Starting phenix.real_space_refine on Wed Sep 17 14:38:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y36_33590/09_2025/7y36_33590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y36_33590/09_2025/7y36_33590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y36_33590/09_2025/7y36_33590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y36_33590/09_2025/7y36_33590.map" model { file = "/net/cci-nas-00/data/ceres_data/7y36_33590/09_2025/7y36_33590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y36_33590/09_2025/7y36_33590.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 58 5.16 5 C 5851 2.51 5 N 1616 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9206 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3053 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 3 Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 1858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1858 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' OH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.73, per 1000 atoms: 0.19 Number of scatterers: 9206 At special positions: 0 Unit cell: (124.722, 97.344, 152.1, 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 58 16.00 O 1681 8.00 N 1616 7.00 C 5851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 346.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 43.3% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'R' and resid 33 through 57 removed outlier: 3.522A pdb=" N ARG R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 172 Processing helix chain 'R' and resid 179 through 212 removed outlier: 4.348A pdb=" N VAL R 183 " --> pdb=" O ARG R 179 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE R 184 " --> pdb=" O GLU R 180 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP R 185 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 216 Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 312 removed outlier: 3.681A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 4.067A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix removed outlier: 3.566A pdb=" N THR R 345 " --> pdb=" O SER R 341 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 420 through 424 removed outlier: 3.633A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 461 removed outlier: 3.605A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 480 Processing helix chain 'P' and resid 2 through 34 Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.925A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.864A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.556A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.615A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.002A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.797A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.787A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.527A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.093A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 126 through 130 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.690A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.641A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.692A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.812A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.502A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.786A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.591A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.618A 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 278 removed outlier: 3.545A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.522A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.170A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1359 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: 1.48 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1503 1.31 - 1.44: 2663 1.44 - 1.56: 5159 1.56 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 9407 Sorted by residual: bond pdb=" C GLN A 227 " pdb=" N ARG A 228 " ideal model delta sigma weight residual 1.330 1.403 -0.072 1.30e-02 5.92e+03 3.08e+01 bond pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.98e+01 bond pdb=" CA THR R 178 " pdb=" C THR R 178 " ideal model delta sigma weight residual 1.523 1.470 0.053 1.34e-02 5.57e+03 1.59e+01 bond pdb=" N LEU R 174 " pdb=" CA LEU R 174 " ideal model delta sigma weight residual 1.459 1.410 0.049 1.23e-02 6.61e+03 1.58e+01 bond pdb=" C CYS R 170 " pdb=" O CYS R 170 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.22e-02 6.72e+03 1.42e+01 ... (remaining 9402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12457 2.04 - 4.08: 233 4.08 - 6.12: 28 6.12 - 8.17: 10 8.17 - 10.21: 4 Bond angle restraints: 12732 Sorted by residual: angle pdb=" N GLU R 169 " pdb=" CA GLU R 169 " pdb=" C GLU R 169 " ideal model delta sigma weight residual 111.71 102.90 8.81 1.15e+00 7.56e-01 5.87e+01 angle pdb=" C GLN A 227 " pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 121.06 131.27 -10.21 1.88e+00 2.83e-01 2.95e+01 angle pdb=" C LEU P 24 " pdb=" N ARG P 25 " pdb=" CA ARG P 25 " ideal model delta sigma weight residual 120.44 113.12 7.32 1.36e+00 5.41e-01 2.90e+01 angle pdb=" N LEU R 174 " pdb=" CA LEU R 174 " pdb=" C LEU R 174 " ideal model delta sigma weight residual 111.33 117.63 -6.30 1.21e+00 6.83e-01 2.71e+01 angle pdb=" N LYS R 172 " pdb=" CA LYS R 172 " pdb=" C LYS R 172 " ideal model delta sigma weight residual 112.38 118.55 -6.17 1.22e+00 6.72e-01 2.56e+01 ... (remaining 12727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5106 17.75 - 35.51: 391 35.51 - 53.26: 69 53.26 - 71.01: 8 71.01 - 88.77: 5 Dihedral angle restraints: 5579 sinusoidal: 2231 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual -86.00 -19.11 -66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CA CYS R 351 " pdb=" C CYS R 351 " pdb=" N TRP R 352 " pdb=" CA TRP R 352 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA PHE A 238 " pdb=" C PHE A 238 " pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta harmonic sigma weight residual 180.00 152.00 28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5576 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1097 0.056 - 0.111: 260 0.111 - 0.167: 40 0.167 - 0.223: 6 0.223 - 0.278: 2 Chirality restraints: 1405 Sorted by residual: chirality pdb=" CA LEU R 174 " pdb=" N LEU R 174 " pdb=" C LEU R 174 " pdb=" CB LEU R 174 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR R 178 " pdb=" N THR R 178 " pdb=" C THR R 178 " pdb=" CB THR R 178 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TYR R 191 " pdb=" N TYR R 191 " pdb=" C TYR R 191 " pdb=" CB TYR R 191 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1402 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER R 168 " 0.035 2.00e-02 2.50e+03 7.17e-02 5.15e+01 pdb=" C SER R 168 " -0.124 2.00e-02 2.50e+03 pdb=" O SER R 168 " 0.048 2.00e-02 2.50e+03 pdb=" N GLU R 169 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO B 236 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.016 2.00e-02 2.50e+03 1.54e-02 4.73e+00 pdb=" CG TYR B 59 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 260 2.70 - 3.25: 8791 3.25 - 3.80: 14683 3.80 - 4.35: 19212 4.35 - 4.90: 32425 Nonbonded interactions: 75371 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.152 3.040 nonbonded pdb=" O ASP R 113 " pdb=" CG1 VAL P 31 " model vdw 2.178 3.460 nonbonded pdb=" OG1 THR R 218 " pdb=" OE2 GLU R 317 " model vdw 2.183 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.207 3.040 nonbonded pdb=" CG2 ILE R 115 " pdb=" NZ LYS P 27 " model vdw 2.229 3.540 ... (remaining 75366 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5207 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 : 0.007 0.171 9414 Z= 0.377 Angle : 0.746 13.025 12744 Z= 0.450 Chirality : 0.049 0.278 1405 Planarity : 0.005 0.072 1621 Dihedral : 12.892 88.766 3395 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.22), residues: 1127 helix: -0.23 (0.22), residues: 449 sheet: -0.68 (0.31), residues: 227 loop : -1.41 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 72 TYR 0.038 0.002 TYR B 59 PHE 0.021 0.002 PHE R 335 TRP 0.024 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00656 ( 9407) covalent geometry : angle 0.73202 (12732) SS BOND : bond 0.00985 ( 6) SS BOND : angle 4.71062 ( 12) hydrogen bonds : bond 0.16462 ( 472) hydrogen bonds : angle 6.24254 ( 1359) Misc. bond : bond 0.17053 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 310 average time/residue: 0.4990 time to fit residues: 165.1035 Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 458 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 463 ASN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 41 HIS B 62 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 176 GLN B 266 HIS B 313 ASN N 77 ASN N 82 GLN N 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.183647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.153266 restraints weight = 15786.491| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.88 r_work: 0.3852 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 9414 Z= 0.220 Angle : 0.744 12.332 12744 Z= 0.392 Chirality : 0.046 0.165 1405 Planarity : 0.005 0.083 1621 Dihedral : 4.896 26.745 1261 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.75 % Allowed : 16.16 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1127 helix: 0.93 (0.24), residues: 451 sheet: -0.15 (0.32), residues: 218 loop : -0.98 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 20 TYR 0.040 0.002 TYR R 191 PHE 0.036 0.002 PHE R 335 TRP 0.019 0.002 TRP B 82 HIS 0.009 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 9407) covalent geometry : angle 0.74213 (12732) SS BOND : bond 0.01622 ( 6) SS BOND : angle 2.06032 ( 12) hydrogen bonds : bond 0.04949 ( 472) hydrogen bonds : angle 4.75226 ( 1359) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7916 (ttp) cc_final: 0.7573 (tpp) REVERT: R 214 ARG cc_start: 0.8210 (mtp85) cc_final: 0.7811 (mtp85) REVERT: R 281 CYS cc_start: 0.5792 (OUTLIER) cc_final: 0.5286 (t) REVERT: R 322 TRP