Starting phenix.real_space_refine on Fri Aug 22 21:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wg7_37504/08_2025/8wg7_37504.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wg7_37504/08_2025/8wg7_37504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wg7_37504/08_2025/8wg7_37504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wg7_37504/08_2025/8wg7_37504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wg7_37504/08_2025/8wg7_37504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wg7_37504/08_2025/8wg7_37504.map" } resolution = 2.54 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= 0.019 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 48 5.16 5 C 5179 2.51 5 N 1412 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8123 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1928 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2205 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 69 Time building chain proxies: 1.95, per 1000 atoms: 0.24 Number of scatterers: 8123 At special positions: 0 Unit cell: (74.97, 96.39, 129.591, 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 48 16.00 O 1484 8.00 N 1412 7.00 C 5179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.48 Conformation dependent library (CDL) restraints added in 309.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.647A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.783A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.661A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.529A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.955A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 Processing helix chain 'R' and resid 174 through 207 removed outlier: 3.918A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 223 Processing helix chain 'R' and resid 224 through 257 removed outlier: 3.916A pdb=" N LEU R 228 " --> pdb=" O LEU R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 275 through 292 removed outlier: 3.633A pdb=" N LEU R 279 " --> pdb=" O GLY R 275 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 294 through 298 removed outlier: 3.693A pdb=" N THR R 298 " --> pdb=" O GLY R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 303 through 336 removed outlier: 4.407A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 343 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 Processing helix chain 'R' and resid 378 through 404 removed outlier: 3.672A pdb=" N ILE R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 424 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.835A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.692A 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: 7.028A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.759A 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: 4.200A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 7.095A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.643A 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: 7.061A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.714A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.515A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (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 10 through 11 removed outlier: 6.036A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1281 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: 1.30 Time building geometry restraints manager: 0.64 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: 2610 1.34 - 1.46: 1384 1.46 - 1.58: 4234 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 8294 Sorted by residual: bond pdb=" CA LYS R 346 " pdb=" C LYS R 346 " ideal model delta sigma weight residual 1.527 1.503 0.024 1.21e-02 6.83e+03 4.03e+00 bond pdb=" CA LYS R 336 " pdb=" C LYS R 336 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" CA ALA R 337 " pdb=" C ALA R 337 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.34e-02 5.57e+03 3.39e+00 bond pdb=" CA THR R 343 " pdb=" C THR R 343 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.41e-02 5.03e+03 2.61e+00 bond pdb=" CA ASN R 338 " pdb=" C ASN R 338 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.34e-02 5.57e+03 2.43e+00 ... (remaining 8289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 10815 