Starting phenix.real_space_refine on Wed Mar 4 13:46:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p1h_13159/03_2026/7p1h_13159_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p1h_13159/03_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_13159/03_2026/7p1h_13159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p1h_13159/03_2026/7p1h_13159.map" model { file = "/net/cci-nas-00/data/ceres_data/7p1h_13159/03_2026/7p1h_13159_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p1h_13159/03_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-5986/lib/python3.9/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, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.50, 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: 1.31 Conformation dependent library (CDL) restraints added in 384.5 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: 0.31 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: 2.88 Time building geometry restraints manager: 1.78 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.290 Find NCS groups from input model: 0.050 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 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 covalent geometry : bond 0.00503 ( 7186) covalent geometry : angle 1.01038 ( 9739) hydrogen bonds : bond 0.17052 ( 339) hydrogen bonds : angle 9.11292 ( 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 : 0.387 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: 0.1932 time to fit residues: 53.4490 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 : 0.363 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 368 ASN B 59 GLN P 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.096934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.079347 restraints weight = 84841.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.082740 restraints weight = 44240.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.085035 restraints weight = 27778.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.086539 restraints weight = 19829.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.087572 restraints weight = 15622.956| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7186 Z= 0.182 Angle : 0.721 7.537 9739 Z= 0.394 Chirality : 0.044 0.176 1082 Planarity : 0.006 0.048 1253 Dihedral : 7.420 40.651 1000 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.57 % Allowed : 12.53 % 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: -0.53 (0.28), residues: 887 helix: 0.39 (0.28), residues: 340 sheet: -0.58 (0.39), residues: 159 loop : -0.81 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 372 TYR 0.029 0.002 TYR A 214 PHE 0.011 0.002 PHE A 321 TRP 0.012 0.002 TRP A 238 HIS 0.013 0.002 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 7186) covalent geometry : angle 0.72125 ( 9739) hydrogen bonds : bond 0.04606 ( 339) hydrogen bonds : angle 6.81700 ( 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 148 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 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: 0.8075 (tmm) cc_final: 0.7711 (tmm) REVERT: B 208 ILE cc_start: 0.9057 (mt) cc_final: 0.8747 (tp) REVERT: B 241 GLU cc_start: 0.8479 (pm20) cc_final: 0.8024 (pm20) REVERT: B 263 GLN cc_start: 0.8486 (mt0) cc_final: 0.8249 (mp10) REVERT: B 292 ASP cc_start: 0.8963 (m-30) cc_final: 0.8339 (t0) REVERT: P 18 ASP cc_start: 0.1930 (t0) cc_final: 0.1420 (t0) REVERT: P 39 PHE cc_start: 0.5103 (m-10) cc_final: 0.4371 (m-10) REVERT: P 125 LYS cc_start: 0.8385 (tttt) cc_final: 0.8143 (tmtt) outliers start: 12 outliers final: 10 residues processed: 143 average time/residue: 0.1527 time to fit residues: 30.8950 Evaluate side-chains 129 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN B 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.096157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.078684 restraints weight = 85062.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.082014 restraints weight = 44255.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.084244 restraints weight = 27920.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.085710 restraints weight = 20138.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.086749 restraints weight = 15950.484| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4431 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= 0.136 Angle : 0.625 7.423 9739 Z= 0.341 Chirality : 0.042 0.149 1082 Planarity : 0.005 0.052 1253 Dihedral : 6.785 38.387 1000 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.31 % Allowed : 13.45 % Favored : 85.25 % 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: 0.61 (0.29), residues: 342 sheet: -0.81 (0.41), residues: 143 loop : -0.69 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 37 TYR 0.034 0.002 TYR A 214 PHE 0.012 0.001 PHE B 266 TRP 0.011 0.001 TRP A 238 HIS 0.007 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7186) covalent geometry : angle 0.62519 ( 9739) hydrogen bonds : bond 0.04028 ( 339) hydrogen bonds : angle 6.26940 ( 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 130 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 120 time to evaluate : 0.384 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: 0.8060 (tmm) cc_final: 0.7684 (tmm) REVERT: B 208 ILE cc_start: 0.9073 (mt) cc_final: 0.8744 (tp) REVERT: B 292 ASP cc_start: 0.8994 (m-30) cc_final: 0.8378 (t0) REVERT: B 341 ILE cc_start: 0.8439 (mt) cc_final: 0.8220 (mt) outliers start: 10 outliers final: 10 residues processed: 124 average time/residue: 0.1641 time to fit residues: 28.4009 Evaluate side-chains 125 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 132 MET 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 Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.089018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071495 restraints weight = 86497.