cc_start: 0.5922 (t60) cc_final: 0.5404 (t60) REVERT: R 441 MET cc_start: 0.7667 (mmm) cc_final: 0.7270 (mmm) REVERT: R 469 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8075 (mm-30) REVERT: P 8 MET cc_start: 0.6412 (ttp) cc_final: 0.5722 (tmm) REVERT: P 11 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5925 (tp) REVERT: A 265 ARG cc_start: 0.6085 (pmt170) cc_final: 0.5863 (ptt-90) REVERT: A 343 ASP cc_start: 0.8537 (m-30) cc_final: 0.8002 (m-30) REVERT: A 347 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7485 (ptp-110) REVERT: A 363 PHE cc_start: 0.8549 (m-80) cc_final: 0.8261 (m-80) REVERT: A 381 ASP cc_start: 0.8587 (t70) cc_final: 0.8285 (t0) REVERT: B 19 ARG cc_start: 0.7752 (ttp-110) cc_final: 0.7226 (ptp-110) REVERT: B 81 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5877 (pt) REVERT: B 123 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7407 (pp) REVERT: B 187 VAL cc_start: 0.6277 (OUTLIER) cc_final: 0.5719 (p) REVERT: B 188 MET cc_start: 0.8190 (mmm) cc_final: 0.7981 (mmm) REVERT: B 290 ASP cc_start: 0.7203 (m-30) cc_final: 0.6816 (m-30) REVERT: N 60 TYR cc_start: 0.8298 (m-80) cc_final: 0.7995 (m-80) REVERT: N 76 LYS cc_start: 0.8384 (tptp) cc_final: 0.8159 (tppp) REVERT: N 87 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7792 (ptpp) REVERT: N 120 GLN cc_start: 0.7396 (mm110) cc_final: 0.7083 (mm-40) outliers start: 47 outliers final: 12 residues processed: 289 average time/residue: 0.4572 time to fit residues: 141.9990 Evaluate side-chains 219 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.1980 chunk 108 optimal weight: 0.0070 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 266 HIS B 295 ASN N 123 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.160877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.125156 restraints weight = 14997.125| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 3.71 r_work: 0.3469 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9414 Z= 0.185 Angle : 0.703 10.520 12744 Z= 0.369 Chirality : 0.045 0.165 1405 Planarity : 0.005 0.062 1621 Dihedral : 4.797 37.374 1259 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.45 % Allowed : 19.90 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.25), residues: 1127 helix: 1.30 (0.24), residues: 456 sheet: -0.09 (0.33), residues: 223 loop : -0.79 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.030 0.002 TYR R 191 PHE 0.016 0.002 PHE R 335 TRP 0.022 0.002 TRP N 36 HIS 0.005 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9407) covalent geometry : angle 0.70094 (12732) SS BOND : bond 0.01796 ( 6) SS BOND : angle 1.71127 ( 12) hydrogen bonds : bond 0.04798 ( 472) hydrogen bonds : angle 4.57667 ( 1359) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.8407 (ttp) cc_final: 0.7773 (pmm) REVERT: R 214 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7887 (mtp85) REVERT: R 278 TYR cc_start: 0.5881 (p90) cc_final: 0.5430 (m-80) REVERT: R 322 TRP cc_start: 0.6009 (t60) cc_final: 0.5439 (t60) REVERT: R 358 ASN cc_start: 0.7823 (m-40) cc_final: 0.7529 (t0) REVERT: R 441 MET cc_start: 0.8544 (mmm) cc_final: 0.8289 (mmm) REVERT: R 469 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8262 (mm-30) REVERT: P 8 MET cc_start: 0.8077 (ttp) cc_final: 0.7768 (tmm) REVERT: A 248 VAL cc_start: 0.8901 (t) cc_final: 0.8574 (m) REVERT: A 265 ARG cc_start: 0.6768 (pmt170) cc_final: 0.6485 (ptt-90) REVERT: A 299 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8803 (pt0) REVERT: A 309 GLU cc_start: 0.8194 (pm20) cc_final: 0.7928 (mt-10) REVERT: A 368 ASP cc_start: 0.4760 (m-30) cc_final: 0.4473 (t0) REVERT: A 370 GLU cc_start: 0.7206 (mp0) cc_final: 0.6844 (mp0) REVERT: A 381 ASP cc_start: 0.8283 (t70) cc_final: 0.7914 (t0) REVERT: A 389 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8311 (ttm110) REVERT: B 19 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7345 (ptp-110) REVERT: B 45 MET cc_start: 0.9365 (mtt) cc_final: 0.9148 (mtt) REVERT: B 89 LYS cc_start: 0.7717 (ptpp) cc_final: 0.7494 (ptpp) REVERT: B 138 GLU cc_start: 0.8599 (mp0) cc_final: 0.8374 (mp0) REVERT: B 176 GLN cc_start: 0.7833 (tt0) cc_final: 0.7081 (tm130) REVERT: B 230 ASN cc_start: 0.8676 (t0) cc_final: 0.8346 (m-40) REVERT: B 292 PHE cc_start: 0.8874 (m-10) cc_final: 0.8288 (m-80) REVERT: B 312 ASP cc_start: 0.8076 (t0) cc_final: 0.7588 (t0) REVERT: G 57 SER cc_start: 0.8976 (t) cc_final: 0.8430 (p) REVERT: G 62 ARG cc_start: 0.7191 (tpt-90) cc_final: 0.6807 (tpp80) REVERT: N 60 TYR cc_start: 0.8715 (m-80) cc_final: 0.8093 (m-80) REVERT: N 83 MET cc_start: 0.6224 (mtp) cc_final: 0.5990 (mtt) REVERT: N 87 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7784 (ptpp) REVERT: N 89 GLU cc_start: 0.9098 (tp30) cc_final: 0.8762 (tp30) outliers start: 54 outliers final: 21 residues processed: 282 average time/residue: 0.5235 time to fit residues: 157.0877 Evaluate side-chains 221 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 431 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.0870 