1.29 - 2.57: 353 2.57 - 3.86: 58 3.86 - 5.15: 10 5.15 - 6.43: 2 Bond angle restraints: 11238 Sorted by residual: angle pdb=" N THR R 343 " pdb=" CA THR R 343 " pdb=" C THR R 343 " ideal model delta sigma weight residual 112.38 108.04 4.34 1.22e+00 6.72e-01 1.27e+01 angle pdb=" N ASP R 344 " pdb=" CA ASP R 344 " pdb=" C ASP R 344 " ideal model delta sigma weight residual 111.75 107.93 3.82 1.28e+00 6.10e-01 8.91e+00 angle pdb=" N LEU R 339 " pdb=" CA LEU R 339 " pdb=" C LEU R 339 " ideal model delta sigma weight residual 112.97 110.15 2.82 1.06e+00 8.90e-01 7.07e+00 angle pdb=" C LYS R 336 " pdb=" CA LYS R 336 " pdb=" CB LYS R 336 " ideal model delta sigma weight residual 111.50 108.20 3.30 1.29e+00 6.01e-01 6.54e+00 angle pdb=" N LYS R 346 " pdb=" CA LYS R 346 " pdb=" C LYS R 346 " ideal model delta sigma weight residual 111.56 107.91 3.65 1.53e+00 4.27e-01 5.68e+00 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4485 17.84 - 35.69: 351 35.69 - 53.53: 65 53.53 - 71.38: 8 71.38 - 89.22: 6 Dihedral angle restraints: 4915 sinusoidal: 1913 harmonic: 3002 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual -86.00 -175.22 89.22 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual 180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PRO N 41 " pdb=" C PRO N 41 " pdb=" N GLY N 42 " pdb=" CA GLY N 42 " ideal model delta harmonic sigma weight residual -180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 809 0.033 - 0.066: 311 0.066 - 0.100: 104 0.100 - 0.133: 37 0.133 - 0.166: 6 Chirality restraints: 1267 Sorted by residual: chirality pdb=" CA GLN A 19 " pdb=" N GLN A 19 " pdb=" C GLN A 19 " pdb=" CB GLN A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA TYR R 152 " pdb=" N TYR R 152 " pdb=" C TYR R 152 " pdb=" CB TYR R 152 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 1264 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 332 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 53 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA N 40 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO N 41 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " -0.024 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 263 2.71 - 3.26: 8170 3.26 - 3.81: 13475 3.81 - 4.35: 16401 4.35 - 4.90: 28505 Nonbonded interactions: 66814 Sorted by model distance: nonbonded pdb=" NE2 GLN A 59 " pdb=" O ASP A 368 " model vdw 2.167 3.120 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.229 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.244 3.040 nonbonded pdb=" OG SER R 136 " pdb=" OE1 GLU R 138 " model vdw 2.265 3.040 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.269 3.120 ... (remaining 66809 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 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:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.003 0.030 8297 Z= 0.146 Angle : 0.544 6.432 11244 Z= 0.326 Chirality : 0.042 0.166 1267 Planarity : 0.004 0.060 1424 Dihedral : 13.039 87.080 2964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.55 % Favored : 96.15 % Rotamer: Outliers : 0.12 % Allowed : 0.58 % Favored : 99.30 % 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 aren not related in a simple way. whole: 1.50 (0.27), residues: 1014 helix: 2.83 (0.27), residues: 379 sheet: 0.42 (0.34), residues: 230 loop : -0.44 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 314 TYR 0.022 0.001 TYR R 152 PHE 0.010 0.001 PHE A 212 TRP 0.028 0.002 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8294) covalent geometry : angle 0.54166 (11238) SS BOND : bond 0.00241 ( 3) SS BOND : angle 2.45696 ( 6) hydrogen bonds : bond 0.13869 ( 454) hydrogen bonds : angle 5.86591 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.290 Fit side-chains REVERT: A 15 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6796 (mm-30) REVERT: A 19 GLN cc_start: 0.7260 (mp10) cc_final: 0.6773 (mp10) REVERT: A 35 GLN cc_start: 0.8196 (tt0) cc_final: 0.7974 (tt0) REVERT: B 175 GLN cc_start: 0.8041 (pp30) cc_final: 0.7818 (pp30) REVERT: G 21 MET cc_start: 0.6486 (ttp) cc_final: 0.6192 (tmt) REVERT: N 31 ASN cc_start: 0.8369 (m110) cc_final: 0.8134 (m110) REVERT: N 87 LYS cc_start: 0.8840 (mtpt) cc_final: 0.8639 (mtpm) REVERT: N 106 ASP cc_start: 0.8552 (p0) cc_final: 0.8119 (p0) REVERT: R 139 GLU cc_start: 0.7668 (pm20) cc_final: 0.6927 (pm20) REVERT: R 306 TRP cc_start: 0.8652 (t60) cc_final: 0.8257 (t-100) REVERT: R 418 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8156 (mm-30) outliers start: 1 outliers final: 0 residues processed: 175 average time/residue: 0.6097 time to fit residues: 111.8664 Evaluate side-chains 137 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 39 GLN N 77 ASN R 180 HIS R 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.121911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084880 restraints weight = 12338.907| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.97 r_work: 0.2933 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 8297 Z= 0.292 Angle : 0.662 7.718 11244 Z= 0.359 Chirality : 0.047 0.182 1267 Planarity : 0.005 0.056 1424 Dihedral : 4.411 21.300 1124 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.24 % Allowed : 13.56 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.27), residues: 1014 helix: 2.59 (0.26), residues: 383 sheet: 0.33 (0.34), residues: 226 loop : -0.44 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 314 TYR 0.022 0.002 TYR R 148 PHE 0.012 0.002 PHE B 234 TRP 0.020 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00691 ( 8294) covalent geometry : angle 0.66059 (11238) SS BOND : bond 0.00164 ( 3) SS BOND : angle 2.24592 ( 6) hydrogen bonds : bond 0.04846 ( 454) hydrogen bonds : angle 4.90134 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8227 (pp30) cc_final: 0.7812 (pp30) REVERT: G 21 MET cc_start: 0.5704 (ttp) cc_final: 0.5446 (tmt) REVERT: N 31 ASN cc_start: 0.8634 (m-40) cc_final: 0.8365 (m110) REVERT: N 53 GLN cc_start: 0.8248 (mp10) cc_final: 0.7942 (mp10) REVERT: N 87 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8030 (mtpm) REVERT: N 106 ASP cc_start: 0.8861 (p0) cc_final: 0.8488 (p0) REVERT: R 139 GLU cc_start: 0.7763 (pm20) cc_final: 0.7312 (pm20) REVERT: R 262 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: R 306 TRP cc_start: 0.8298 (t60) cc_final: 0.7823 (t-100) REVERT: R 418 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8224 (mm-30) REVERT: R 420 TRP cc_start: 0.6872 (t60) cc_final: 0.6624 (t60) outliers start: 28 outliers final: 14 residues processed: 156 average time/residue: 0.5439 time to fit residues: 89.4048 Evaluate side-chains 144 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 194 VAL Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.087987 restraints weight = 11930.896| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.92 r_work: 0.2993 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8297 Z= 0.133 Angle : 0.547 8.189 11244 Z= 0.294 Chirality : 0.042 0.135 1267 Planarity : 0.004 0.052 1424 Dihedral : 4.144 20.906 1124 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.90 % Allowed : 17.27 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.27), residues: 1014 helix: 2.86 (0.26), residues: 378 sheet: 0.27 (0.34), residues: 218 loop : -0.27 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.014 0.001 TYR R 148 PHE 0.021 0.001 PHE R 169 TRP 0.018 0.002 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8294) covalent geometry : angle 0.54626 (11238) SS BOND : bond 0.00163 ( 3) SS BOND : angle 1.27223 ( 6) hydrogen bonds : bond 0.03883 ( 454) hydrogen bonds : angle 4.63281 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8215 (pp30) cc_final: 0.7759 (pp30) REVERT: N 31 ASN cc_start: 0.8467 (m-40) cc_final: 0.8260 (m-40) REVERT: N 53 GLN cc_start: 0.8184 (mp10) cc_final: 0.7915 (mp10) REVERT: N 87 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8232 (mtpm) REVERT: N 105 ARG cc_start: 0.8432 (ttp-110) cc_final: 0.8191 (ttp-110) REVERT: N 106 ASP cc_start: 0.8833 (p0) cc_final: 0.8540 (OUTLIER) REVERT: N 117 TYR cc_start: 0.8135 (m-80) cc_final: 0.7920 (m-80) REVERT: R 139 GLU cc_start: 0.7809 (pm20) cc_final: 0.7423 (pm20) REVERT: R 197 LYS cc_start: 0.8754 (tmtm) cc_final: 0.8469 (tmmm) REVERT: R 306 TRP cc_start: 0.8252 (t60) cc_final: 0.7896 (t-100) REVERT: R 418 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8180 (mm-30) REVERT: R 420 TRP cc_start: 0.6887 (t60) cc_final: 0.6603 (t60) outliers start: 25 outliers final: 14 residues processed: 