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.074609 restraints weight = 45084.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.076590 restraints weight = 28524.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.078015 restraints weight = 20873.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.078984 restraints weight = 16581.594| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7186 Z= 0.230 Angle : 0.705 7.402 9739 Z= 0.387 Chirality : 0.044 0.174 1082 Planarity : 0.006 0.075 1253 Dihedral : 6.917 42.340 1000 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.61 % Allowed : 13.45 % Favored : 83.94 % 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: -0.73 (0.28), residues: 887 helix: 0.28 (0.28), residues: 342 sheet: -1.01 (0.38), residues: 159 loop : -0.81 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 37 TYR 0.030 0.002 TYR A 223 PHE 0.018 0.003 PHE B 279 TRP 0.015 0.002 TRP A 238 HIS 0.008 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 7186) covalent geometry : angle 0.70545 ( 9739) hydrogen bonds : bond 0.04183 ( 339) hydrogen bonds : angle 6.27323 ( 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 131 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.411 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: A 223 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (m-80) REVERT: B 263 GLN cc_start: 0.8682 (mt0) cc_final: 0.8233 (mp10) REVERT: B 369 ILE cc_start: 0.9092 (tt) cc_final: 0.8769 (tp) outliers start: 20 outliers final: 15 residues processed: 124 average time/residue: 0.1752 time to fit residues: 29.7929 Evaluate side-chains 115 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 304 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 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 Chi-restraints excluded: chain P residue 113 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 0.0670 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.091054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.073465 restraints weight = 84918.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.076770 restraints weight = 42873.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.079006 restraints weight = 26549.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.080468 restraints weight = 18763.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.081487 restraints weight = 14732.605| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.6326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7186 Z= 0.118 Angle : 0.595 7.783 9739 Z= 0.319 Chirality : 0.042 0.140 1082 Planarity : 0.005 0.061 1253 Dihedral : 6.418 55.738 1000 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.70 % Allowed : 16.19 % Favored : 82.11 % 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: -0.31 (0.29), residues: 887 helix: 0.77 (0.29), residues: 340 sheet: -0.85 (0.39), residues: 159 loop : -0.70 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 107 TYR 0.015 0.001 TYR A 223 PHE 0.013 0.001 PHE A 343 TRP 0.012 0.001 TRP A 238 HIS 0.006 0.001 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7186) covalent geometry : angle 0.59496 ( 9739) hydrogen bonds : bond 0.03440 ( 339) hydrogen bonds : angle 5.83495 ( 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 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.393 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: 0.7962 (tmm) cc_final: 0.7600 (tmm) REVERT: B 208 ILE cc_start: 0.9074 (mm) cc_final: 0.8451 (tp) REVERT: B 241 GLU cc_start: 0.8659 (pm20) cc_final: 0.8179 (pm20) REVERT: B 263 GLN cc_start: 0.8643 (mt0) cc_final: 0.8184 (mp10) REVERT: B 289 ILE cc_start: 0.8297 (pt) cc_final: 0.7882 (mt) REVERT: B 369 ILE cc_start: 0.9101 (tt) cc_final: 0.8809 (tp) outliers start: 13 outliers final: 9 residues processed: 113 average time/residue: 0.1732 time to fit residues: 27.0076 Evaluate side-chains 112 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL 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 190 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 363 ASP 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: 2.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.089335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.072024 restraints weight = 85458.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.075150 restraints weight = 43782.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.077242 restraints weight = 27474.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.078652 restraints weight = 19780.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.079579 restraints weight = 15678.752| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7186 Z= 0.164 Angle : 0.613 7.732 9739 Z= 0.332 Chirality : 0.042 0.142 1082 Planarity : 0.006 0.071 1253 Dihedral : 6.411 50.495 1000 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.57 % Allowed : 16.97 % Favored : 81.46 % 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: 0.72 (0.28), residues: 341 sheet: -0.78 (0.40), residues: 151 loop : -0.81 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.019 0.002 TYR A 223 PHE 0.011 0.002 PHE A 321 TRP 0.013 0.001 TRP A 238 HIS 0.008 0.002 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 7186) covalent geometry : angle 0.61341 ( 9739) hydrogen bonds : bond 0.03539 ( 339) hydrogen bonds : angle 5.80817 ( 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 113 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.254 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: 0.8452 (m-40) cc_final: 0.8158 (m110) REVERT: B 208 ILE cc_start: 0.9119 (mm) cc_final: 0.8576 (tp) REVERT: B 263 GLN cc_start: 0.8626 (mt0) cc_final: 0.8193 (mp10) REVERT: B 289 ILE cc_start: 0.8460 (pt) cc_final: 0.8083 (mt) REVERT: B 369 ILE cc_start: 0.9066 (tt) cc_final: 0.8749 (tp) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 0.1784 time to fit residues: 26.3445 Evaluate side-chains 110 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE 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 190 MET 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 87 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 81 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.090540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.072790 restraints weight = 83030.