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 9 HIS P 10 ASN A 236 GLN B 6 GLN B 293 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.159881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123775 restraints weight = 15102.164| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.70 r_work: 0.3470 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.9148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9414 Z= 0.128 Angle : 0.624 10.134 12744 Z= 0.326 Chirality : 0.043 0.157 1405 Planarity : 0.004 0.030 1621 Dihedral : 4.361 28.791 1259 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.75 % Allowed : 24.75 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.25), residues: 1127 helix: 1.77 (0.25), residues: 453 sheet: 0.28 (0.33), residues: 226 loop : -0.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.025 0.001 TYR R 191 PHE 0.013 0.001 PHE R 335 TRP 0.016 0.001 TRP P 23 HIS 0.003 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9407) covalent geometry : angle 0.62258 (12732) SS BOND : bond 0.00404 ( 6) SS BOND : angle 1.51834 ( 12) hydrogen bonds : bond 0.04035 ( 472) hydrogen bonds : angle 4.23437 ( 1359) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 214 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7855 (mtp85) REVERT: R 322 TRP cc_start: 0.6215 (t60) cc_final: 0.5585 (t60) REVERT: R 349 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.8057 (p) REVERT: R 358 ASN cc_start: 0.7802 (m-40) cc_final: 0.7570 (t0) REVERT: R 469 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8492 (mm-30) REVERT: P 8 MET cc_start: 0.8188 (ttp) cc_final: 0.7820 (ttm) REVERT: A 35 GLN cc_start: 0.8266 (mt0) cc_final: 0.7788 (mp10) REVERT: A 265 ARG cc_start: 0.6796 (pmt170) cc_final: 0.6485 (ptt-90) REVERT: A 309 GLU cc_start: 0.8193 (pm20) cc_final: 0.7949 (mt-10) REVERT: A 368 ASP cc_start: 0.4720 (m-30) cc_final: 0.4331 (t0) REVERT: A 370 GLU cc_start: 0.7252 (mp0) cc_final: 0.6779 (mp0) REVERT: A 378 ASP cc_start: 0.8161 (m-30) cc_final: 0.7931 (m-30) REVERT: A 381 ASP cc_start: 0.8343 (t70) cc_final: 0.7985 (t0) REVERT: A 389 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8296 (ttm110) REVERT: B 19 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7173 (ptp-110) REVERT: B 57 LYS cc_start: 0.8569 (pttm) cc_final: 0.8217 (ptpp) REVERT: B 76 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8319 (p0) REVERT: B 123 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7926 (mm) REVERT: B 176 GLN cc_start: 0.8024 (tt0) cc_final: 0.7268 (tm130) REVERT: B 217 MET cc_start: 0.8658 (mmm) cc_final: 0.8353 (mmm) REVERT: B 229 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7784 (mt) REVERT: B 230 ASN cc_start: 0.8687 (t0) cc_final: 0.8310 (m-40) REVERT: B 292 PHE cc_start: 0.8859 (m-10) cc_final: 0.8335 (m-80) REVERT: B 312 ASP cc_start: 0.8128 (t0) cc_final: 0.7594 (t0) REVERT: G 62 ARG cc_start: 0.7051 (tpt-90) cc_final: 0.6714 (tpp80) REVERT: N 38 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7842 (ptt180) REVERT: N 60 TYR cc_start: 0.8698 (m-80) cc_final: 0.8078 (m-80) REVERT: N 73 ASP cc_start: 0.5640 (p0) cc_final: 0.5354 (p0) REVERT: N 76 LYS cc_start: 0.8894 (tppp) cc_final: 0.8476 (ttmt) REVERT: N 87 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7874 (ptpp) REVERT: N 89 GLU cc_start: 0.9091 (tp30) cc_final: 0.8722 (tp30) REVERT: N 109 ASP cc_start: 0.7346 (p0) cc_final: 0.6581 (p0) outliers start: 47 outliers final: 21 residues processed: 240 average time/residue: 0.5623 time to fit residues: 143.4454 Evaluate side-chains 211 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 389 LEU Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 33 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.145802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110143 restraints weight = 14827.832| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.49 r_work: 0.3291 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 1.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9414 Z= 0.174 Angle : 0.677 10.076 12744 Z= 0.355 Chirality : 0.045 0.204 1405 Planarity : 0.004 0.036 1621 Dihedral : 4.585 29.998 1259 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.77 % Allowed : 23.64 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1127 helix: 1.70 (0.24), residues: 453 sheet: 0.26 (0.33), residues: 227 loop : -0.52 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.028 0.002 TYR R 191 PHE 0.016 0.002 PHE G 61 TRP 0.023 0.002 TRP B 82 HIS 0.007 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 9407) covalent geometry : angle 0.67571 (12732) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.49683 ( 12) hydrogen bonds : bond 0.04835 ( 472) hydrogen bonds : angle 4.39979 ( 1359) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 THR cc_start: 0.8570 (m) cc_final: 0.8339 (p) REVERT: R 214 ARG cc_start: 0.8335 (mtp85) cc_final: 0.7870 (mtp85) REVERT: R 322 TRP cc_start: 0.6183 (t60) cc_final: 0.5544 (t60) REVERT: R 349 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8941 (p) REVERT: R 358 ASN cc_start: 0.8285 (m-40) cc_final: 0.7709 (t0) REVERT: R 469 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8573 (mm-30) REVERT: P 8 MET cc_start: 0.8590 (ttp) cc_final: 0.8269 (ttm) REVERT: A 31 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8722 (mm110) REVERT: A 35 GLN cc_start: 0.8451 (mt0) cc_final: 0.7876 (mp10) REVERT: A 213 GLN cc_start: 0.9099 (tt0) cc_final: 0.8817 (tm-30) REVERT: A 265 ARG cc_start: 0.6982 (pmt170) cc_final: 0.6711 (ptt-90) REVERT: A 297 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 299 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8870 (pm20) REVERT: A 300 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7398 (mtmt) REVERT: A 309 GLU cc_start: 0.8255 (pm20) cc_final: 0.7960 (mt-10) REVERT: A 381 ASP cc_start: 0.8303 (t70) cc_final: 0.7996 (t0) REVERT: A 389 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8269 (ttm110) REVERT: B 19 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7923 (ttm110) REVERT: B 37 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6651 (tt) REVERT: B 59 TYR cc_start: 0.8737 (OUTLIER) cc_final: 0.7721 (m-80) REVERT: B 76 ASP cc_start: 0.8663 (p0) cc_final: 0.8358 (p0) REVERT: B 156 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: B 189 SER cc_start: 0.8972 (t) cc_final: 0.8630 (t) REVERT: B 197 ARG cc_start: 0.8327 (mmm-85) cc_final: 0.7986 (mmm-85) REVERT: B 217 MET cc_start: 0.8667 (mmm) cc_final: 0.8231 (mpp) REVERT: B 219 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8280 (mmm-85) REVERT: B 229 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7912 (mt) REVERT: B 230 ASN cc_start: 0.8847 (t0) cc_final: 0.8466 (m-40) REVERT: B 292 PHE cc_start: 0.9081 (m-10) cc_final: 0.8716 (m-80) REVERT: B 304 ARG cc_start: 0.8580 (mtp180) cc_final: 0.8178 (ttm110) REVERT: B 312 ASP cc_start: 0.8377 (t0) cc_final: 0.8001 (t0) REVERT: G 58 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: G 62 ARG cc_start: 0.6990 (tpt-90) cc_final: 0.6768 (tpp80) REVERT: N 38 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8258 (ptm160) REVERT: N 89 GLU cc_start: 0.9080 (tp30) cc_final: 0.8711 (tp30) REVERT: N 109 ASP cc_start: 0.7599 (p0) cc_final: 0.7083 (p0) outliers start: 67 outliers final: 23 residues processed: 283 average time/residue: 0.5363 time to fit residues: 161.5188 Evaluate side-chains 231 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 99 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 348 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 176 GLN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101149 restraints weight = 15099.481| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.41 r_work: 0.3164 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 1.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9414 Z= 0.258 Angle : 0.749 13.135 12744 Z= 0.394 Chirality : 0.047 0.192 1405 Planarity : 0.005 0.054 1621 Dihedral : 4.899 27.165 1259 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.97 % Allowed : 25.56 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.25), residues: 1127 helix: 1.63 (0.24), residues: 450 sheet: 0.24 (0.33), residues: 224 loop : -0.71 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 27 TYR 0.026 0.002 TYR B 59 PHE 0.019 0.002 PHE B 234 TRP 0.023 0.002 TRP P 23 HIS 0.008 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00606 ( 9407) covalent geometry : angle 0.74755 (12732) SS BOND : bond 0.00450 ( 6) SS BOND : angle 1.71529 ( 12) hydrogen bonds : bond 0.05355 ( 472) hydrogen bonds : angle 4.54821 ( 1359) Misc. bond : bond 0.00102 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 234 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 THR cc_start: 0.8602 (m) cc_final: 0.8336 (p) REVERT: R 214 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7847 (mtp85) REVERT: R 349 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9063 (p) REVERT: R 431 GLU cc_start: 0.8226 (pp20) cc_final: 0.7904 (pp20) REVERT: R 469 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8547 (mm-30) REVERT: A 21 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7926 (pp20) REVERT: A 31 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8792 (mm-40) REVERT: A 35 GLN cc_start: 0.8538 (mt0) cc_final: 0.7972 (mp10) REVERT: A 213 GLN cc_start: 0.9024 (tt0) cc_final: 0.8704 (tm-30) REVERT: A 229 ASP cc_start: 0.7860 (p0) cc_final: 0.7483 (p0) REVERT: A 237 CYS cc_start: 0.8587 (t) cc_final: 0.8237 (t) REVERT: A 265 ARG cc_start: 0.7100 (pmt170) cc_final: 0.6760 (ptt-90) REVERT: A 267 GLN cc_start: 0.8733 (tp40) cc_final: 0.8491 (mm-40) REVERT: A 300 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7203 (mtmt) REVERT: A 309 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: A 381 ASP cc_start: 0.8340 (t70) cc_final: 0.8021 (t0) REVERT: A 389 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (ttm110) REVERT: B 59 TYR cc_start: 0.8732 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: B 76 ASP cc_start: 0.8655 (p0) cc_final: 0.8451 (p0) REVERT: B 135 