Starting phenix.real_space_refine on Tue Mar 3 19:55:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oya_20223/03_2026/6oya_20223.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oya_20223/03_2026/6oya_20223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2026/6oya_20223.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2026/6oya_20223.map" model { file = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2026/6oya_20223.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oya_20223/03_2026/6oya_20223.cif" } resolution = 3.3 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= -0.023 sd= 0.464 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 67 5.16 5 C 5312 2.51 5 N 1389 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 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: 8321 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1655 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2592 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 18, 'TRANS': 307} Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'RET': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.22 Number of scatterers: 8321 At special positions: 0 Unit cell: (85.86, 117.66, 113.42, 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 67 16.00 O 1553 8.00 N 1389 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 228.9 milliseconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.6% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 27 removed outlier: 3.752A pdb=" N GLU A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.609A pdb=" N ILE A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.521A pdb=" N CYS A 210 " --> pdb=" O TRP A 207 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.566A pdb=" N MET A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 4.122A pdb=" N GLU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 Processing helix chain 'A' and resid 326 through 348 removed outlier: 3.670A pdb=" N ASP A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 removed outlier: 3.863A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.767A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 25 Processing helix chain 'G' and resid 32 through 47 removed outlier: 3.672A pdb=" N ARG G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 51 removed outlier: 3.897A pdb=" N ASP G 51 " --> pdb=" O SER G 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 48 through 51' Processing helix chain 'R' and resid 14 through 18 removed outlier: 4.172A pdb=" N THR R 17 " --> pdb=" O SER R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 31 removed outlier: 4.548A pdb=" N TYR R 30 " --> pdb=" O PRO R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 65 Proline residue: R 53 - end of helix removed outlier: 4.382A pdb=" N THR R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU R 59 " --> pdb=" O ASN R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 89 Processing helix chain 'R' and resid 89 through 101 removed outlier: 4.260A pdb=" N THR R 93 " --> pdb=" O GLY R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 140 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.704A pdb=" N ALA R 153 " --> pdb=" O GLY R 149 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE R 154 " --> pdb=" O GLU R 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA R 169 " --> pdb=" O LEU R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 211 Processing helix chain 'R' and resid 212 through 235 removed outlier: 3.673A pdb=" N ALA R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 263 removed outlier: 3.856A pdb=" N LYS R 248 " --> pdb=" O GLN R 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 278 removed outlier: 3.966A pdb=" N ALA R 269 " --> pdb=" O TRP R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 307 removed outlier: 3.904A pdb=" N ILE R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 3.615A pdb=" N SER R 298 " --> pdb=" O PHE R 294 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA R 299 " --> pdb=" O ALA R 295 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL R 300 " --> pdb=" O LYS R 296 " (cutoff:3.500A) Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 312 through 322 removed outlier: 3.856A pdb=" N CYS R 316 " --> pdb=" O GLN R 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 removed outlier: 7.047A pdb=" N VAL A 30 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE A 195 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 183 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.712A pdb=" N LEU A 33 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 217 " --> pdb=" O ILE A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.953A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.262A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET B 61 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.698A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.086A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.899A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.576A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.623A pdb=" N VAL N 12 " --> pdb=" O THR N 125 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'N' and resid 45 through 51 removed outlier: 6.340A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 4 through 5 327 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2672 1.35 - 1.47: 2121 1.47 - 1.59: 3609 1.59 - 1.71: 0 1.71 - 1.84: 99 Bond restraints: 8501 Sorted by residual: bond pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.25e+00 