Starting phenix.real_space_refine on Tue Mar 3 19:16:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d3s_30566/03_2026/7d3s_30566.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d3s_30566/03_2026/7d3s_30566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2026/7d3s_30566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2026/7d3s_30566.map" model { file = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2026/7d3s_30566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d3s_30566/03_2026/7d3s_30566.cif" } resolution = 2.9 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= 0.006 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5286 2.51 5 N 1473 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 8338 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2179 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain breaks: 2 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1921 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8338 At special positions: 0 Unit cell: (122.84, 98.4936, 107.347, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1529 8.00 N 1473 7.00 C 5286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 314.4 milliseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.2% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'P' and resid 1 through 27 Processing helix chain 'R' and resid 132 through 166 Processing helix chain 'R' and resid 167 through 171 removed outlier: 3.509A pdb=" N LEU R 170 " --> pdb=" O PHE R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 200 removed outlier: 3.527A pdb=" N ILE R 177 " --> pdb=" O THR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 246 Processing helix chain 'R' and resid 250 through 281 removed outlier: 3.832A pdb=" N GLN R 256 " --> pdb=" O ARG R 252 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY R 257 " --> pdb=" O LYS R 253 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 291 through 327 removed outlier: 4.202A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.867A pdb=" N GLN R 327 " --> pdb=" O LYS R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'R' and resid 347 through 352 Processing helix chain 'R' and resid 365 through 377 Processing helix chain 'R' and resid 379 through 391 Processing helix chain 'R' and resid 392 through 405 removed outlier: 3.560A pdb=" N LYS R 402 " --> pdb=" O GLU R 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.724A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 252 through 268 removed outlier: 4.212A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.026A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 343 removed outlier: 3.591A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.886A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.659A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.286A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.819A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.939A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.927A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.985A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.444A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.644A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.898A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2750 1.34 - 1.46: 1906 1.46 - 1.58: 3780 1.58 - 1.70: 0 1.70 - 1.81: 71 Bond restraints: 8507 Sorted by residual: bond pdb=" CA TYR A 381 " pdb=" C TYR A 381 " ideal model delta sigma weight residual 1.523 1.490 0.033 1.41e-02 5.03e+03 5.38e+00 bond pdb=" CB TRP B 63 " pdb=" CG TRP B 63 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.72e+00 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.33e+00 bond pdb=" N CYS R 389 " pdb=" CA CYS R 389 " ideal model delta sigma weight residual 1.460 1.446 0.014 1.27e-02 6.20e+03 1.21e+00 bond pdb=" CA PHE R 371 " pdb=" C PHE R 371 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.37e-02 5.33e+03 1.17e+00 ... (remaining 8502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 10991 1.41 - 2.81: 448 2.81 - 4.22: 51 4.22 - 5.62: 6 5.62 - 7.03: 3 Bond angle restraints: 11499 Sorted by residual: angle pdb=" N HIS R 211 " pdb=" CA HIS R 211 " pdb=" C HIS R 211 " ideal model delta sigma weight residual 112.58 108.88 3.70 1.22e+00 6.72e-01 9.19e+00 angle pdb=" C LEU R 374 " pdb=" N ALA R 375 " pdb=" CA ALA R 375 " ideal model delta sigma weight residual 122.06 116.46 5.60 1.86e+00 2.89e-01 