 19595.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.082222 restraints weight = 15462.384| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7186 Z= 0.161 Angle : 0.622 7.586 9739 Z= 0.338 Chirality : 0.042 0.141 1082 Planarity : 0.005 0.058 1253 Dihedral : 6.515 32.789 1000 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.35 % Allowed : 13.58 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.20 (0.29), residues: 887 helix: 0.76 (0.29), residues: 341 sheet: -0.70 (0.39), residues: 159 loop : -0.57 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.021 0.002 TYR A 223 PHE 0.015 0.002 PHE B 266 TRP 0.013 0.001 TRP A 238 HIS 0.008 0.002 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 7186) covalent geometry : angle 0.62179 / 0.34 ( 9739) hydrogen bonds : bond 0.03616 / 2.48 ( 339) hydrogen bonds : angle 5.97689 / 4.13 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.359 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7967 (tmm) cc_final: 0.7531 (tmm) REVERT: B 208 ILE cc_start: 0.9112 (mt) cc_final: 0.8836 (tp) REVERT: B 241 GLU cc_start: 0.8680 (pm20) cc_final: 0.8438 (pm20) REVERT: B 369 ILE cc_start: 0.9046 (tt) cc_final: 0.8710 (tp) REVERT: P 39 PHE cc_start: 0.5371 (m-10) cc_final: 0.5149 (m-10) outliers start: 18 outliers final: 12 residues processed: 127 average time/residue: 0.1647 time to fit residues: 29.0242 Evaluate side-chains 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 396 HIS Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.091653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.074306 restraints weight = 85900.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.077648 restraints weight = 43830.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.079844 restraints weight = 27127.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.081319 restraints weight = 19297.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.082283 restraints weight = 15113.556| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7186 Z= 0.140 Angle : 0.595 7.709 9739 Z= 0.323 Chirality : 0.042 0.136 1082 Planarity : 0.005 0.060 1253 Dihedral : 6.371 32.576 1000 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.83 % Allowed : 16.19 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.10 (0.29), residues: 887 helix: 0.87 (0.29), residues: 341 sheet: -0.67 (0.39), residues: 159 loop : -0.53 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.015 0.002 TYR A 223 PHE 0.012 0.001 PHE A 343 TRP 0.012 0.001 TRP A 238 HIS 0.015 0.002 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 7186) covalent geometry : angle 0.59529 / 0.32 ( 9739) hydrogen bonds : bond 0.03417 / 2.38 ( 339) hydrogen bonds : angle 5.81092 / 4.04 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.382 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: A 298 MET cc_start: 0.8888 (ttm) cc_final: 0.8610 (ttm) REVERT: B 153 MET cc_start: 0.7975 (tmm) cc_final: 0.7540 (tmm) REVERT: B 208 ILE cc_start: 0.9120 (mt) cc_final: 0.8831 (tp) REVERT: B 334 GLU cc_start: 0.8334 (pm20) cc_final: 0.8133 (pt0) REVERT: B 369 ILE cc_start: 0.9055 (tt) cc_final: 0.8747 (tp) outliers start: 14 outliers final: 11 residues processed: 114 average time/residue: 0.1576 time to fit residues: 25.3951 Evaluate side-chains 111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.089032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.071924 restraints weight = 85498.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.075122 restraints weight = 43661.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.077246 restraints weight = 27162.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.078661 restraints weight = 19354.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.079592 restraints weight = 15236.285| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7186 Z= 0.183 Angle : 0.624 7.669 9739 Z= 0.338 Chirality : 0.042 0.140 1082 Planarity : 0.006 0.070 1253 Dihedral : 6.410 32.698 1000 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.35 % Allowed : 16.06 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.38 (0.28), residues: 887 helix: 0.66 (0.28), residues: 342 sheet: -0.84 (0.39), residues: 159 loop : -0.71 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.020 0.002 TYR A 223 PHE 0.013 0.002 PHE A 321 TRP 0.014 0.001 TRP A 238 HIS 0.007 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 7186) covalent geometry : angle 0.62376 / 0.34 ( 9739) hydrogen bonds : bond 0.03607 / 2.48 ( 339) hydrogen bonds : angle 5.84069 / 4.05 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.378 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: 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: symmetry clash REVERT: A 223 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: A 298 MET cc_start: 0.8943 (ttm) cc_final: 0.8630 (ttm) REVERT: B 119 MET cc_start: 0.8667 (mmm) cc_final: 0.8366 (mtm) REVERT: B 153 MET cc_start: 0.8004 (tmm) cc_final: 0.7555 (tmm) REVERT: B 196 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7444 (tpt-90) REVERT: B 208 ILE cc_start: 0.9168 (mt) cc_final: 0.8898 (tp) REVERT: B 289 ILE cc_start: 0.8485 (pt) cc_final: 0.8093 (mt) REVERT: P 74 ARG cc_start: 0.6349 (mtm180) cc_final: 0.5420 (ttp-110) outliers start: 18 outliers final: 16 residues processed: 116 average time/residue: 0.1682 time to fit residues: 26.5999 Evaluate side-chains 117 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.3980 chunk 23 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 63 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.090754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073890 restraints weight = 83301.