bond pdb=" C ILE R 214 " pdb=" N PRO R 215 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.20e+00 bond pdb=" C ILE R 290 " pdb=" N PRO R 291 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.23e-02 6.61e+03 2.12e+00 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.532 1.554 -0.022 1.56e-02 4.11e+03 2.00e+00 bond pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 1.460 1.479 -0.020 1.42e-02 4.96e+03 1.91e+00 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 11183 2.19 - 4.38: 261 4.38 - 6.57: 35 6.57 - 8.76: 18 8.76 - 10.96: 5 Bond angle restraints: 11502 Sorted by residual: angle pdb=" C ASN R 310 " pdb=" N LYS R 311 " pdb=" CA LYS R 311 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 115.28 -4.58 1.22e+00 6.72e-01 1.41e+01 angle pdb=" N ALA R 169 " pdb=" CA ALA R 169 " pdb=" C ALA R 169 " ideal model delta sigma weight residual 109.81 118.10 -8.29 2.21e+00 2.05e-01 1.41e+01 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 122.82 127.91 -5.09 1.42e+00 4.96e-01 1.28e+01 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4436 17.68 - 35.36: 499 35.36 - 53.04: 74 53.04 - 70.72: 21 70.72 - 88.40: 9 Dihedral angle restraints: 5039 sinusoidal: 1986 harmonic: 3053 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 163.25 -70.25 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -132.79 46.79 1 1.00e+01 1.00e-02 3.03e+01 dihedral pdb=" CA CYS B 166 " pdb=" C CYS B 166 " pdb=" N ALA B 167 " pdb=" CA ALA B 167 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 957 0.054 - 0.108: 247 0.108 - 0.161: 59 0.161 - 0.215: 10 0.215 - 0.269: 3 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASP A 189 " pdb=" N ASP A 189 " pdb=" C ASP A 189 " pdb=" CB ASP A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 80 " pdb=" CA ILE B 80 " pdb=" CG1 ILE B 80 " pdb=" CG2 ILE B 80 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1273 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.062 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO R 171 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 70 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.19e+00 pdb=" N PRO R 71 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 283 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO A 284 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2821 2.84 - 3.36: 7395 3.36 - 3.87: 13818 3.87 - 4.39: 15242 4.39 - 4.90: 26585 Nonbonded interactions: 65861 Sorted by model distance: nonbonded pdb=" OG1 THR A 320 " pdb=" OD2 ASP A 324 " model vdw 2.329 3.040 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.331 3.040 nonbonded pdb=" OE1 GLU B 226 " pdb=" OH TYR N 32 " model vdw 2.341 3.040 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.347 3.040 nonbonded pdb=" NZ LYS A 341 " pdb=" OG1 THR R 243 " model vdw 2.351 3.120 ... (remaining 65856 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: 0.850 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 0.096 8505 Z= 0.219 Angle : 0.877 10.956 11508 Z= 0.470 Chirality : 0.054 0.269 1276 Planarity : 0.007 0.094 1468 Dihedral : 15.281 88.402 3066 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.11 % Allowed : 10.19 % Favored : 89.70 % 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: -4.69 (0.20), residues: 1042 helix: -2.67 (0.19), residues: 369 sheet: -2.86 (0.31), residues: 206 loop : -3.55 (0.22), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 72 TYR 0.025 0.002 TYR R 301 PHE 0.024 0.002 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8501) covalent geometry : angle 0.87669 (11502) SS BOND : bond 0.00527 ( 3) SS BOND : angle 1.29584 ( 6) hydrogen bonds : bond 0.15123 ( 327) hydrogen bonds : angle 7.11329 ( 936) Misc. bond : bond 0.09587 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8849 (tt0) cc_final: 0.8580 (tt0) REVERT: A 212 GLU cc_start: 0.8663 (tt0) cc_final: 0.8406 (tm-30) REVERT: A 240 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8953 (tp-100) REVERT: A 267 LYS cc_start: 0.7444 (mmpt) cc_final: 0.7015 (ttpt) REVERT: A 302 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8825 (mm110) REVERT: A 326 GLN cc_start: 0.8268 (mm110) cc_final: 0.7871 (mm110) REVERT: A 337 ASP cc_start: 0.8694 (t0) cc_final: 0.8387 (t0) REVERT: B 125 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0) REVERT: B 264 TYR cc_start: 0.8696 (m-80) cc_final: 0.8465 (m-10) REVERT: B 289 TYR cc_start: 0.8239 (m-10) cc_final: 0.7900 (m-10) REVERT: B 308 LEU cc_start: 0.9212 (mm) cc_final: 0.8645 (mt) REVERT: B 333 ASP cc_start: 0.7945 (p0) cc_final: 0.7724 (p0) REVERT: B 337 LYS cc_start: 0.8604 (mttt) cc_final: 0.8246 (mmtm) REVERT: B 339 TRP cc_start: 0.8548 (m100) cc_final: 0.8082 (m100) REVERT: G 51 ASP cc_start: 0.7973 (t0) cc_final: 0.7268 (t70) REVERT: G 65 LYS cc_start: 0.8081 (mttt) cc_final: 0.7872 (mttm) REVERT: N 6 GLU cc_start: 0.7804 (mp0) cc_final: 0.7425 (mp0) REVERT: N 22 CYS cc_start: 0.7485 (t) cc_final: 0.7184 (t) REVERT: N 76 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8253 (mptt) REVERT: N 77 ASN cc_start: 0.7865 (t0) cc_final: 0.7376 (t0) REVERT: N 112 SER cc_start: 0.8901 (m) cc_final: 0.8679 (m) REVERT: N 123 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8281 (tp40) REVERT: R 44 MET cc_start: 0.8555 (mmp) cc_final: 0.7571 (mmm) REVERT: R 60 TYR cc_start: 0.8569 (t80) cc_final: 0.8301 (t80) REVERT: R 78 ASN cc_start: 0.9040 (t0) cc_final: 0.8721 (t0) REVERT: R 134 GLU cc_start: 0.8259 (pt0) cc_final: 0.7944 (pt0) REVERT: R 147 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: R 