9.07e+00 angle pdb=" N PRO N 102 " pdb=" CA PRO N 102 " pdb=" C PRO N 102 " ideal model delta sigma weight residual 114.80 118.98 -4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" CA TYR R 146 " pdb=" CB TYR R 146 " pdb=" CG TYR R 146 " ideal model delta sigma weight residual 113.90 118.91 -5.01 1.80e+00 3.09e-01 7.75e+00 angle pdb=" N ALA R 245 " pdb=" CA ALA R 245 " pdb=" C ALA R 245 " ideal model delta sigma weight residual 114.31 111.14 3.17 1.29e+00 6.01e-01 6.02e+00 ... (remaining 11494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 4560 17.79 - 35.57: 431 35.57 - 53.36: 50 53.36 - 71.14: 17 71.14 - 88.93: 7 Dihedral angle restraints: 5065 sinusoidal: 2025 harmonic: 3040 Sorted by residual: dihedral pdb=" CA LEU B 70 " pdb=" C LEU B 70 " pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta harmonic sigma weight residual 180.00 159.97 20.03 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA PHE R 358 " pdb=" C PHE R 358 " pdb=" N ALA R 359 " pdb=" CA ALA R 359 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 788 0.036 - 0.071: 365 0.071 - 0.107: 97 0.107 - 0.142: 26 0.142 - 0.178: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" CA PRO N 102 " pdb=" N PRO N 102 " pdb=" C PRO N 102 " pdb=" CB PRO N 102 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 ... (remaining 1274 not shown) Planarity restraints: 1469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 372 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C PHE R 372 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE R 372 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU R 373 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 387 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LEU R 387 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU R 387 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR R 388 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 386 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C VAL R 386 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL R 386 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU R 387 " -0.017 2.00e-02 2.50e+03 ... (remaining 1466 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1551 2.77 - 3.30: 7877 3.30 - 3.83: 14171 3.83 - 4.37: 17502 4.37 - 4.90: 29472 Nonbonded interactions: 70573 Sorted by model distance: nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.237 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.241 3.040 nonbonded pdb=" NZ LYS R 323 " pdb=" OE1 GLN A 374 " model vdw 2.266 3.120 nonbonded pdb=" NE2 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.285 3.120 ... (remaining 70568 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.940 Find NCS groups from input model: 0.030 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8510 Z= 0.193 Angle : 0.644 7.026 11505 Z= 0.394 Chirality : 0.043 0.178 1277 Planarity : 0.005 0.058 1469 Dihedral : 13.878 88.926 3090 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.23), residues: 1030 helix: -0.99 (0.23), residues: 423 sheet: -0.95 (0.32), residues: 219 loop : -2.31 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 98 TYR 0.016 0.002 TYR R 146 PHE 0.025 0.002 PHE R 313 TRP 0.025 0.002 TRP B 82 HIS 0.008 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8507) covalent geometry : angle 0.64307 (11499) SS BOND : bond 0.00382 ( 3) SS BOND : angle 1.40973 ( 6) hydrogen bonds : bond 0.15912 ( 448) hydrogen bonds : angle 6.53666 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.358 Fit side-chains REVERT: R 346 LEU cc_start: 0.8167 (mp) cc_final: 0.7678 (mt) REVERT: R 368 ILE cc_start: 0.7624 (tt) cc_final: 0.7414 (tp) REVERT: A 27 GLU cc_start: 0.6300 (tp30) cc_final: 0.5629 (tp30) REVERT: A 60 MET cc_start: 0.7722 (mmm) cc_final: 0.7407 (mmt) REVERT: A 209 GLU cc_start: 0.7343 (tt0) cc_final: 0.7071 (tt0) REVERT: A 258 GLU cc_start: 0.7778 (pt0) cc_final: 0.7489 (pt0) REVERT: A 321 ASP cc_start: 0.7469 (t70) cc_final: 0.7076 (t0) REVERT: A 382 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 96 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7541 (mtt180) REVERT: B 124 TYR cc_start: 0.7729 (m-80) cc_final: 0.7314 (m-80) REVERT: B 138 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6323 (mt-10) REVERT: N 5 GLN cc_start: 0.6876 (tp-100) cc_final: 0.6434 (mt0) REVERT: N 82 GLN cc_start: 0.7193 (tp40) cc_final: 0.6925 (tp-100) REVERT: N 94 TYR cc_start: 0.7943 (m-80) cc_final: 