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.077186 restraints weight = 41500.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.079333 restraints weight = 25378.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.080784 restraints weight = 17902.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.081751 restraints weight = 13981.353| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7186 Z= 0.122 Angle : 0.580 7.689 9739 Z= 0.310 Chirality : 0.041 0.142 1082 Planarity : 0.005 0.062 1253 Dihedral : 6.156 34.953 1000 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.57 % Allowed : 16.71 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.07 (0.29), residues: 887 helix: 0.95 (0.29), residues: 342 sheet: -0.69 (0.39), residues: 161 loop : -0.56 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 136 TYR 0.013 0.001 TYR P 128 PHE 0.009 0.001 PHE B 200 TRP 0.012 0.001 TRP A 238 HIS 0.012 0.002 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7186) covalent geometry : angle 0.58022 / 0.31 ( 9739) hydrogen bonds : bond 0.03217 / 2.21 ( 339) hydrogen bonds : angle 5.59681 / 3.88 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.251 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7976 (tmm) cc_final: 0.7518 (tmm) REVERT: B 208 ILE cc_start: 0.9144 (mt) cc_final: 0.8861 (tp) REVERT: B 289 ILE cc_start: 0.8469 (pt) cc_final: 0.8087 (mt) REVERT: P 74 ARG cc_start: 0.6256 (mtm180) cc_final: 0.5408 (ttp-110) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 0.1608 time to fit residues: 25.8880 Evaluate side-chains 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.089132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.071822 restraints weight = 84684.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075020 restraints weight = 42948.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.077009 restraints weight = 26838.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.078434 restraints weight = 19637.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.079397 restraints weight = 15530.384| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.7379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7186 Z= 0.164 Angle : 0.599 7.677 9739 Z= 0.322 Chirality : 0.041 0.141 1082 Planarity : 0.006 0.069 1253 Dihedral : 6.231 35.756 1000 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.96 % Allowed : 16.97 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.24 (0.29), residues: 887 helix: 0.84 (0.28), residues: 342 sheet: -0.87 (0.38), residues: 161 loop : -0.64 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 196 TYR 0.013 0.002 TYR P 128 PHE 0.013 0.002 PHE A 321 TRP 0.013 0.001 TRP A 238 HIS 0.007 0.002 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 7186) covalent geometry : angle 0.59904 / 0.32 ( 9739) hydrogen bonds : bond 0.03359 / 2.29 ( 339) hydrogen bonds : angle 5.65840 / 3.94 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.376 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: 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 298 MET cc_start: 0.8936 (ttm) cc_final: 0.8728 (ttm) REVERT: B 111 ASN cc_start: 0.6390 (t0) cc_final: 0.6119 (t0) REVERT: B 119 MET cc_start: 0.8564 (mmm) cc_final: 0.8310 (mtm) REVERT: B 153 MET cc_start: 0.8009 (tmm) cc_final: 0.7163 (tmm) REVERT: B 190 MET cc_start: 0.9042 (ttt) cc_final: 0.8228 (tpt) REVERT: B 208 ILE cc_start: 0.9179 (mt) cc_final: 0.8924 (tp) REVERT: B 289 ILE cc_start: 0.8655 (pt) cc_final: 0.8292 (mt) REVERT: B 369 ILE cc_start: 0.9071 (tt) cc_final: 0.8745 (tp) REVERT: P 74 ARG cc_start: 0.6341 (mtm180) cc_final: 0.5475 (ttp-110) outliers start: 15 outliers final: 14 residues processed: 116 average time/residue: 0.1667 time to fit residues: 26.5183 Evaluate side-chains 113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 64 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.091043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.073516 restraints weight = 83485.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.076856 restraints weight = 41098.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.079085 restraints weight = 25223.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.080563 restraints weight = 17829.