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.076082 restraints weight = 42075.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.078281 restraints weight = 26069.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.079773 restraints weight = 18540.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.080610 restraints weight = 14555.802| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7017 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= 0.117 Angle : 0.577 7.823 9739 Z= 0.308 Chirality : 0.041 0.138 1082 Planarity : 0.005 0.062 1253 Dihedral : 6.167 59.565 1000 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.57 % Allowed : 16.97 % Favored : 81.46 % 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: -0.11 (0.29), residues: 887 helix: 0.95 (0.29), residues: 341 sheet: -0.72 (0.40), residues: 155 loop : -0.63 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 196 TYR 0.014 0.001 TYR P 128 PHE 0.009 0.001 PHE A 316 TRP 0.012 0.001 TRP A 238 HIS 0.007 0.002 HIS A 396 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7186) covalent geometry : angle 0.57723 ( 9739) hydrogen bonds : bond 0.03126 ( 339) hydrogen bonds : angle 5.59854 ( 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 119 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.299 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: A 223 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: A 287 ASN cc_start: 0.8505 (m-40) cc_final: 0.7969 (t0) REVERT: A 298 MET cc_start: 0.8844 (ttm) cc_final: 0.8618 (ttm) REVERT: B 132 MET cc_start: 0.7770 (tmm) cc_final: 0.7291 (tmm) REVERT: B 208 ILE cc_start: 0.9112 (mm) cc_final: 0.8503 (tp) REVERT: B 263 GLN cc_start: 0.8663 (mt0) cc_final: 0.8192 (mp10) REVERT: B 289 ILE cc_start: 0.8541 (pt) cc_final: 0.8160 (mt) REVERT: B 369 ILE cc_start: 0.9098 (tt) cc_final: 0.8784 (tp) outliers start: 12 outliers final: 7 residues processed: 113 average time/residue: 0.1830 time to fit residues: 28.0491 Evaluate side-chains 111 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 108 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.088965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.071427 restraints weight = 83926.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.074597 restraints weight = 42071.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.076711 restraints weight = 26178.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.078125 restraints weight = 18754.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.079076 restraints weight = 14850.516| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.7383 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= 0.148 Angle : 0.591 7.608 9739 Z= 0.318 Chirality : 0.041 0.135 1082 Planarity : 0.005 0.069 1253 Dihedral : 6.180 54.039 1000 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.31 % Allowed : 17.89 % Favored : 80.81 % 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: -0.22 (0.29), residues: 887 helix: 0.91 (0.29), residues: 342 sheet: -0.79 (0.39), residues: 157 loop : -0.72 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 136 TYR 0.017 0.002 TYR A 223 PHE 0.011 0.001 PHE A 321 TRP 0.013 0.001 TRP A 238 HIS 0.006 0.002 HIS A 300 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7186) covalent geometry : angle 0.59119 ( 9739) hydrogen bonds : bond 0.03246 ( 339) hydrogen bonds : angle 5.64305 ( 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 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.391 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: A 158 MET cc_start: 0.5668 (mtm) cc_final: 0.5261 (mtm) REVERT: A 223 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: A 287 ASN cc_start: 0.8515 (m-40) cc_final: 0.8008 (t0) REVERT: B 111 ASN cc_start: 0.6350 (t0) cc_final: 0.6120 (t0) REVERT: B 119 MET cc_start: 0.8592 (mmm) cc_final: 0.8305 (mtm) REVERT: B 208 ILE cc_start: 0.9145 (mm) cc_final: 0.8624 (tp) REVERT: B 263 GLN cc_start: 0.8664 (mt0) cc_final: 0.8212 (mp10) REVERT: B 289 ILE cc_start: 0.8660 (pt) cc_final: 0.8299 (mt) REVERT: B 369 ILE cc_start: 0.9081 (tt) cc_final: 0.8771 (tp) outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 0.1800 time to fit residues: 28.5020 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain B residue 101 HIS 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 87 LEU Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 111 LEU 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: 1.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.090460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.072546 restraints weight = 83695.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.075792 restraints weight = 42055.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.077994 restraints weight = 26149.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.079420 restraints weight = 18674.