0.7627 (m-80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.6511 time to fit residues: 107.7697 Evaluate side-chains 120 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.0870 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN P 24 GLN R 132 ASN R 241 HIS R 336 HIS R 354 HIS A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 ASN A 269 ASN B 88 ASN B 91 HIS B 176 GLN B 268 ASN B 340 ASN N 31 ASN N 39 GLN N 120 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.165109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130116 restraints weight = 8778.200| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.65 r_work: 0.3375 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8510 Z= 0.150 Angle : 0.552 8.014 11505 Z= 0.304 Chirality : 0.042 0.141 1277 Planarity : 0.005 0.051 1469 Dihedral : 4.715 24.298 1148 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.23 % Allowed : 12.47 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1030 helix: 0.68 (0.25), residues: 420 sheet: -0.54 (0.33), residues: 218 loop : -1.70 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.030 0.002 TYR R 146 PHE 0.017 0.002 PHE R 313 TRP 0.025 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8507) covalent geometry : angle 0.55136 (11499) SS BOND : bond 0.00157 ( 3) SS BOND : angle 1.57431 ( 6) hydrogen bonds : bond 0.04516 ( 448) hydrogen bonds : angle 5.12244 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.309 Fit side-chains REVERT: R 246 ILE cc_start: 0.7825 (mt) cc_final: 0.7586 (mp) REVERT: R 281 GLU cc_start: 0.7397 (tt0) cc_final: 0.7114 (mm-30) REVERT: A 27 GLU cc_start: 0.6778 (tp30) cc_final: 0.6125 (tp30) REVERT: A 58 LYS cc_start: 0.6610 (ttpp) cc_final: 0.5814 (mmmt) REVERT: A 301 TYR cc_start: 0.8199 (m-80) cc_final: 0.7749 (m-80) REVERT: A 346 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6209 (mtp180) REVERT: A 382 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7881 (mt-10) REVERT: B 124 TYR cc_start: 0.7849 (m-80) cc_final: 0.7377 (m-80) REVERT: B 138 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7208 (mt-10) REVERT: B 175 GLN cc_start: 0.7732 (mm110) cc_final: 0.7526 (mm110) REVERT: N 5 GLN cc_start: 0.6992 (tp-100) cc_final: 0.6355 (mt0) REVERT: N 82 GLN cc_start: 0.7376 (tp40) cc_final: 0.7128 (tp-100) REVERT: N 94 TYR cc_start: 0.7995 (m-80) cc_final: 0.7755 (m-80) outliers start: 20 outliers final: 9 residues processed: 142 average time/residue: 0.6860 time to fit residues: 102.8814 Evaluate side-chains 125 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 ASN B 176 GLN B 340 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.165334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.130402 restraints weight = 8764.405| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.65 r_work: 0.3366 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 8510 Z= 0.146 Angle : 0.545 14.125 11505 Z= 0.299 Chirality : 0.042 0.138 1277 Planarity : 0.004 0.048 1469 Dihedral : 4.514 18.950 1148 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.56 % Allowed : 15.81 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.25), residues: 1030 helix: 1.29 (0.25), residues: 422 sheet: -0.36 (0.33), residues: 216 loop : -1.54 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.024 0.001 TYR R 146 PHE 0.018 0.001 PHE R 313 TRP 0.022 0.001 TRP B 82 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8507) covalent geometry : angle 0.52829 (11499) SS BOND : bond 0.00168 ( 3) SS BOND : angle 5.86001 ( 6) hydrogen bonds : bond 0.04190 ( 448) hydrogen bonds : angle 4.87348 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.307 Fit side-chains REVERT: R 133 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6933 (mm-30) REVERT: R 165 CYS cc_start: 0.7344 (t) cc_final: 0.6878 (m) REVERT: R 246 ILE cc_start: 0.7798 (mt) cc_final: 0.7541 (mp) REVERT: R 281 GLU cc_start: 0.7340 (tt0) cc_final: 0.7099 (mm-30) REVERT: R 348 ILE cc_start: 0.8276 (mt) cc_final: 0.8063 (mt) REVERT: R 367 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6730 (mp0) REVERT: A 27 GLU cc_start: 0.6783 (tp30) cc_final: 0.6134 (tp30) REVERT: A 58 LYS cc_start: 0.6941 (ttpp) cc_final: 0.6115 (mmmt) REVERT: A 60 MET cc_start: 0.7503 (mmt) cc_final: 0.7004 (mmt) REVERT: A 301 TYR cc_start: 0.8148 (m-80) cc_final: 0.7684 (m-80) REVERT: A 346 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6156 (mtp180) REVERT: A 360 GLU cc_start: 0.7648 (tt0) cc_final: 0.7433 (tt0) REVERT: A 382 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7441 (mt-10) REVERT: B 124 TYR cc_start: 0.7784 (m-80) cc_final: 0.7279 (m-80) REVERT: B 146 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 175 GLN cc_start: 0.7717 (mm110) cc_final: 0.7460 (mm110) REVERT: B 197 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.6797 (mmm-85) REVERT: N 5 GLN cc_start: 0.7027 (tp-100) cc_final: 0.6397 (mt0) REVERT: N 82 GLN cc_start: 0.7337 (tp40) cc_final: 0.7070 (tp-100) REVERT: N 94 TYR cc_start: 0.7939 (m-80) cc_final: 0.7696 (m-80) outliers start: 23 outliers final: 9 residues processed: 136 average time/residue: 0.6528 time to fit residues: 93.8726 Evaluate side-chains 130 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 64 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 0.0670 chunk 65 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 192 ASN A 31 GLN A 254 ASN A 380 GLN B 176 GLN B 340 ASN N 120 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125278 restraints weight = 8981.606| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.67 r_work: 0.3301 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 8510 Z= 0.228 Angle : 0.627 15.219 11505 Z= 0.342 Chirality : 0.045 0.192 1277 Planarity : 0.005 0.054 1469 Dihedral : 4.773 19.414 1148 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.45 % Allowed : 16.15 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1030 helix: 1.41 (0.25), residues: 420 sheet: -0.30 (0.33), residues: 214 loop : -1.49 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.027 0.002 TYR R 146 PHE 0.024 0.002 PHE R 313 TRP 0.022 0.002 TRP B 82 HIS 0.010 0.002 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 8507) covalent geometry : angle 0.61026 (11499) SS BOND : bond 0.00421 ( 3) SS BOND : angle 6.31297 ( 6) hydrogen bonds : bond 0.04807 ( 448) hydrogen bonds : angle 5.18701 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.333 Fit side-chains REVERT: R 133 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7059 (mm-30) REVERT: R 164 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7421 (mt) REVERT: R 246 ILE cc_start: 0.7872 (mt) cc_final: 0.7631 (mt) REVERT: R 344 THR cc_start: 0.8251 (m) cc_final: 0.7957 (m) REVERT: R 367 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6911 (mp0) REVERT: A 27 GLU cc_start: 0.6847 (tp30) cc_final: 0.6097 (tp30) REVERT: A 223 ASP cc_start: 0.8101 (t0) cc_final: 0.7886 (t70) REVERT: A 301 TYR cc_start: 0.8219 (m-80) cc_final: 0.7796 (m-80) REVERT: A 346 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6268 (mtp180) REVERT: A 382 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 82 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.7110 (m-90) REVERT: B 124 TYR cc_start: 0.7818 (m-80) cc_final: 0.7279 (m-80) REVERT: B 146 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8283 (tt) REVERT: B 175 GLN cc_start: 0.7790 (mm110) cc_final: 0.7559 (mm110) REVERT: B 197 ARG cc_start: 0.7199 (mtt-85) cc_final: 0.6775 (mmt90) REVERT: N 1 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.6227 (tt0) REVERT: N 5 GLN cc_start: 0.7093 (tp-100) cc_final: 0.6382 (mt0) REVERT: N 82 GLN cc_start: 0.7480 (tp40) cc_final: 0.7235 (tp-100) REVERT: N 94 TYR cc_start: 0.8049 (m-80) cc_final: 0.7804 (m-80) outliers start: 40 outliers final: 18 residues processed: 141 average time/residue: 0.6106 time to fit residues: 91.2792 Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 380 GLN B 176 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.128515 restraints weight = 8874.486| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.68 r_work: 0.3343 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 8510 Z= 0.150 Angle : 0.552 15.110 11505 Z= 0.300 Chirality : 0.042 0.179 1277 Planarity : 0.005 0.051 1469 Dihedral : 4.521 19.604 1148 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.79 % Allowed : 17.71 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1030 helix: 1.77 (0.25), residues: 418 sheet: -0.21 (0.34), residues: 213 loop : -1.38 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.023 0.002 TYR R 146 PHE 0.020 0.002 PHE R 313 TRP 0.022 0.002 TRP B 82 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8507) covalent geometry : angle 0.53322 (11499) SS BOND : bond 0.00116 ( 3) SS BOND : angle 6.33644 ( 6) hydrogen bonds : bond 0.04118 ( 448) hydrogen bonds : angle 4.95498 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.335 