155 MET cc_start: 0.8488 (ttt) cc_final: 0.8274 (ttm) REVERT: R 183 MET cc_start: 0.8629 (mmm) cc_final: 0.8298 (mmt) REVERT: R 236 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8092 (mm110) REVERT: R 308 MET cc_start: 0.8655 (mmm) cc_final: 0.8046 (mmm) REVERT: R 310 ASN cc_start: 0.8921 (t0) cc_final: 0.8233 (t0) REVERT: R 317 MET cc_start: 0.8656 (mtp) cc_final: 0.8413 (mtp) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.0878 time to fit residues: 32.1273 Evaluate side-chains 205 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS B 6 GLN B 13 GLN B 62 HIS B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 73 ASN R 310 ASN R 312 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.112414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095869 restraints weight = 16631.491| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.55 r_work: 0.3216 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8505 Z= 0.127 Angle : 0.623 8.518 11508 Z= 0.324 Chirality : 0.042 0.183 1276 Planarity : 0.004 0.050 1468 Dihedral : 5.771 69.307 1145 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.66 % Allowed : 16.72 % Favored : 81.62 % 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: -3.09 (0.23), residues: 1042 helix: -0.73 (0.26), residues: 360 sheet: -2.27 (0.34), residues: 200 loop : -3.01 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.020 0.002 TYR R 301 PHE 0.013 0.001 PHE B 151 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8501) covalent geometry : angle 0.62265 (11502) SS BOND : bond 0.00262 ( 3) SS BOND : angle 1.25505 ( 6) hydrogen bonds : bond 0.03411 ( 327) hydrogen bonds : angle 4.87942 ( 936) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9086 (tt0) cc_final: 0.8813 (tt0) REVERT: A 182 GLU cc_start: 0.8502 (tt0) cc_final: 0.8300 (tp30) REVERT: A 194 MET cc_start: 0.8867 (mtt) cc_final: 0.8193 (mtp) REVERT: A 212 GLU cc_start: 0.9017 (tt0) cc_final: 0.8797 (tm-30) REVERT: A 240 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8315 (tp40) REVERT: A 268 ASP cc_start: 0.7007 (m-30) cc_final: 0.6370 (p0) REVERT: A 302 GLN cc_start: 0.9380 (mm-40) cc_final: 0.8906 (mm110) REVERT: A 326 GLN cc_start: 0.8679 (mm110) cc_final: 0.8270 (mm110) REVERT: A 337 ASP cc_start: 0.9338 (t0) cc_final: 0.8960 (t0) REVERT: B 17 GLN cc_start: 0.7810 (mt0) cc_final: 0.7558 (tm-30) REVERT: B 19 ARG cc_start: 0.7821 (tmt-80) cc_final: 0.6996 (ttm-80) REVERT: B 101 MET cc_start: 0.9026 (mmm) cc_final: 0.8801 (mmm) REVERT: B 125 ASN cc_start: 0.8933 (t0) cc_final: 0.8488 (t0) REVERT: B 186 ASP cc_start: 0.8293 (p0) cc_final: 0.7884 (p0) REVERT: B 226 GLU cc_start: 0.7792 (mp0) cc_final: 0.7439 (mp0) REVERT: B 228 ASP cc_start: 0.8821 (m-30) cc_final: 0.8095 (m-30) REVERT: B 235 PHE cc_start: 0.8979 (t80) cc_final: 0.8627 (t80) REVERT: B 262 MET cc_start: 0.8615 (mmm) cc_final: 0.8382 (mmt) REVERT: B 268 ASN cc_start: 0.8951 (m110) cc_final: 0.8689 (m110) REVERT: B 293 ASN cc_start: 0.7730 (t0) cc_final: 0.7319 (t0) REVERT: B 308 LEU cc_start: 0.9320 (mm) cc_final: 0.8953 (mp) REVERT: B 337 LYS cc_start: 0.8318 (mttt) cc_final: 0.8097 (mmtm) REVERT: B 339 TRP cc_start: 0.8876 (m100) cc_final: 0.8408 (m100) REVERT: N 22 CYS cc_start: 0.7772 (t) cc_final: 0.7467 (t) REVERT: N 76 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8234 (mptt) REVERT: N 77 ASN cc_start: 0.8237 (t0) cc_final: 0.7717 (t0) REVERT: N 123 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8404 (tp40) REVERT: R 60 TYR cc_start: 0.8599 (t80) cc_final: 0.8369 (t80) REVERT: R 78 ASN cc_start: 0.9094 (t0) cc_final: 0.8719 (t0) REVERT: R 147 ARG cc_start: 0.8853 (mmm-85) cc_final: 0.8239 (tpp80) REVERT: R 155 MET cc_start: 0.8709 (ttt) cc_final: 0.8405 (ttm) REVERT: R 183 MET cc_start: 0.8698 (mmm) cc_final: 0.8365 (tpp) REVERT: R 287 PHE cc_start: 0.9092 (t80) cc_final: 0.8856 (t80) REVERT: R 308 MET cc_start: 0.8805 (mmm) cc_final: 0.8252 (mmm) REVERT: R 310 ASN cc_start: 0.9266 (t0) cc_final: 0.8461 (t0) REVERT: R 317 MET cc_start: 0.8899 (mtp) cc_final: 0.8619 (mtp) outliers start: 15 outliers final: 9 residues processed: 245 average time/residue: 0.0831 time to fit residues: 28.4269 Evaluate side-chains 212 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 203 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS R 28 GLN R 236 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.107648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.090654 restraints weight = 16769.299| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.52 r_work: 0.3130 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8505 Z= 0.203 Angle : 0.663 9.385 11508 Z= 0.343 Chirality : 0.044 0.170 1276 Planarity : 0.004 0.047 1468 Dihedral : 5.294 50.081 1145 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.21 % Allowed : 16.06 % Favored : 80.73 % 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: -2.54 (0.25), residues: 1042 helix: -0.05 (0.27), residues: 374 sheet: -2.04 (0.34), residues: 209 loop : -2.93 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 314 TYR 0.014 0.002 TYR R 178 PHE 0.027 0.002 PHE R 293 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 8501) covalent geometry : angle 0.66141 (11502) SS BOND : bond 0.00437 ( 3) SS BOND : angle 2.08737 ( 6) hydrogen bonds : bond 0.03485 ( 327) hydrogen bonds : angle 4.66850 ( 936) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9123 (tt0) cc_final: 0.8871 (tt0) REVERT: A 24 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7499 (pp20) REVERT: A 194 MET cc_start: 0.8951 (mtt) cc_final: 