VAL cc_start: 0.8992 (m) cc_final: 0.8759 (t) REVERT: B 156 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8020 (mm110) REVERT: B 197 ARG cc_start: 0.8472 (mmm-85) cc_final: 0.8229 (mmm-85) REVERT: B 219 ARG cc_start: 0.8804 (mmm-85) cc_final: 0.8273 (mmm-85) REVERT: B 229 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 230 ASN cc_start: 0.8896 (t0) cc_final: 0.8579 (m-40) REVERT: B 233 CYS cc_start: 0.9235 (t) cc_final: 0.8775 (t) REVERT: B 259 GLN cc_start: 0.7878 (mp10) cc_final: 0.7596 (mp10) REVERT: B 304 ARG cc_start: 0.8709 (mtp180) cc_final: 0.8305 (ttm-80) REVERT: B 312 ASP cc_start: 0.8546 (t0) cc_final: 0.8173 (t0) REVERT: G 13 ARG cc_start: 0.7759 (ptm-80) cc_final: 0.7528 (ptp-170) REVERT: G 36 ASP cc_start: 0.8650 (t0) cc_final: 0.8398 (m-30) REVERT: G 58 GLU cc_start: 0.8085 (mp0) cc_final: 0.7712 (mp0) REVERT: G 62 ARG cc_start: 0.7174 (tpt-90) cc_final: 0.6769 (tpp80) REVERT: N 4 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7272 (mt) REVERT: N 89 GLU cc_start: 0.9111 (tp30) cc_final: 0.8715 (pp20) REVERT: N 90 ASP cc_start: 0.8486 (m-30) cc_final: 0.7944 (m-30) outliers start: 69 outliers final: 34 residues processed: 279 average time/residue: 0.5798 time to fit residues: 171.6655 Evaluate side-chains 228 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 86 optimal weight: 0.0570 chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.106401 restraints weight = 14968.025| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 3.48 r_work: 0.3236 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 1.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9414 Z= 0.138 Angle : 0.698 10.914 12744 Z= 0.361 Chirality : 0.044 0.198 1405 Planarity : 0.004 0.052 1621 Dihedral : 4.561 25.317 1259 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.85 % Allowed : 29.39 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.26), residues: 1127 helix: 1.91 (0.25), residues: 451 sheet: 0.65 (0.35), residues: 223 loop : -0.57 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.025 0.001 TYR N 60 PHE 0.027 0.001 PHE R 335 TRP 0.024 0.001 TRP P 23 HIS 0.004 0.001 HIS R 420 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9407) covalent geometry : angle 0.69692 (12732) SS BOND : bond 0.00291 ( 6) SS BOND : angle 1.49862 ( 12) hydrogen bonds : bond 0.04301 ( 472) hydrogen bonds : angle 4.36668 ( 1359) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 THR cc_start: 0.8627 (m) cc_final: 0.8366 (p) REVERT: R 214 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8030 (mtp85) REVERT: R 349 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.9060 (p) REVERT: R 431 GLU cc_start: 0.7992 (pp20) cc_final: 0.7734 (pp20) REVERT: R 438 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: A 31 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8751 (mm-40) REVERT: A 35 GLN cc_start: 0.8492 (mt0) cc_final: 0.7927 (mp10) REVERT: A 213 GLN cc_start: 0.9089 (tt0) cc_final: 0.8837 (tm-30) REVERT: A 237 CYS cc_start: 0.8609 (t) cc_final: 0.8317 (t) REVERT: A 265 ARG cc_start: 0.7117 (pmt170) cc_final: 0.6879 (ptt180) REVERT: A 299 GLU cc_start: 0.8181 (pp20) cc_final: 0.7820 (pm20) REVERT: A 309 GLU cc_start: 0.8385 (pm20) cc_final: 0.8009 (mt-10) REVERT: A 381 ASP cc_start: 0.8388 (t70) cc_final: 0.8108 (t0) REVERT: A 389 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: B 44 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8215 (mt0) REVERT: B 59 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: B 156 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7730 (mm110) REVERT: B 197 ARG cc_start: 0.8385 (mmm-85) cc_final: 0.8116 (mmm-85) REVERT: B 215 GLU cc_start: 0.8394 (mp0) cc_final: 0.7514 (pm20) REVERT: B 217 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6159 (pmt) REVERT: B 219 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8177 (mmt90) REVERT: B 229 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 230 ASN cc_start: 0.8791 (t0) cc_final: 0.8539 (m110) REVERT: B 233 CYS cc_start: 0.9207 (t) cc_final: 0.8762 (t) REVERT: B 258 ASP cc_start: 0.7321 (t0) cc_final: 0.6660 (t0) REVERT: B 294 CYS cc_start: 0.8026 (m) cc_final: 0.7786 (t) REVERT: B 304 ARG cc_start: 0.8734 (mtp180) cc_final: 0.8277 (ttm-80) REVERT: B 312 ASP cc_start: 0.8535 (t0) cc_final: 0.8215 (t0) REVERT: B 314 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8085 (tmm-80) REVERT: G 58 GLU cc_start: 0.8101 (mp0) cc_final: 0.7755 (mm-30) REVERT: G 62 ARG cc_start: 0.7179 (tpt-90) cc_final: 0.6795 (tpp80) REVERT: N 30 SER cc_start: 0.9440 (p) cc_final: 0.9223 (m) REVERT: N 38 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8155 (ptm160) REVERT: N 53 GLN cc_start: 0.7908 (mp10) cc_final: 0.7591 (mp10) REVERT: N 73 ASP cc_start: 0.5343 (p0) cc_final: 0.5038 (p0) REVERT: N 76 LYS cc_start: 0.9251 (tppp) cc_final: 0.8637 (ttmp) REVERT: N 89 GLU cc_start: 0.9081 (tp30) cc_final: 0.8768 (pp20) REVERT: N 90 ASP cc_start: 0.8412 (m-30) cc_final: 0.7912 (m-30) REVERT: N 123 GLN cc_start: 0.8806 (tp-100) cc_final: 0.8549 (tm-30) outliers start: 48 outliers final: 24 residues processed: 252 average time/residue: 0.5603 time to fit residues: 150.0464 Evaluate side-chains 231 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 346 LEU Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 438 GLN Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 91 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 420 HIS A 292 ASN A 384 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 176 GLN B 266 HIS N 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106194 restraints weight = 14857.116| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.45 r_work: 0.3224 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 1.