156 average time/residue: 0.5267 time to fit residues: 86.3636 Evaluate side-chains 143 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 110 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.086338 restraints weight = 12304.810| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.96 r_work: 0.2966 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8297 Z= 0.179 Angle : 0.568 8.014 11244 Z= 0.305 Chirality : 0.043 0.163 1267 Planarity : 0.004 0.051 1424 Dihedral : 4.199 21.587 1124 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.71 % Allowed : 18.66 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.27), residues: 1014 helix: 2.88 (0.26), residues: 378 sheet: 0.01 (0.32), residues: 239 loop : -0.22 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.016 0.002 TYR R 148 PHE 0.018 0.001 PHE R 169 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 8294) covalent geometry : angle 0.56729 (11238) SS BOND : bond 0.00120 ( 3) SS BOND : angle 1.47018 ( 6) hydrogen bonds : bond 0.04044 ( 454) hydrogen bonds : angle 4.62109 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9193 (mt) REVERT: A 283 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7515 (mtp-110) REVERT: B 175 GLN cc_start: 0.8231 (pp30) cc_final: 0.7731 (pp30) REVERT: N 31 ASN cc_start: 0.8549 (m-40) cc_final: 0.8321 (m110) REVERT: N 53 GLN cc_start: 0.8237 (mp10) cc_final: 0.7943 (mp10) REVERT: N 87 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8084 (mtpm) REVERT: N 105 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.8221 (ttp-110) REVERT: N 106 ASP cc_start: 0.8782 (p0) cc_final: 0.8543 (OUTLIER) REVERT: R 138 GLU cc_start: 0.7909 (pm20) cc_final: 0.7684 (pm20) REVERT: R 139 GLU cc_start: 0.7820 (pm20) cc_final: 0.7417 (pm20) REVERT: R 197 LYS cc_start: 0.8787 (tmtm) cc_final: 0.8458 (tmmm) REVERT: R 262 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: R 306 TRP cc_start: 0.8269 (t60) cc_final: 0.7880 (t-100) REVERT: R 418 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8191 (mm-30) REVERT: R 420 TRP cc_start: 0.6903 (t60) cc_final: 0.6614 (t60) outliers start: 32 outliers final: 16 residues processed: 154 average time/residue: 0.5229 time to fit residues: 84.9566 Evaluate side-chains 147 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS A 279 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.125543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.088994 restraints weight = 12183.860| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.97 r_work: 0.3001 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8297 Z= 0.118 Angle : 0.537 8.136 11244 Z= 0.287 Chirality : 0.042 0.133 1267 Planarity : 0.004 0.049 1424 Dihedral : 4.070 21.069 1124 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.13 % Allowed : 20.16 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.27), residues: 1014 helix: 3.13 (0.26), residues: 372 sheet: 0.00 (0.32), residues: 242 loop : -0.13 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.013 0.001 TYR R 148 PHE 0.013 0.001 PHE A 212 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8294) covalent geometry : angle 0.53701 (11238) SS BOND : bond 0.00203 ( 3) SS BOND : angle 1.11794 ( 6) hydrogen bonds : bond 0.03554 ( 454) hydrogen bonds : angle 4.47106 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7442 (mtp-110) REVERT: B 175 GLN cc_start: 0.8296 (pp30) cc_final: 0.7700 (pp30) REVERT: B 217 MET cc_start: 0.8401 (pp-130) cc_final: 0.8193 (pp-130) REVERT: B 243 THR cc_start: 0.8447 (p) cc_final: 0.8104 (p) REVERT: B 334 SER cc_start: 0.8566 (m) cc_final: 0.8285 (p) REVERT: G 58 GLU cc_start: 0.7830 (pm20) cc_final: 0.7428 (pm20) REVERT: N 31 ASN cc_start: 0.8438 (m-40) cc_final: 0.8230 (m-40) REVERT: N 53 GLN cc_start: 0.8190 (mp10) cc_final: 0.7881 (mp10) REVERT: N 87 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8237 (mtpm) REVERT: N 105 ARG cc_start: 0.8442 (ttp-110) cc_final: 0.8159 (ttp-110) REVERT: R 138 GLU cc_start: 0.7961 (pm20) cc_final: 0.7737 (pm20) REVERT: R 139 GLU cc_start: 0.7860 (pm20) cc_final: 0.7457 (pm20) REVERT: R 197 LYS cc_start: 0.8772 (tmtm) cc_final: 0.8449 (tmmm) REVERT: R 262 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: R 306 TRP cc_start: 0.8299 (t60) cc_final: 0.7906 (t-100) REVERT: R 418 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8164 (mm-30) REVERT: R 420 TRP cc_start: 0.6866 (t60) cc_final: 0.6587 (t60) outliers start: 27 outliers final: 15 residues processed: 160 average time/residue: 0.5298 time to fit residues: 89.4810 Evaluate side-chains 151 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 64 HIS N 39 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.125109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.088814 restraints weight = 12068.441| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.94 r_work: 0.3003 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8297 Z= 0.131 Angle : 0.552 8.618 11244 Z= 0.294 Chirality : 0.042 0.140 1267 Planarity : 0.004 0.048 1424 Dihedral : 4.062 20.836 1124 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.82 % Allowed : 19.58 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.27), residues: 1014 helix: 3.17 (0.26), residues: 372 sheet: 0.04 (0.32), residues: 242 loop : -0.15 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 38 TYR 0.014 0.001 TYR R 148 PHE 0.012 0.001 PHE A 212 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8294) covalent geometry : angle 0.55119 (11238) SS BOND : bond 0.00106 ( 3) SS BOND : angle 1.14696 ( 6) hydrogen bonds : bond 0.03587 ( 454) hydrogen bonds : angle 4.43967 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.7747 (mtm110) cc_final: 0.7512 (mtp-110) REVERT: B 175 GLN cc_start: 0.8212 (pp30) cc_final: 0.7718 (pp30) REVERT: B 217 MET cc_start: 0.8384 (pp-130) cc_final: 0.7946 (ppp) REVERT: B 243 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 334 SER cc_start: 0.8516 (m) cc_final: 0.8255 (p) REVERT: N 31 ASN cc_start: 0.8468 (m-40) cc_final: 0.8232 (m110) REVERT: N 53 GLN cc_start: 0.8225 (mp10) cc_final: 0.7901 (mp10) REVERT: N 87 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8244 (mtpm) REVERT: N 105 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8141 (ttp-110) REVERT: R 138 GLU cc_start: 0.7964 (pm20) cc_final: 0.7726 (pm20) REVERT: R 139 GLU cc_start: 0.7881 (pm20) cc_final: 0.7440 (pm20) REVERT: R 197 LYS cc_start: 0.8786 (tmtm) cc_final: 0.8467 (tmmm) REVERT: R 262 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7511 (pm20) REVERT: R 306 TRP cc_start: 0.8293 (t60) cc_final: 0.7902 (t-100) REVERT: R 418 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8131 (mm-30) REVERT: R 420 TRP cc_start: 0.6916 (t60) cc_final: 0.6642 (t60) outliers start: 33 outliers final: 18 residues processed: 163 average time/residue: 0.5210 time to fit residues: 89.7373 Evaluate side-chains 157 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 54 ASN A 64 HIS N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.124238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.087666 restraints weight = 12236.838| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.97 r_work: 0.2977 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8297 Z= 0.153 Angle : 0.574 9.287 11244 Z= 0.303 Chirality : 0.043 0.154 1267 Planarity : 0.004 0.057 1424 Dihedral : 4.079 20.984 1124 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.48 % Allowed : 20.74 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.27), residues: 1014 helix: 3.16 (0.26), residues: 372 sheet: 0.02 (0.32), residues: 242 loop : -0.19 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 38 TYR 0.014 0.001 TYR R 148 PHE 0.012 0.001 PHE A 212 TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8294) covalent geometry : angle 0.57344 (11238) SS BOND : bond 0.00140 ( 3) SS BOND : angle 1.32882 ( 6) hydrogen bonds : bond 0.03699 ( 454) hydrogen bonds : angle 4.45769 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 ARG cc_start: 0.8335 (mtm110) cc_final: 0.8130 (mtm-85) REVERT: B 175 GLN cc_start: 0.8257 (pp30) cc_final: 0.7657 (pp30) REVERT: B 217 MET cc_start: 0.8420 (pp-130) cc_final: 0.7970 (ppp) REVERT: B 243 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8084 (p) REVERT: N 31 ASN cc_start: 0.8498 (m-40) cc_final: 0.8257 (m110) REVERT: N 53 GLN cc_start: 0.8244 (mp10) cc_final: 0.7921 (mp10) REVERT: N 87 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8039 (mtpm) REVERT: N 105 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8167 (ttp-110) REVERT: R 138 GLU cc_start: 0.7996 (pm20) cc_final: 0.7757 (pm20) REVERT: R 139 GLU cc_start: 0.7941 (pm20) cc_final: 0.7486 (pm20) REVERT: R 197 LYS cc_start: 0.8778 (tmtm) cc_final: 0.8466 (tmmm) REVERT: R 262 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7481 (pm20) REVERT: R 306 TRP cc_start: 0.8291 (t60) cc_final: 0.7941 (t-100) REVERT: R 418 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8175 (mm-30) outliers start: 30 outliers final: 19 residues processed: 155 average time/residue: 0.5236 time to fit residues: 85.7189 Evaluate side-chains 154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 152 TYR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.122694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086149 restraints weight = 12111.942| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.94 r_work: 0.2961 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8297 Z= 0.194 Angle : 0.617 13.341 11244 Z= 0.322 Chirality : 0.044 0.162 1267 Planarity : 0.005 0.060 1424 Dihedral : 4.194 21.533 1124 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.36 % Allowed : 21.21 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.27), residues: 1014 helix: 3.01 (0.26), residues: 377 sheet: -0.01 (0.32), residues: 242 loop : -0.30 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 38 TYR 0.017 0.002 TYR N 32 PHE 0.015 0.001 PHE R 367 TRP 0.017 0.001 TRP A 234 HIS 0.005 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8294) covalent geometry : angle 0.61651 (11238) SS BOND : bond 0.00143 ( 3) SS BOND : angle 1.48125 ( 6) hydrogen bonds : bond 0.03982 ( 454) hydrogen bonds : angle 4.54321 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8678 (p90) cc_final: 0.8448 (p90) REVERT: B 175 GLN cc_start: 0.8281 (pp30) cc_final: 0.7703 (pp30) REVERT: B 217 MET cc_start: 0.8366 (pp-130) cc_final: 0.8125 (pp-130) REVERT: B 243 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8093 (p) REVERT: N 31 ASN cc_start: 0.8565 (m-40) cc_final: 0.8329 (m110) REVERT: N 53 GLN cc_start: 0.8303 (mp10) cc_final: 0.7975 (mp10) REVERT: N 87 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8025 (mtpm) REVERT: N 105 ARG cc_start: 0.8383 (ttp-110) cc_final: 0.8118 (ttp-110) REVERT: R 138 GLU cc_start: 0.7960 (pm20) cc_final: 0.7721 (pm20) REVERT: R 139 GLU cc_start: 0.7965 (pm20) cc_final: 0.7438 (pm20) REVERT: R 197 LYS cc_start: 0.8807 (tmtm) cc_final: 0.8480 (tmmm) REVERT: R 262 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: R 292 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8144 (tp30) REVERT: R 306 TRP cc_start: 0.8299 (t60) cc_final: 0.7946 (t-100) REVERT: R 418 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8182 (mm-30) outliers start: 29 outliers final: 18 residues processed: 152 average time/residue: 0.5271 time to fit residues: 84.5265 Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.123816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.087485 restraints weight = 12094.158| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.94 r_work: 0.2987 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8297 Z= 0.148 Angle : 0.603 13.937 11244 Z= 0.313 Chirality : 0.043 0.166 1267 Planarity : 0.005 0.063 1424 Dihedral : 4.144 21.457 1124 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.13 % Allowed : 22.02 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.27), residues: 1014 helix: 3.16 (0.26), residues: 371 sheet: -0.03 (0.32), residues: 242 loop : -0.23 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 38 TYR 0.014 0.001 TYR R 148 PHE 0.012 0.001 PHE A 212 TRP 0.020 0.002 TRP R 420 HIS 0.005 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 8294) covalent geometry : angle 0.60254 (11238) SS BOND : bond 0.00148 ( 3) SS BOND : angle 1.18680 ( 6) hydrogen bonds : bond 0.03701 ( 454) hydrogen bonds : angle 4.47116 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 TYR cc_start: 0.8692 (p90) cc_final: 0.8484 (p90) REVERT: B 175 GLN cc_start: 0.8262 (pp30) cc_final: 0.7683 (pp30) REVERT: B 243 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8075 (p) REVERT: N 31 ASN cc_start: 0.8489 (m-40) cc_final: 0.8187 (m-40) REVERT: N 53 GLN cc_start: 0.8231 (mp10) cc_final: 0.7930 (mp10) REVERT: N 87 