0.8706 (ttm) REVERT: A 202 ASP cc_start: 0.8685 (t0) cc_final: 0.8450 (t0) REVERT: A 212 GLU cc_start: 0.9116 (tt0) cc_final: 0.8791 (tm-30) REVERT: A 240 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8365 (tp-100) REVERT: A 268 ASP cc_start: 0.7099 (m-30) cc_final: 0.6463 (p0) REVERT: A 302 GLN cc_start: 0.9431 (mm-40) cc_final: 0.8944 (mm110) REVERT: A 326 GLN cc_start: 0.8669 (mm110) cc_final: 0.8182 (mm110) REVERT: B 19 ARG cc_start: 0.7710 (tmt-80) cc_final: 0.6900 (ttm-80) REVERT: B 235 PHE cc_start: 0.9040 (t80) cc_final: 0.8756 (t80) REVERT: B 261 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9127 (mm) REVERT: B 289 TYR cc_start: 0.8094 (m-10) cc_final: 0.7825 (m-80) REVERT: B 293 ASN cc_start: 0.7940 (t0) cc_final: 0.7536 (t0) REVERT: B 308 LEU cc_start: 0.9295 (mm) cc_final: 0.9041 (mp) REVERT: B 325 MET cc_start: 0.8846 (mmt) cc_final: 0.8609 (mmt) REVERT: B 339 TRP cc_start: 0.8907 (m100) cc_final: 0.8605 (m100) REVERT: G 31 MET cc_start: 0.8132 (ttp) cc_final: 0.7932 (ttp) REVERT: N 76 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8279 (mptt) REVERT: N 77 ASN cc_start: 0.8426 (t0) cc_final: 0.7837 (t0) REVERT: N 123 GLN cc_start: 0.9008 (tp-100) cc_final: 0.8325 (tp-100) REVERT: R 60 TYR cc_start: 0.8616 (t80) cc_final: 0.8363 (t80) REVERT: R 69 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8537 (mtm-85) REVERT: R 78 ASN cc_start: 0.9142 (t0) cc_final: 0.8846 (t0) REVERT: R 147 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8305 (tpp80) REVERT: R 155 MET cc_start: 0.8758 (ttt) cc_final: 0.8378 (ttm) REVERT: R 183 MET cc_start: 0.8748 (mmm) cc_final: 0.8452 (tpp) REVERT: R 308 MET cc_start: 0.8865 (mmm) cc_final: 0.8382 (mmm) REVERT: R 310 ASN cc_start: 0.9382 (t0) cc_final: 0.8574 (t0) REVERT: R 317 MET cc_start: 0.8909 (mtp) cc_final: 0.8617 (mtp) outliers start: 29 outliers final: 18 residues processed: 220 average time/residue: 0.0859 time to fit residues: 26.2525 Evaluate side-chains 209 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 34 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 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 209 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096153 restraints weight = 17104.792| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.42 r_work: 0.3273 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8505 Z= 0.141 Angle : 0.615 8.006 11508 Z= 0.315 Chirality : 0.043 0.166 1276 Planarity : 0.004 0.047 1468 Dihedral : 5.121 55.327 1145 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.10 % Allowed : 19.82 % Favored : 77.08 % 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: -2.13 (0.25), residues: 1042 helix: 0.29 (0.27), residues: 374 sheet: -1.75 (0.35), residues: 201 loop : -2.72 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.016 0.002 TYR R 301 PHE 0.019 0.001 PHE R 287 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8501) covalent geometry : angle 0.61294 (11502) SS BOND : bond 0.00413 ( 3) SS BOND : angle 2.10646 ( 6) hydrogen bonds : bond 0.03171 ( 327) hydrogen bonds : angle 4.45825 ( 936) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9101 (tt0) cc_final: 0.8841 (tt0) REVERT: A 24 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7598 (pp20) REVERT: A 194 MET cc_start: 0.9035 (mtt) cc_final: 0.8775 (ttm) REVERT: A 202 ASP cc_start: 0.8761 (t0) cc_final: 0.8478 (t0) REVERT: A 212 GLU cc_start: 0.9115 (tt0) cc_final: 0.8810 (tm-30) REVERT: A 240 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8364 (tp-100) REVERT: A 268 ASP cc_start: 0.7062 (m-30) cc_final: 0.6676 (p0) REVERT: A 302 GLN cc_start: 0.9367 (mm-40) cc_final: 0.8933 (mm110) REVERT: A 326 GLN cc_start: 0.8662 (mm110) cc_final: 0.8176 (mm110) REVERT: A 337 ASP cc_start: 0.9197 (t0) cc_final: 0.8996 (t0) REVERT: B 17 GLN cc_start: 0.7701 (mt0) cc_final: 0.7467 (tm-30) REVERT: B 58 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8602 (pt) REVERT: B 235 PHE cc_start: 0.9034 (t80) cc_final: 0.8769 (t80) REVERT: B 251 ARG cc_start: 0.8688 (mtt180) cc_final: 0.8236 (mmm-85) REVERT: B 293 ASN cc_start: 0.7995 (t0) cc_final: 0.7627 (t0) REVERT: B 308 LEU cc_start: 0.9279 (mm) cc_final: 0.8997 (mp) REVERT: B 325 MET cc_start: 0.8820 (mmt) cc_final: 0.8605 (mmt) REVERT: B 339 TRP cc_start: 0.8906 (m100) cc_final: 0.8652 (m100) REVERT: G 55 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8506 (mmtm) REVERT: N 6 GLU cc_start: 0.7862 (mp0) cc_final: 0.7236 (mp0) REVERT: N 22 CYS cc_start: 0.8050 (t) cc_final: 0.7828 (t) REVERT: N 76 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8292 (mptt) REVERT: N 77 ASN cc_start: 0.8296 (t0) cc_final: 0.7819 (t0) REVERT: N 123 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8407 (tp-100) REVERT: R 60 TYR cc_start: 0.8676 (t80) cc_final: 0.8433 (t80) REVERT: R 78 ASN cc_start: 0.9155 (t0) cc_final: 0.8864 (t0) REVERT: R 147 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8389 (tpp80) REVERT: R 155 MET cc_start: 0.8792 (ttt) cc_final: 0.8341 (mtp) REVERT: R 183 MET cc_start: 0.8893 (mmm) cc_final: 0.8521 (tpp) REVERT: R 308 MET cc_start: 0.8870 (mmm) cc_final: 0.8424 (mmm) REVERT: R 310 ASN cc_start: 0.9281 (t0) cc_final: 0.8478 (t0) REVERT: R 317 MET cc_start: 0.8822 (mtp) cc_final: 0.8524 (mtp) outliers start: 28 outliers final: 19 residues processed: 227 average time/residue: 0.0861 time to fit residues: 27.0808 Evaluate side-chains 212 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096395 restraints weight = 16832.589| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.33 