Fit side-chains REVERT: R 133 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6987 (mm-30) REVERT: R 164 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7338 (mt) REVERT: R 246 ILE cc_start: 0.7803 (mt) cc_final: 0.7537 (mt) REVERT: R 253 LYS cc_start: 0.7857 (tptp) cc_final: 0.7531 (tmtt) REVERT: R 367 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6873 (mp0) REVERT: A 301 TYR cc_start: 0.8157 (m-80) cc_final: 0.7747 (m-80) REVERT: A 346 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6165 (mtp180) REVERT: A 382 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 82 TRP cc_start: 0.7350 (OUTLIER) cc_final: 0.7065 (m-90) REVERT: B 124 TYR cc_start: 0.7773 (m-80) cc_final: 0.7216 (m-80) REVERT: B 146 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8307 (tp) REVERT: B 175 GLN cc_start: 0.7688 (mm110) cc_final: 0.7460 (mm110) REVERT: B 197 ARG cc_start: 0.7201 (mtt-85) cc_final: 0.6782 (mmt90) REVERT: N 5 GLN cc_start: 0.7104 (tp-100) cc_final: 0.6454 (mt0) REVERT: N 94 TYR cc_start: 0.7923 (m-80) cc_final: 0.7714 (m-80) outliers start: 34 outliers final: 13 residues processed: 141 average time/residue: 0.5979 time to fit residues: 89.4723 Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 85 optimal weight: 0.0070 chunk 29 optimal weight: 4.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 380 GLN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133117 restraints weight = 8780.629| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.54 r_work: 0.3410 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8510 Z= 0.126 Angle : 0.520 10.257 11505 Z= 0.282 Chirality : 0.042 0.181 1277 Planarity : 0.004 0.050 1469 Dihedral : 4.401 22.122 1148 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.90 % Allowed : 18.49 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.26), residues: 1030 helix: 1.99 (0.25), residues: 418 sheet: -0.13 (0.34), residues: 218 loop : -1.27 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.022 0.001 TYR R 146 PHE 0.020 0.001 PHE R 313 TRP 0.021 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8507) covalent geometry : angle 0.51179 (11499) SS BOND : bond 0.00198 ( 3) SS BOND : angle 4.09250 ( 6) hydrogen bonds : bond 0.03874 ( 448) hydrogen bonds : angle 4.82073 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.311 Fit side-chains REVERT: R 164 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7280 (mt) REVERT: R 246 ILE cc_start: 0.7806 (mt) cc_final: 0.7564 (mt) REVERT: R 367 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6938 (mp0) REVERT: A 301 TYR cc_start: 0.8120 (m-80) cc_final: 0.7755 (m-80) REVERT: A 346 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6227 (mtp180) REVERT: A 382 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 82 TRP cc_start: 0.7298 (OUTLIER) cc_final: 0.7058 (m-90) REVERT: B 124 TYR cc_start: 0.7777 (m-80) cc_final: 0.7230 (m-80) REVERT: B 146 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8280 (tp) REVERT: B 197 ARG cc_start: 0.7212 (mtt-85) cc_final: 0.6810 (mmt90) REVERT: N 5 GLN cc_start: 0.7093 (tp-100) cc_final: 0.6530 (mt0) REVERT: N 94 TYR cc_start: 0.8019 (m-80) cc_final: 0.7734 (m-80) outliers start: 35 outliers final: 15 residues processed: 142 average time/residue: 0.5759 time to fit residues: 86.8736 Evaluate side-chains 132 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 51 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 211 HIS A 380 GLN B 176 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127195 restraints weight = 8890.520| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.67 r_work: 0.3327 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8510 Z= 0.181 Angle : 0.580 10.190 11505 Z= 0.313 Chirality : 0.044 0.182 1277 Planarity : 0.005 0.052 1469 Dihedral : 4.573 22.227 1148 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.56 % Allowed : 19.27 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1030 helix: 1.90 (0.25), residues: 417 sheet: -0.07 (0.34), residues: 217 loop : -1.32 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.024 0.002 TYR R 146 PHE 0.022 0.002 PHE R 313 TRP 0.021 0.002 TRP B 82 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8507) covalent geometry : angle 0.57263 (11499) SS BOND : bond 0.00171 ( 3) SS BOND : angle 3.98013 ( 6) hydrogen bonds : bond 0.04382 ( 448) hydrogen bonds : angle 5.03206 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 