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8006 (mtpm) REVERT: N 105 ARG cc_start: 0.8433 (ttp-110) cc_final: 0.8156 (ttp-110) REVERT: R 138 GLU cc_start: 0.7962 (pm20) cc_final: 0.7724 (pm20) REVERT: R 139 GLU cc_start: 0.7970 (pm20) cc_final: 0.7437 (pm20) REVERT: R 197 LYS cc_start: 0.8808 (tmtm) cc_final: 0.8478 (tmmm) REVERT: R 262 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: R 306 TRP cc_start: 0.8300 (t60) cc_final: 0.7906 (t-100) REVERT: R 418 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8184 (mm-30) outliers start: 27 outliers final: 22 residues processed: 152 average time/residue: 0.5102 time to fit residues: 81.9448 Evaluate side-chains 154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 chunk 92 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.088553 restraints weight = 12106.754| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.94 r_work: 0.3001 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8297 Z= 0.134 Angle : 0.600 13.310 11244 Z= 0.311 Chirality : 0.043 0.194 1267 Planarity : 0.004 0.047 1424 Dihedral : 4.086 21.161 1124 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 22.36 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.27), residues: 1014 helix: 3.20 (0.26), residues: 371 sheet: -0.01 (0.32), residues: 242 loop : -0.21 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.014 0.001 TYR A 311 PHE 0.012 0.001 PHE A 212 TRP 0.029 0.002 TRP R 420 HIS 0.006 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8294) covalent geometry : angle 0.59942 (11238) SS BOND : bond 0.00156 ( 3) SS BOND : angle 1.11019 ( 6) hydrogen bonds : bond 0.03560 ( 454) hydrogen bonds : angle 4.42094 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8067 (mt0) REVERT: B 175 GLN cc_start: 0.8248 (pp30) cc_final: 0.7635 (pp30) REVERT: B 243 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8037 (p) REVERT: B 262 MET cc_start: 0.7348 (tpp) cc_final: 0.7102 (tpp) REVERT: N 31 ASN cc_start: 0.8482 (m-40) cc_final: 0.8252 (m110) REVERT: N 53 GLN cc_start: 0.8198 (mp10) cc_final: 0.7884 (mp10) REVERT: N 87 LYS cc_start: 0.8469 (mtpt) cc_final: 0.7994 (mtpm) REVERT: N 105 ARG cc_start: 0.8464 (ttp-110) cc_final: 0.8228 (ttp-110) REVERT: N 125 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8648 (p) REVERT: R 138 GLU cc_start: 0.7963 (pm20) cc_final: 0.7723 (pm20) REVERT: R 139 GLU cc_start: 0.7975 (pm20) cc_final: 0.7437 (pm20) REVERT: R 197 LYS cc_start: 0.8829 (tmtm) cc_final: 0.8516 (tmmm) REVERT: R 262 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: R 306 TRP cc_start: 0.8275 (t60) cc_final: 0.7946 (t-100) REVERT: R 418 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8185 (mm-30) outliers start: 25 outliers final: 19 residues processed: 148 average time/residue: 0.5446 time to fit residues: 85.1066 Evaluate side-chains 150 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 0.0020 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 47 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 237 ASN B 239 ASN N 39 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.125693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089380 restraints weight = 12172.681| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.97 r_work: 0.3006 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8297 Z= 0.125 Angle : 0.592 13.863 11244 Z= 0.307 Chirality : 0.042 0.191 1267 Planarity : 0.004 0.047 1424 Dihedral : 4.064 20.909 1124 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.01 % Allowed : 22.36 % Favored : 74.62 % 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 aren not related in a simple way. whole: 1.68 (0.27), residues: 1014 helix: 3.20 (0.26), residues: 372 sheet: 0.10 (0.33), residues: 232 loop : -0.22 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.013 0.001 TYR R 148 PHE 0.011 0.001 PHE A 212 TRP 0.027 0.002 TRP R 420 HIS 0.006 0.001 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8294) covalent geometry : angle 0.59132 (11238) SS BOND : bond 0.00171 ( 3) SS BOND : angle 1.12006 ( 6) hydrogen bonds : bond 0.03437 ( 454) hydrogen bonds : angle 4.37225 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2840.37 seconds wall clock time: 48 minutes 56.74 seconds (2936.74 seconds total)