r_work: 0.3295 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8505 Z= 0.130 Angle : 0.614 9.084 11508 Z= 0.314 Chirality : 0.043 0.164 1276 Planarity : 0.004 0.047 1468 Dihedral : 4.964 55.718 1145 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.10 % Allowed : 21.37 % Favored : 74.53 % 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: -1.92 (0.26), residues: 1042 helix: 0.45 (0.27), residues: 379 sheet: -1.66 (0.35), residues: 203 loop : -2.61 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 205 TYR 0.015 0.001 TYR R 301 PHE 0.023 0.001 PHE R 287 TRP 0.014 0.001 TRP B 82 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8501) covalent geometry : angle 0.61365 (11502) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.33294 ( 6) hydrogen bonds : bond 0.03099 ( 327) hydrogen bonds : angle 4.34541 ( 936) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9076 (tt0) cc_final: 0.8821 (tt0) REVERT: A 24 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7613 (pp20) REVERT: A 25 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8640 (mtmm) REVERT: A 202 ASP cc_start: 0.8773 (t0) cc_final: 0.8475 (t0) REVERT: A 212 GLU cc_start: 0.9066 (tt0) cc_final: 0.8777 (tm-30) REVERT: A 240 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8360 (tp-100) REVERT: A 268 ASP cc_start: 0.7014 (m-30) cc_final: 0.6604 (p0) REVERT: A 302 GLN cc_start: 0.9331 (mm-40) cc_final: 0.8905 (mm110) REVERT: A 326 GLN cc_start: 0.8692 (mm110) cc_final: 0.8227 (mm110) REVERT: A 337 ASP cc_start: 0.9229 (t0) cc_final: 0.8898 (t0) REVERT: B 17 GLN cc_start: 0.7666 (mt0) cc_final: 0.7440 (tm-30) REVERT: B 19 ARG cc_start: 0.7733 (tmt-80) cc_final: 0.6974 (ttm-80) REVERT: B 58 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8579 (pt) REVERT: B 220 GLN cc_start: 0.8548 (mt0) cc_final: 0.8169 (tt0) REVERT: B 235 PHE cc_start: 0.9046 (t80) cc_final: 0.8798 (t80) REVERT: B 264 TYR cc_start: 0.8732 (m-10) cc_final: 0.8469 (m-10) REVERT: B 289 TYR cc_start: 0.7893 (m-10) cc_final: 0.7181 (m-10) REVERT: B 293 ASN cc_start: 0.8045 (t0) cc_final: 0.7527 (t0) REVERT: B 308 LEU cc_start: 0.9288 (mm) cc_final: 0.8970 (mp) REVERT: B 333 ASP cc_start: 0.8582 (p0) cc_final: 0.8259 (p0) REVERT: B 339 TRP cc_start: 0.8899 (m100) cc_final: 0.8636 (m100) REVERT: N 6 GLU cc_start: 0.7686 (mp0) cc_final: 0.6965 (mp0) REVERT: N 22 CYS cc_start: 0.7981 (t) cc_final: 0.7622 (t) REVERT: N 76 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8250 (mptt) REVERT: N 77 ASN cc_start: 0.8281 (t0) cc_final: 0.7719 (t0) REVERT: R 60 TYR cc_start: 0.8669 (t80) cc_final: 0.8413 (t80) REVERT: R 78 ASN cc_start: 0.9142 (t0) cc_final: 0.8841 (t0) REVERT: R 147 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8374 (tpp80) REVERT: R 155 MET cc_start: 0.8794 (ttt) cc_final: 0.8542 (ttm) REVERT: R 183 MET cc_start: 0.8878 (mmm) cc_final: 0.8490 (tpp) REVERT: R 308 MET cc_start: 0.8841 (mmm) cc_final: 0.8358 (mmm) REVERT: R 310 ASN cc_start: 0.9266 (t0) cc_final: 0.8545 (t0) REVERT: R 317 MET cc_start: 0.8825 (mtp) cc_final: 0.8521 (mtp) outliers start: 37 outliers final: 24 residues processed: 234 average time/residue: 0.0836 time to fit residues: 27.3337 Evaluate side-chains 213 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.112312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095990 restraints weight = 16849.379| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.39 r_work: 0.3286 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8505 Z= 0.137 Angle : 0.619 8.674 11508 Z= 0.316 Chirality : 0.043 0.162 1276 Planarity : 0.004 0.047 1468 Dihedral : 4.908 55.171 1145 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.54 % Allowed : 22.15 % Favored : 74.31 % 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: -1.69 (0.26), residues: 1042 helix: 0.65 (0.28), residues: 375 sheet: -1.54 (0.35), residues: 202 loop : -2.46 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.015 0.001 TYR R 301 PHE 0.026 0.001 PHE R 293 TRP 0.014 0.001 TRP B 82 HIS 0.010 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8501) covalent geometry : angle 0.61842 (11502) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.09652 ( 6) hydrogen bonds : bond 0.03080 ( 327) hydrogen bonds : angle 4.31782 ( 936) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9099 (tt0) cc_final: 0.8869 (tt0) REVERT: A 24 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7556 (pp20) REVERT: A 25 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8662 (mtmm) REVERT: A 202 ASP cc_start: 0.8821 (t0) cc_final: 0.8483 (t0) REVERT: A 212 GLU cc_start: 0.9065 (tt0) cc_final: 0.8767 (tm-30) REVERT: A 240 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8359 (tp-100) REVERT: A 268 ASP cc_start: 0.7085 (m-30) cc_final: 0.6714 (p0) REVERT: A 302 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8889 (mm110) REVERT: A 326 GLN cc_start: 0.8731 (mm110) cc_final: 0.8280 (mm110) REVERT: A 337 ASP cc_start: 0.9265 (t0) cc_final: 0.8919 (t0) REVERT: B 17 GLN cc_start: 0.7699 (mt0) cc_final: 0.7468 (tm-30) REVERT: B 57 LYS cc_start: 0.8941 (ptpp) cc_final: 0.8513 (ptmm) REVERT: B 89 LYS cc_start: 0.8615 (mttp) cc_final: 0.8306 (mptt) REVERT: B 186 ASP cc_start: 0.8560 (p0) cc_final: 0.8148 (p0) REVERT: B 215 GLU cc_start: 0.7397 (pt0) cc_final: 0.7186 (tm-30) REVERT: B 220 GLN cc_start: 0.8586 (mt0) cc_final: 0.8173 (tt0) REVERT: B 228 ASP cc_start: 0.8877 (m-30) cc_final: 0.8380 (m-30) REVERT: B 235 PHE cc_start: 0.9027 (t80) cc_final: 0.8764 (t80) REVERT: B 264 TYR cc_start: 0.8790 (m-10) cc_final: 0.8532 (m-10) REVERT: B 289 TYR cc_start: 0.7899 (m-10) cc_final: 0.7187 (m-10) REVERT: B 293 ASN cc_start: 0.8014 (t0) cc_final: 0.7491 (t0) REVERT: B 308 LEU cc_start: 0.9264 (mm) cc_final: 0.8963 (mp) REVERT: B 339 TRP cc_start: 0.8913 (m100) cc_final: 0.8653 (m100) REVERT: N 76 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8250 (mptt) REVERT: N 77 ASN cc_start: 0.8399 (t0) cc_final: 0.7812 (t0) REVERT: N 123 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8538 (tp40) REVERT: R 60 TYR cc_start: 0.8648 (t80) cc_final: 0.8410 (t80) REVERT: R 69 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8447 (mtm-85) REVERT: R 78 ASN cc_start: 0.9168 (t0) cc_final: 0.8862 (t0) REVERT: R 147 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8333 (tpp80) REVERT: R 155 MET cc_start: 0.8801 (ttt) cc_final: 0.8500 (ttm) REVERT: R 183 MET cc_start: 0.8883 (mmm) cc_final: 0.8483 (tpp) REVERT: R 308 MET cc_start: 0.8905 (mmm) cc_final: 0.8419 (mmm) REVERT: R 310 ASN cc_start: 0.9281 (t0) cc_final: 0.8504 (t0) REVERT: R 317 MET cc_start: 0.8858 (mtp) cc_final: 0.8545 (mtp) outliers start: 32 outliers final: 23 residues processed: 217 average time/residue: 0.0862 time to fit residues: 26.0999 Evaluate side-chains 212 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 1 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.113947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.097405 restraints weight = 17159.383| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.46 r_work: 0.3299 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8505 Z= 0.121 Angle : 0.627 10.473 11508 Z= 0.316 Chirality : 0.042 0.164 1276 Planarity : 0.004 0.047 1468 Dihedral : 4.746 56.344 1145 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.99 % Allowed : 23.03 % Favored : 73.98 % 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: -1.46 (0.26), residues: 1042 helix: 0.77 (0.28), residues: 378 sheet: -1.31 (0.36), residues: 201 loop : -2.32 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.021 0.001 TYR A 283 PHE 0.028 0.001 PHE R 287 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8501) covalent geometry : angle 0.62522 (11502) SS BOND : bond 0.00298 ( 3) SS BOND : angle 2.03767 ( 6) hydrogen bonds : bond 0.03023 ( 327) hydrogen bonds : angle 4.21586 ( 936) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9102 (tt0) cc_final: 0.8874 (tt0) REVERT: A 24 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7542 (pp20) REVERT: A 25 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8634 (mtmm) REVERT: A 202 ASP cc_start: 0.8859 (t0) cc_final: 0.8537 (t0) REVERT: A 212 GLU cc_start: 0.9046 (tt0) cc_final: 0.8713 (tm-30) REVERT: A 240 GLN cc_start: 0.8955 (tp-100) cc_final: 0.8304 (tp-100) REVERT: A 268 ASP cc_start: 0.7073 (m-30) cc_final: 0.6729 (p0) REVERT: A 298 TYR cc_start: 0.8821 (t80) cc_final: 0.8283 (t80) REVERT: A 326 GLN cc_start: 0.8753 (mm110) cc_final: 0.8303 (mm110) REVERT: A 337 ASP cc_start: 0.9300 (t0) cc_final: 0.8984 (t0) REVERT: B 19 ARG cc_start: 0.7731 (tmt-80) cc_final: 0.7061 (ttm-80) REVERT: B 58 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8621 (pt) REVERT: B 89 LYS cc_start: 0.8526 (mttp) cc_final: 0.8278 (mptt) REVERT: B 215 GLU cc_start: 0.7459 (pt0) cc_final: 0.7200 (tm-30) REVERT: B 220 GLN cc_start: 0.8547 (mt0) cc_final: 0.8105 (tt0) REVERT: B 228 ASP cc_start: 0.8891 (m-30) cc_final: 0.8351 (m-30) REVERT: B 235 PHE cc_start: 0.9012 (t80) cc_final: 0.8805 (t80) REVERT: B 262 MET cc_start: 0.8869 (mmm) cc_final: 0.8658 (mmm) REVERT: B 289 TYR cc_start: 0.7807 (m-10) cc_final: 0.7120 (m-10) REVERT: B 293 ASN cc_start: 0.7992 (t0) cc_final: 0.7452 (t0) REVERT: B 308 LEU cc_start: 0.9262 (mm) cc_final: 0.8962 (mp) REVERT: B 333 ASP cc_start: 0.8553 (p0) cc_final: 0.8269 (p0) REVERT: B 339 TRP cc_start: 0.8938 (m100) cc_final: 0.8675 (m100) REVERT: N 6 GLU cc_start: 0.7756 (mp0) cc_final: 0.6947 (mp0) REVERT: N 27 PHE cc_start: 0.8965 (p90) cc_final: 0.8591 (p90) REVERT: N 73 ASP cc_start: 0.6747 (t0) cc_final: 0.6311 (t0) REVERT: N 76 LYS cc_start: 0.8837 (mmmt) cc_final: 0.7976 (mppt) REVERT: N 77 ASN cc_start: 0.8412 (t0) cc_final: 0.7865 (t0) REVERT: N 123 GLN cc_start: 0.9063 (tp-100) cc_final: 0.8728 (tp40) REVERT: R 30 TYR cc_start: 0.7997 (p90) cc_final: 0.7662 (p90) REVERT: R 60 TYR cc_start: 0.8633 (t80) cc_final: 0.8415 (t80) REVERT: R 69 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8637 (mtm-85) REVERT: R 78 ASN cc_start: 0.9136 (t0) cc_final: 0.8877 (t0) REVERT: R 147 ARG cc_start: 0.8882 (mmm-85) cc_final: 0.8243 (tpp80) REVERT: R 155 MET cc_start: 0.8780 (ttt) cc_final: 0.8447 (ttm) REVERT: R 183 MET cc_start: 0.8884 (mmm) cc_final: 0.8451 (tpp) REVERT: R 310 ASN cc_start: 0.9275 (t0) cc_final: 0.8494 (t0) REVERT: R 317 MET cc_start: 0.8865 (mtp) cc_final: 0.8658 (ttp) outliers start: 27 outliers final: 19 residues processed: 231 average time/residue: 0.0812 time to fit residues: 26.3581 Evaluate side-chains 220 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097652 restraints weight = 17043.329| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.43 r_work: 0.3308 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8505 Z= 0.129 Angle : 0.653 9.470 11508 Z= 0.330 Chirality : 0.043 0.164 1276 Planarity : 0.004 0.046 1468 Dihedral : 4.726 55.602 1145 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.33 % Allowed : 24.81 % Favored : 72.87 % 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: -1.32 (0.27), residues: 1042 helix: 0.89 (0.28), residues: 