115 time to evaluate : 0.325 Fit side-chains REVERT: R 164 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7301 (mt) REVERT: R 246 ILE cc_start: 0.7742 (mt) cc_final: 0.7500 (mt) REVERT: R 367 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6916 (mp0) REVERT: A 223 ASP cc_start: 0.7980 (t0) cc_final: 0.7745 (t70) REVERT: A 301 TYR cc_start: 0.8226 (m-80) cc_final: 0.7850 (m-80) REVERT: A 346 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6212 (mtp180) REVERT: A 382 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 124 TYR cc_start: 0.7793 (m-80) cc_final: 0.7253 (m-80) REVERT: B 146 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8319 (tp) REVERT: N 1 GLN cc_start: 0.6486 (OUTLIER) cc_final: 0.6230 (tt0) REVERT: N 5 GLN cc_start: 0.7016 (tp-100) cc_final: 0.6391 (mt0) REVERT: N 94 TYR cc_start: 0.7990 (m-80) cc_final: 0.7679 (m-80) outliers start: 32 outliers final: 17 residues processed: 132 average time/residue: 0.6021 time to fit residues: 84.1534 Evaluate side-chains 133 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 96 optimal weight: 0.0570 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 380 GLN B 176 GLN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127609 restraints weight = 8814.808| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.67 r_work: 0.3338 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8510 Z= 0.163 Angle : 0.558 8.982 11505 Z= 0.304 Chirality : 0.043 0.181 1277 Planarity : 0.005 0.051 1469 Dihedral : 4.536 22.407 1148 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.67 % Allowed : 19.15 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1030 helix: 1.96 (0.25), residues: 417 sheet: -0.04 (0.34), residues: 217 loop : -1.22 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.023 0.002 TYR R 146 PHE 0.022 0.002 PHE R 313 TRP 0.021 0.002 TRP R 232 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 8507) covalent geometry : angle 0.55246 (11499) SS BOND : bond 0.00154 ( 3) SS BOND : angle 3.59164 ( 6) hydrogen bonds : bond 0.04282 ( 448) hydrogen bonds : angle 4.97298 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.210 Fit side-chains REVERT: R 164 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7431 (mt) REVERT: R 246 ILE cc_start: 0.7777 (mt) cc_final: 0.7524 (mt) REVERT: R 367 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6870 (mp0) REVERT: R 400 GLN cc_start: 0.6172 (tt0) cc_final: 0.5969 (tt0) REVERT: A 223 ASP cc_start: 0.8026 (t0) cc_final: 0.7770 (t70) REVERT: A 301 TYR cc_start: 0.8246 (m-80) cc_final: 0.7891 (m-80) REVERT: A 346 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6179 (mtp180) REVERT: A 382 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7362 (mt-10) REVERT: B 124 TYR cc_start: 0.7816 (m-80) cc_final: 0.7280 (m-80) REVERT: B 146 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8324 (tp) REVERT: N 1 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.6214 (tt0) REVERT: N 5 GLN cc_start: 0.7008 (tp-100) cc_final: 0.6407 (mt0) REVERT: N 94 TYR cc_start: 0.7947 (m-80) cc_final: 0.7668 (m-80) outliers start: 33 outliers final: 17 residues processed: 137 average time/residue: 0.5686 time to fit residues: 82.6439 Evaluate side-chains 134 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 153 SER Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 20 GLN ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 ASN A 380 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.165754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130837 restraints weight = 8816.210| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.65 r_work: 0.3368 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8510 Z= 0.116 Angle : 0.511 7.320 11505 Z= 0.278 Chirality : 0.041 0.154 1277 Planarity : 0.004 0.054 1469 Dihedral : 4.337 21.230 1148 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.01 % Allowed : 20.04 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.27), residues: 1030 helix: 2.17 (0.25), residues: 416 sheet: -0.03 (0.34), residues: 220 loop : -1.10 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.021 0.001 TYR R 146 PHE 0.018 0.001 PHE R 313 TRP 0.020 0.001 TRP R 232 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8507) covalent geometry : angle 0.50635 (11499) SS BOND : bond 0.00155 ( 3) SS BOND : angle 2.99742 ( 6) hydrogen bonds : bond 0.03831 ( 448) hydrogen bonds : angle 4.77594 