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9414 Z= 0.139 Angle : 0.684 11.260 12744 Z= 0.353 Chirality : 0.044 0.276 1405 Planarity : 0.004 0.035 1621 Dihedral : 4.400 22.863 1259 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.75 % Allowed : 28.79 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.26), residues: 1127 helix: 1.91 (0.25), residues: 453 sheet: 0.72 (0.35), residues: 223 loop : -0.57 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.025 0.001 TYR R 191 PHE 0.028 0.001 PHE R 335 TRP 0.026 0.001 TRP P 23 HIS 0.006 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9407) covalent geometry : angle 0.68315 (12732) SS BOND : bond 0.00300 ( 6) SS BOND : angle 1.52882 ( 12) hydrogen bonds : bond 0.04159 ( 472) hydrogen bonds : angle 4.32946 ( 1359) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 THR cc_start: 0.8600 (m) cc_final: 0.8328 (p) REVERT: R 214 ARG cc_start: 0.8379 (mtp85) cc_final: 0.7911 (mtp85) REVERT: R 469 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8485 (mm-30) REVERT: A 35 GLN cc_start: 0.8594 (mt0) cc_final: 0.8222 (mp10) REVERT: A 213 GLN cc_start: 0.9076 (tt0) cc_final: 0.8827 (tm-30) REVERT: A 309 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8000 (mt-10) REVERT: A 381 ASP cc_start: 0.8407 (t70) cc_final: 0.8079 (t0) REVERT: A 389 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8089 (ttm110) REVERT: B 44 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: B 59 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: B 156 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7756 (mm110) REVERT: B 197 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.8080 (mmm-85) REVERT: B 215 GLU cc_start: 0.8370 (mp0) cc_final: 0.7452 (pm20) REVERT: B 217 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6143 (pmt) REVERT: B 219 ARG cc_start: 0.8740 (mmm-85) cc_final: 0.8191 (mmt90) REVERT: B 233 CYS cc_start: 0.9205 (t) cc_final: 0.8740 (t) REVERT: B 234 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: B 294 CYS cc_start: 0.7936 (m) cc_final: 0.7717 (t) REVERT: B 304 ARG cc_start: 0.8712 (mtp180) cc_final: 0.8365 (ttm-80) REVERT: B 312 ASP cc_start: 0.8535 (t0) cc_final: 0.8328 (t0) REVERT: B 314 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8078 (tmm-80) REVERT: G 58 GLU cc_start: 0.8112 (mp0) cc_final: 0.7737 (mm-30) REVERT: G 62 ARG cc_start: 0.7183 (tpt-90) cc_final: 0.6817 (tpp80) REVERT: N 30 SER cc_start: 0.9449 (p) cc_final: 0.9232 (m) REVERT: N 38 ARG cc_start: 0.8527 (ptm-80) cc_final: 0.8157 (ptm160) REVERT: N 53 GLN cc_start: 0.7841 (mp10) cc_final: 0.7487 (mp10) REVERT: N 73 ASP cc_start: 0.5323 (p0) cc_final: 0.4994 (p0) REVERT: N 76 LYS cc_start: 0.9243 (tppp) cc_final: 0.8579 (ttmp) REVERT: N 89 GLU cc_start: 0.9097 (tp30) cc_final: 0.8830 (pp20) REVERT: N 90 ASP cc_start: 0.8312 (m-30) cc_final: 0.7704 (m-30) REVERT: N 123 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8440 (tm-30) outliers start: 47 outliers final: 26 residues processed: 240 average time/residue: 0.5374 time to fit residues: 137.1618 Evaluate side-chains 234 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 266 HIS N 77 ASN N 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.140752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.106915 restraints weight = 14926.685| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.42 r_work: 0.3227 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 1.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9414 Z= 0.140 Angle : 0.677 11.548 12744 Z= 0.350 Chirality : 0.044 0.246 1405 Planarity : 0.004 0.039 1621 Dihedral : 4.250 21.460 1259 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.14 % Allowed : 30.30 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.26), residues: 1127 helix: 2.00 (0.25), residues: 447 sheet: 0.49 (0.35), residues: 216 loop : -0.43 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 347 TYR 0.025 0.001 TYR R 191 PHE 0.029 0.001 PHE R 335 TRP 0.028 0.001 TRP P 23 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9407) covalent geometry : angle 0.67528 (12732) SS BOND : bond 0.00248 ( 6) SS BOND : angle 1.65660 ( 12) hydrogen bonds : bond 0.04164 ( 472) hydrogen bonds : angle 4.31328 ( 1359) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 218 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 