374 sheet: -1.09 (0.37), residues: 197 loop : -2.30 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.032 0.002 TYR A 283 PHE 0.028 0.001 PHE R 287 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8501) covalent geometry : angle 0.65230 (11502) SS BOND : bond 0.00331 ( 3) SS BOND : angle 1.51958 ( 6) hydrogen bonds : bond 0.03084 ( 327) hydrogen bonds : angle 4.24897 ( 936) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9108 (tt0) cc_final: 0.8861 (tt0) REVERT: A 24 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7565 (pp20) REVERT: A 25 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8657 (mtmm) REVERT: A 202 ASP cc_start: 0.8867 (t0) cc_final: 0.8530 (t0) REVERT: A 212 GLU cc_start: 0.9055 (tt0) cc_final: 0.8713 (tm-30) REVERT: A 240 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8300 (tp-100) REVERT: A 252 ASN cc_start: 0.8587 (p0) cc_final: 0.8383 (p0) REVERT: A 268 ASP cc_start: 0.7061 (m-30) cc_final: 0.6730 (p0) REVERT: A 298 TYR cc_start: 0.8825 (t80) cc_final: 0.8289 (t80) REVERT: A 326 GLN cc_start: 0.8806 (mm110) cc_final: 0.8357 (mm110) REVERT: A 337 ASP cc_start: 0.9261 (t0) cc_final: 0.8938 (t0) REVERT: B 58 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8627 (pt) REVERT: B 215 GLU cc_start: 0.7414 (pt0) cc_final: 0.7184 (tm-30) REVERT: B 220 GLN cc_start: 0.8541 (mt0) cc_final: 0.8101 (tt0) REVERT: B 228 ASP cc_start: 0.8861 (m-30) cc_final: 0.8346 (m-30) REVERT: B 289 TYR cc_start: 0.7794 (m-10) cc_final: 0.7214 (m-10) REVERT: B 293 ASN cc_start: 0.8003 (t0) cc_final: 0.7468 (t0) REVERT: B 308 LEU cc_start: 0.9254 (mm) cc_final: 0.8985 (mp) REVERT: B 333 ASP cc_start: 0.8505 (p0) cc_final: 0.8246 (p0) REVERT: B 339 TRP cc_start: 0.8935 (m100) cc_final: 0.8675 (m100) REVERT: N 27 PHE cc_start: 0.8983 (p90) cc_final: 0.8632 (p90) REVERT: N 73 ASP cc_start: 0.6779 (t0) cc_final: 0.6337 (t0) REVERT: N 76 LYS cc_start: 0.8832 (mmmt) cc_final: 0.7981 (mppt) REVERT: N 77 ASN cc_start: 0.8428 (t0) cc_final: 0.7864 (t0) REVERT: N 123 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8722 (tp40) REVERT: R 60 TYR cc_start: 0.8559 (t80) cc_final: 0.8245 (t80) REVERT: R 64 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: R 69 ARG cc_start: 0.8876 (mtm-85) cc_final: 0.8576 (mtm-85) REVERT: R 78 ASN cc_start: 0.9136 (t0) cc_final: 0.8885 (t0) REVERT: R 147 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8204 (tpp80) REVERT: R 155 MET cc_start: 0.8779 (ttt) cc_final: 0.8455 (ttm) REVERT: R 183 MET cc_start: 0.8877 (mmm) cc_final: 0.8468 (tpp) REVERT: R 253 MET cc_start: 0.9260 (mmm) cc_final: 0.9024 (mmm) REVERT: R 257 MET cc_start: 0.7903 (mtm) cc_final: 0.7013 (mtp) REVERT: R 310 ASN cc_start: 0.9162 (t0) cc_final: 0.8419 (t0) outliers start: 21 outliers final: 17 residues processed: 219 average time/residue: 0.0815 time to fit residues: 25.0603 Evaluate side-chains 214 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 9 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 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 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.114547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098158 restraints weight = 17080.958| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.42 r_work: 0.3313 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8505 Z= 0.131 Angle : 0.673 10.541 11508 Z= 0.341 Chirality : 0.043 0.163 1276 Planarity : 0.004 0.046 1468 Dihedral : 4.805 53.851 1145 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.55 % Allowed : 25.03 % Favored : 72.43 % 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 are not related in a simple way. whole: -1.32 (0.27), residues: 1042 helix: 0.84 (0.28), residues: 373 sheet: -1.10 (0.37), residues: 199 loop : -2.25 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.027 0.002 TYR A 283 PHE 0.031 0.001 PHE R 287 TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8501) covalent geometry : angle 0.67272 (11502) SS BOND : bond 0.00337 ( 3) SS BOND : angle 1.36249 ( 6) hydrogen bonds : bond 0.03064 ( 327) hydrogen bonds : angle 4.28463 ( 936) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9089 (tt0) cc_final: 0.8847 (tt0) REVERT: A 202 ASP cc_start: 0.8849 (t0) cc_final: 0.8515 (t0) REVERT: A 212 GLU cc_start: 0.9060 (tt0) cc_final: 0.8713 (tm-30) REVERT: A 240 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8297 (tp-100) REVERT: A 268 ASP cc_start: 0.7084 (m-30) cc_final: 0.6592 (p0) REVERT: A 298 TYR cc_start: 0.8849 (t80) cc_final: 0.8328 (t80) REVERT: A 307 ASN cc_start: 0.8460 (t0) cc_final: 0.8251 (t0) REVERT: A 319 MET cc_start: 0.8103 (mmm) cc_final: 0.7896 (tpp) REVERT: A 326 GLN cc_start: 0.8829 (mm110) cc_final: 0.8400 (mm110) REVERT: A 337 ASP cc_start: 0.9245 (t0) cc_final: 0.8928 (t0) REVERT: B 58 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8623 (pt) REVERT: B 186 ASP cc_start: 0.8521 (p0) cc_final: 0.8104 (p0) REVERT: B 215 GLU cc_start: 0.7354 (pt0) cc_final: 0.7137 (tm-30) REVERT: B 220 GLN cc_start: 0.8517 (mt0) cc_final: 0.8080 (tt0) REVERT: B 228 ASP cc_start: 0.8834 (m-30) cc_final: 0.8316 (m-30) REVERT: B 289 TYR cc_start: 0.7955 (m-10) cc_final: 0.7298 (m-10) REVERT: B 293 ASN cc_start: 0.7993 (t0) cc_final: 0.7350 (t0) REVERT: B 308 LEU cc_start: 0.9240 (mm) cc_final: 0.8985 (mp) REVERT: B 333 ASP cc_start: 0.8498 (p0) cc_final: 0.8238 (p0) REVERT: B 339 TRP cc_start: 0.8903 (m100) cc_final: 0.8648 (m100) REVERT: N 27 PHE cc_start: 0.9007 (p90) cc_final: 0.8734 (p90) REVERT: N 73 ASP cc_start: 0.6664 (t0) cc_final: 0.6223 (t0) REVERT: N 76 LYS cc_start: 0.8801 (mmmt) cc_final: 0.7971 (mppt) REVERT: N 77 ASN cc_start: 0.8411 (t0) cc_final: 0.7902 (t0) REVERT: R 60 TYR cc_start: 0.8494 (t80) cc_final: 0.8204 (t80) REVERT: R 64 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: R 78 ASN cc_start: 0.9086 (t0) cc_final: 0.8825 (t0) REVERT: R 147 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8176 (tpp80) REVERT: R 155 MET cc_start: 0.8781 (ttt) cc_final: 0.8442 (ttm) REVERT: R 183 MET cc_start: 0.8872 (mmm) cc_final: 0.8482 (tpp) REVERT: R 236 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8420 (mm110) REVERT: R 310 ASN cc_start: 0.9159 (t0) cc_final: 0.7763 (t0) outliers start: 23 outliers final: 16 residues processed: 224 average time/residue: 0.0854 time to fit residues: 26.4917 Evaluate side-chains 209 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 45 optimal weight: 0.0370 chunk 75 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.110820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.093925 restraints weight = 17171.468| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.53 r_work: 0.3261 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8505 Z= 0.186 Angle : 0.728 10.561 11508 Z= 0.367 Chirality : 0.044 0.165 1276 Planarity : 0.004 0.045 1468 Dihedral : 4.984 48.715 1145 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.55 % Allowed : 24.81 % Favored : 72.65 % 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: -1.36 (0.27), residues: 1042 helix: 0.80 (0.28), residues: 376 sheet: -1.16 (0.37), residues: 198 loop : -2.25 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.026 0.002 TYR A 283 PHE 0.034 0.002 PHE B 235 TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS R 278 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8501) covalent geometry : angle 0.72690 (11502) SS BOND : bond 0.00451 ( 3) SS BOND : angle 1.52317 ( 6) hydrogen bonds : bond 0.03254 ( 327) hydrogen bonds : angle 4.41889 ( 936) Misc. bond : bond 0.00028 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9124 (tt0) cc_final: 0.8899 (tt0) REVERT: A 24 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7543 (pp20) REVERT: A 193 ARG cc_start: 0.8632 (mtp-110) cc_final: 0.8381 (mtp-110) REVERT: A 202 ASP cc_start: 0.8859 (t0) cc_final: 0.8486 (t0) REVERT: A 212 GLU cc_start: 0.9129 (tt0) cc_final: 0.8699 (tm-30) REVERT: A 240 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8298 (tp-100) REVERT: A 268 ASP cc_start: 0.7153 (m-30) cc_final: 0.6573 (p0) REVERT: A 298 TYR cc_start: 0.8918 (t80) cc_final: 0.8612 (t80) REVERT: A 307 ASN cc_start: 0.8537 (t0) cc_final: 0.8292 (t0) REVERT: A 326 GLN cc_start: 0.8891 (mm110) cc_final: 0.8477 (mm110) REVERT: A 337 ASP cc_start: 0.9285 (t0) cc_final: 0.8970 (t0) REVERT: B 58 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8644 (pt) REVERT: B 89 LYS cc_start: 0.8556 (mttp) cc_final: 0.8320 (mptt) REVERT: B 228 ASP cc_start: 0.8876 (m-30) cc_final: 0.8309 (m-30) REVERT: B 262 MET cc_start: 0.8849 (mmm) cc_final: 0.8545 (mmm) REVERT: B 289 TYR cc_start: 0.7949 (m-10) cc_final: 0.7249 (m-10) REVERT: B 293 ASN cc_start: 0.8119 (t0) cc_final: 0.7496 (t0) REVERT: B 308 LEU cc_start: 0.9253 (mm) cc_final: 0.9040 (mp) REVERT: B 333 ASP cc_start: 0.8547 (p0) cc_final: 0.8280 (p0) REVERT: B 339 TRP cc_start: 0.8914 (m100) cc_final: 0.8677 (m100) REVERT: G 46 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8118 (tp30) REVERT: N 73 ASP cc_start: 0.6705 (t0) cc_final: 0.6242 (t0) REVERT: N 76 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8024 (mppt) REVERT: N 77 ASN cc_start: 0.8432 (t0) cc_final: 0.7941 (t0) REVERT: N 123 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8516 (tp-100) REVERT: R 60 TYR cc_start: 0.8505 (t80) cc_final: 0.8204 (t80) REVERT: R 64 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7619 (mt0) REVERT: R 69 ARG cc_start: 0.8816 (mtm-85) cc_final: 0.8519 (mtm-85) REVERT: R 78 ASN cc_start: 0.9173 (t0) cc_final: 0.8904 (t0) REVERT: R 147 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8252 (tpp80) REVERT: R 155 MET cc_start: 0.8815 (ttt) cc_final: 0.8489 (ttm) REVERT: R 183 MET cc_start: 0.8903 (mmm) cc_final: 0.8582 (tpp) REVERT: R 310 ASN cc_start: 0.9054 (t0) cc_final: 0.8217 (t0) outliers start: 23 outliers final: 20 residues processed: 208 average time/residue: 0.0860 time to fit residues: 24.9950 Evaluate side-chains 210 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098219 restraints weight = 16987.004| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 3.42 r_work: 0.3318 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8505 Z= 0.130 Angle : 0.699 10.328 11508 Z= 0.351 Chirality : 0.043 0.164 1276 Planarity : 0.004 0.041 1468 Dihedral : 4.949 55.807 1145 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.99 % Allowed : 25.47 % Favored : 72.54 % 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: -1.31 (0.27), residues: 1042 helix: 0.81 (0.28), residues: 374 sheet: -1.06 (0.37), residues: 199 loop : -2.22 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 205 TYR 0.024 0.002 TYR A 283 PHE 0.028 0.001 PHE R 287 TRP 0.026 0.001 TRP N 47 HIS 0.008 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8501) covalent geometry : angle 0.69868 (11502) SS BOND : bond 0.00496 ( 3) SS BOND : angle 1.01949 ( 6) hydrogen bonds : bond 0.03088 ( 327) hydrogen bonds : angle 4.33393 ( 936) Misc. bond : bond 0.00009 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1708.76 seconds wall clock time: 30 minutes 6.80 seconds (1806.80 seconds total)