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.272 Fit side-chains REVERT: R 164 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7344 (mt) REVERT: R 367 GLU cc_start: 0.7478 (mt-10) cc_final: 0.6952 (mp0) REVERT: A 223 ASP cc_start: 0.8047 (t0) cc_final: 0.7798 (t70) REVERT: A 301 TYR cc_start: 0.8099 (m-80) cc_final: 0.7734 (m-80) REVERT: A 346 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6210 (mtp180) REVERT: A 382 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7377 (mt-10) REVERT: B 124 TYR cc_start: 0.7795 (m-80) cc_final: 0.7263 (m-80) REVERT: B 146 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8289 (tp) REVERT: N 1 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.6218 (tt0) REVERT: N 5 GLN cc_start: 0.7021 (tp-100) cc_final: 0.6487 (mt0) REVERT: N 94 TYR cc_start: 0.7942 (m-80) cc_final: 0.7682 (m-80) outliers start: 27 outliers final: 13 residues processed: 135 average time/residue: 0.5578 time to fit residues: 79.9744 Evaluate side-chains 128 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 192 ASN Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 1 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 76 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.0040 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 ASN R 400 GLN A 31 GLN A 380 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.168048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.134525 restraints weight = 8811.890| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.58 r_work: 0.3428 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8510 Z= 0.106 Angle : 0.500 7.114 11505 Z= 0.272 Chirality : 0.041 0.139 1277 Planarity : 0.004 0.055 1469 Dihedral : 4.194 20.190 1148 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.78 % Allowed : 20.82 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 1030 helix: 2.23 (0.25), residues: 419 sheet: 0.06 (0.34), residues: 225 loop : -1.05 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.017 0.001 TYR R 146 PHE 0.021 0.001 PHE R 390 TRP 0.020 0.001 TRP R 232 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8507) covalent geometry : angle 0.49602 (11499) SS BOND : bond 0.00133 ( 3) SS BOND : angle 2.82881 ( 6) hydrogen bonds : bond 0.03622 ( 448) hydrogen bonds : angle 4.65304 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.287 Fit side-chains REVERT: R 366 MET cc_start: 0.7326 (ttp) cc_final: 0.7112 (tmm) REVERT: R 367 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6934 (mp0) REVERT: A 58 LYS cc_start: 0.7144 (ttpp) cc_final: 0.6373 (mmmt) REVERT: A 301 TYR cc_start: 0.8097 (m-80) cc_final: 0.7735 (m-80) REVERT: A 346 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6192 (mtp180) REVERT: A 382 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7415 (mt-10) REVERT: B 124 TYR cc_start: 0.7741 (m-80) cc_final: 0.7181 (m-80) REVERT: B 146 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8273 (tp) REVERT: N 5 GLN cc_start: 0.7068 (tp-100) cc_final: 0.6585 (mt0) REVERT: N 94 TYR cc_start: 0.7890 (m-80) cc_final: 0.7654 (m-80) REVERT: N 104 THR cc_start: 0.6715 (p) cc_final: 0.6438 (t) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.5523 time to fit residues: 76.2034 Evaluate side-chains 127 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 400 GLN A 31 GLN A 380 GLN B 176 GLN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.167938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.132659 restraints weight = 8739.206| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.65 r_work: 0.3365 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8510 Z= 0.137 Angle : 0.531 7.105 11505 Z= 0.289 Chirality : 0.042 0.152 1277 Planarity : 0.004 0.050 1469 Dihedral : 4.322 21.426 1148 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.12 % Allowed : 21.16 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.27), residues: 1030 helix: 2.27 (0.25), residues: 417 sheet: 0.13 (0.34), residues: 223 loop : -1.13 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.021 0.002 TYR R 146 PHE 0.020 0.002 PHE R 313 TRP 0.021 0.001 TRP R 232 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8507) covalent geometry : angle 0.52692 (11499) SS BOND : bond 0.00160 ( 3) SS BOND : angle 3.06458 ( 6) hydrogen bonds : bond 0.03963 ( 448) hydrogen bonds : angle 4.75497 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.00 seconds wall clock time: 56 minutes 17.78 seconds (3377.78 seconds total)