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.081540 restraints weight = 13981.361| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.7500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7186 Z= 0.106 Angle : 0.582 7.668 9739 Z= 0.307 Chirality : 0.041 0.136 1082 Planarity : 0.005 0.060 1253 Dihedral : 6.011 36.340 1000 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.17 % Allowed : 18.80 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.00 (0.29), residues: 887 helix: 1.09 (0.29), residues: 342 sheet: -0.78 (0.39), residues: 161 loop : -0.54 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 136 TYR 0.012 0.001 TYR P 128 PHE 0.009 0.001 PHE A 316 TRP 0.012 0.001 TRP B 340 HIS 0.010 0.002 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7186) covalent geometry : angle 0.58211 / 0.31 ( 9739) hydrogen bonds : bond 0.03063 / 2.09 ( 339) hydrogen bonds : angle 5.51188 / 3.85 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.240 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8975 (mm-30) REVERT: B 119 MET cc_start: 0.8586 (mmm) cc_final: 0.8272 (mtm) REVERT: B 153 MET cc_start: 0.7946 (tmm) cc_final: 0.7639 (tmm) REVERT: B 208 ILE cc_start: 0.9145 (mt) cc_final: 0.8866 (tp) REVERT: B 267 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8447 (tp) REVERT: B 284 LYS cc_start: 0.9163 (mttm) cc_final: 0.8888 (mtpt) REVERT: B 289 ILE cc_start: 0.8642 (pt) cc_final: 0.8277 (mt) REVERT: P 74 ARG cc_start: 0.6273 (mtm180) cc_final: 0.5457 (ttp-110) outliers start: 9 outliers final: 8 residues processed: 116 average time/residue: 0.1503 time to fit residues: 23.7602 Evaluate side-chains 115 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.089972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.072587 restraints weight = 83858.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.075888 restraints weight = 41255.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.078087 restraints weight = 25287.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.079549 restraints weight = 17902.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.080528 restraints weight = 14039.673| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7186 Z= 0.127 Angle : 0.579 7.655 9739 Z= 0.307 Chirality : 0.041 0.137 1082 Planarity : 0.005 0.065 1253 Dihedral : 5.988 37.160 1000 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.44 % Allowed : 18.15 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.00 (0.29), residues: 887 helix: 1.10 (0.29), residues: 342 sheet: -0.81 (0.38), residues: 161 loop : -0.55 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 136 TYR 0.013 0.001 TYR P 128 PHE 0.011 0.001 PHE A 321 TRP 0.012 0.001 TRP A 238 HIS 0.008 0.001 HIS A 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 ( 7186) covalent geometry : angle 0.57874 / 0.31 ( 9739) hydrogen bonds : bond 0.03062 / 2.09 ( 339) hydrogen bonds : angle 5.54661 / 3.88 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.456 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: 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: symmetry clash revert: symmetry clash REVERT: A 287 ASN cc_start: 0.8564 (m-40) cc_final: 0.8244 (m110) REVERT: A 298 MET cc_start: 0.8783 (ttm) cc_final: 0.8459 (ttp) REVERT: B 111 ASN cc_start: 0.6466 (t0) cc_final: 0.6231 (t0) REVERT: B 117 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8973 (mm-30) REVERT: B 119 MET cc_start: 0.8573 (mmm) cc_final: 0.8225 (mtm) REVERT: B 153 MET cc_start: 0.7941 (tmm) cc_final: 0.7638 (tmm) REVERT: B 208 ILE cc_start: 0.9166 (mt) cc_final: 0.8889 (tp) REVERT: B 267 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8499 (tp) REVERT: B 289 ILE cc_start: 0.8731 (pt) cc_final: 0.8392 (mt) REVERT: P 74 ARG cc_start: 0.6337 (mtm180) cc_final: 0.5543 (ttp-110) outliers start: 11 outliers final: 9 residues processed: 110 average time/residue: 0.1677 time to fit residues: 24.6921 Evaluate side-chains 112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 15 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN P 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.087403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.070204 restraints weight = 85877.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.073324 restraints weight = 42503.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.075407 restraints weight = 26445.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.076807 restraints weight = 18963.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.077583 restraints weight = 15024.538| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.8136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7186 Z= 0.196 Angle : 0.640 7.450 9739 Z= 0.344 Chirality : 0.043 0.161 1082 Planarity : 0.006 0.090 1253 Dihedral : 6.381 42.486 1000 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.57 % Allowed : 18.41 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.38 (0.29), residues: 887 helix: 0.82 (0.28), residues: 340 sheet: -1.04 (0.37), residues: 166 loop : -0.76 (0.34), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 136 TYR 0.013 0.002 TYR A 221 PHE 0.020 0.002 PHE A 321 TRP 0.019 0.002 TRP A 238 HIS 0.006 0.002 HIS A 300 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 ( 7186) covalent geometry : angle 0.64030 / 0.34 ( 9739) hydrogen bonds : bond 0.03490 / 2.37 ( 339) hydrogen bonds : angle 5.79951 / 4.07 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.02 seconds wall clock time: 46 minutes 16.42 seconds (2776.42 seconds total)