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080248 restraints weight = 14822.074| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7186 Z= 0.116 Angle : 0.586 7.710 9739 Z= 0.310 Chirality : 0.041 0.138 1082 Planarity : 0.005 0.062 1253 Dihedral : 6.052 59.794 1000 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.44 % Allowed : 18.67 % Favored : 79.90 % 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: 1.12 (0.29), residues: 342 sheet: -0.69 (0.40), residues: 157 loop : -0.63 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 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 0.012 0.002 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 7186) covalent geometry : angle 0.58575 ( 9739) hydrogen bonds : bond 0.03089 ( 339) hydrogen bonds : angle 5.53750 ( 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 124 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.302 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: A 223 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: A 287 ASN cc_start: 0.8500 (m-40) cc_final: 0.7989 (t0) REVERT: A 298 MET cc_start: 0.8802 (ttm) cc_final: 0.8529 (ttm) REVERT: B 119 MET cc_start: 0.8542 (mmm) cc_final: 0.8243 (mtm) REVERT: B 208 ILE cc_start: 0.9112 (mm) cc_final: 0.8544 (tp) REVERT: B 263 GLN cc_start: 0.8654 (mt0) cc_final: 0.8187 (mp10) REVERT: B 267 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8471 (tp) REVERT: B 284 LYS cc_start: 0.9231 (mttm) cc_final: 0.8941 (mtpt) REVERT: B 289 ILE cc_start: 0.8670 (pt) cc_final: 0.8317 (mt) outliers start: 11 outliers final: 7 residues processed: 121 average time/residue: 0.1890 time to fit residues: 30.5110 Evaluate side-chains 118 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 109 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 TYR 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 267 LEU Chi-restraints excluded: chain B residue 363 ASP 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: 1.9990 chunk 57 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.089803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.072427 restraints weight = 84923.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075650 restraints weight = 42274.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.077785 restraints weight = 26146.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.079225 restraints weight = 18683.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.080216 restraints weight = 14755.003| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7186 Z= 0.130 Angle : 0.584 7.619 9739 Z= 0.310 Chirality : 0.041 0.134 1082 Planarity : 0.006 0.066 1253 Dihedral : 6.013 56.520 1000 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.31 % Allowed : 19.06 % Favored : 79.63 % 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: -0.04 (0.29), residues: 887 helix: 1.10 (0.29), residues: 342 sheet: -0.74 (0.39), residues: 161 loop : -0.64 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 136 TYR 0.014 0.001 TYR A 223 PHE 0.010 0.001 PHE A 321 TRP 0.013 0.001 TRP A 238 HIS 0.007 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7186) covalent geometry : angle 0.58412 ( 9739) hydrogen bonds : bond 0.03093 ( 339) hydrogen bonds : angle 5.54902 ( 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 120 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.362 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: A 223 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: A 287 ASN cc_start: 0.8492 (m-40) cc_final: 0.7998 (t0) REVERT: B 111 ASN cc_start: 0.6418 (t0) cc_final: 0.6180 (t0) REVERT: B 119 MET cc_start: 0.8510 (mmm) cc_final: 0.8223 (mtm) REVERT: B 208 ILE cc_start: 0.9137 (mm) cc_final: 0.8569 (tp) REVERT: B 263 GLN cc_start: 0.8650 (mt0) cc_final: 0.8193 (mp10) REVERT: B 267 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8541 (tp) REVERT: B 289 ILE cc_start: 0.8752 (pt) cc_final: 0.8424 (mt) REVERT: B 369 ILE cc_start: 0.9082 (tt) cc_final: 0.8768 (tp) REVERT: P 74 ARG cc_start: 0.5913 (mtm180) cc_final: 0.5062 (ttp-110) outliers start: 10 outliers final: 7 residues processed: 117 average time/residue: 0.1871 time to fit residues: 29.4282 Evaluate side-chains 116 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 TYR 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 267 LEU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain P residue 16 CYS Chi-restraints excluded: chain P residue 87 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: 0.9980 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.089350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.071906 restraints weight = 84595.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075009 restraints weight = 42969.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.077092 restraints weight = 27041.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.078467 restraints weight = 19566.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.079423 restraints weight = 15645.216| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.7978 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= 0.135 Angle : 0.586 7.744 9739 Z= 0.310 Chirality : 0.041 0.134 1082 Planarity : 0.005 0.066 1253 Dihedral : 6.000 57.615 1000 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.31 % Allowed : 19.45 % Favored : 79.24 % 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: -0.03 (0.29), residues: 887 helix: 1.07 (0.29), residues: 342 sheet: -0.73 (0.40), residues: 153 loop : -0.61 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 136 TYR 0.015 0.002 TYR A 223 PHE 0.013 0.001 PHE A 321 TRP 0.014 0.002 TRP A 238 HIS 0.008 0.002 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7186) covalent geometry : angle 0.58641 ( 9739) hydrogen bonds : bond 0.03095 ( 339) hydrogen bonds : angle 5.55492 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2760.26 seconds wall clock time: 47 minutes 38.99 seconds (2858.99 seconds total)