203 THR cc_start: 0.8629 (m) cc_final: 0.8346 (p) REVERT: R 214 ARG cc_start: 0.8370 (mtp85) cc_final: 0.7916 (mtp85) REVERT: R 438 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: R 469 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8516 (mm-30) REVERT: A 21 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7744 (pp20) REVERT: A 35 GLN cc_start: 0.8598 (mt0) cc_final: 0.8195 (mp10) REVERT: A 213 GLN cc_start: 0.9101 (tt0) cc_final: 0.8871 (tm-30) REVERT: A 265 ARG cc_start: 0.7470 (ptt180) cc_final: 0.7148 (ptt-90) REVERT: A 299 GLU cc_start: 0.8281 (pp20) cc_final: 0.7998 (pm20) REVERT: A 309 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: A 381 ASP cc_start: 0.8379 (t70) cc_final: 0.8092 (t0) REVERT: A 389 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8031 (ttm110) REVERT: B 44 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8396 (mt0) REVERT: B 59 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: B 156 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7758 (mm110) REVERT: B 197 ARG cc_start: 0.8371 (mmm-85) cc_final: 0.8086 (mmm-85) REVERT: B 215 GLU cc_start: 0.8483 (mp0) cc_final: 0.7472 (pm20) REVERT: B 217 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.6092 (pmt) REVERT: B 219 ARG cc_start: 0.8703 (mmm-85) cc_final: 0.8284 (mmt90) REVERT: B 233 CYS cc_start: 0.9208 (t) cc_final: 0.8739 (t) REVERT: B 254 ASP cc_start: 0.8662 (m-30) cc_final: 0.8191 (t70) REVERT: B 294 CYS cc_start: 0.8054 (m) cc_final: 0.7749 (t) REVERT: B 312 ASP cc_start: 0.8518 (t0) cc_final: 0.8302 (t0) REVERT: G 24 ASN cc_start: 0.8701 (p0) cc_final: 0.8390 (p0) REVERT: G 36 ASP cc_start: 0.8599 (t0) cc_final: 0.8344 (m-30) REVERT: G 58 GLU cc_start: 0.8094 (mp0) cc_final: 0.7686 (mm-30) REVERT: G 62 ARG cc_start: 0.6974 (tpt-90) cc_final: 0.6754 (tpp80) REVERT: N 73 ASP cc_start: 0.5780 (p0) cc_final: 0.5503 (p0) REVERT: N 76 LYS cc_start: 0.9223 (tppp) cc_final: 0.8480 (ttmp) REVERT: N 90 ASP cc_start: 0.8335 (m-30) cc_final: 0.7986 (m-30) REVERT: N 91 THR cc_start: 0.9160 (t) cc_final: 0.8703 (m) REVERT: N 117 TYR cc_start: 0.8115 (m-80) cc_final: 0.7862 (m-80) REVERT: N 123 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8420 (tm-30) outliers start: 41 outliers final: 24 residues processed: 240 average time/residue: 0.5699 time to fit residues: 145.2623 Evaluate side-chains 229 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 438 GLN Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106533 restraints weight = 14923.384| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.43 r_work: 0.3222 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 1.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9414 Z= 0.144 Angle : 0.691 10.852 12744 Z= 0.358 Chirality : 0.044 0.185 1405 Planarity : 0.004 0.033 1621 Dihedral : 4.235 21.790 1259 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.74 % Allowed : 31.11 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.26), residues: 1127 helix: 1.96 (0.25), residues: 447 sheet: 0.52 (0.37), residues: 205 loop : -0.40 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 105 TYR 0.025 0.001 TYR R 191 PHE 0.029 0.001 PHE R 335 TRP 0.030 0.002 TRP P 23 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9407) covalent geometry : angle 0.68919 (12732) SS BOND : bond 0.00241 ( 6) SS BOND : angle 1.57948 ( 12) hydrogen bonds : bond 0.04140 ( 472) hydrogen bonds : angle 4.25626 ( 1359) Misc. bond : bond 0.00005 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7038 (tmm) cc_final: 0.6745 (tpt) REVERT: R 203 THR cc_start: 0.8612 (m) cc_final: 0.8330 (p) REVERT: R 214 ARG cc_start: 0.8372 (mtp85) cc_final: 0.7918 (mtp85) REVERT: R 358 ASN cc_start: 0.8201 (m-40) cc_final: 0.7605 (t0) REVERT: R 438 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: R 469 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8569 (mm-30) REVERT: A 21 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7930 (pp20) REVERT: A 33 ASP cc_start: 0.8356 (m-30) cc_final: 0.7957 (m-30) REVERT: A 35 GLN cc_start: 0.8595 (mt0) cc_final: 0.8200 (mp10) REVERT: A 210 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7980 (p) REVERT: A 213 GLN cc_start: 0.9094 (tt0) cc_final: 0.8859 (tm-30) REVERT: A 265 ARG cc_start: 0.7379 (ptt180) cc_final: 0.7141 (ppt170) REVERT: A 299 GLU cc_start: 0.8187 (pp20) cc_final: 0.7838 (pm20) REVERT: A 309 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: A 381 ASP cc_start: 0.8406 (t70) cc_final: 0.8127 (t0) REVERT: A 389 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8046 (ttm110) REVERT: B 44 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: B 46 ARG cc_start: 0.8007 (mtp180) cc_final: 0.7453 (mtt90) REVERT: B 57 LYS cc_start: 0.8296 (pttm) cc_final: 0.7761 (pttm) REVERT: B 59 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: B 156 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7700 (mm110) REVERT: B 197 ARG cc_start: 0.8323 (mmm-85) cc_final: 0.8030 (mmm-85) REVERT: B 215 GLU cc_start: 0.8400 (mp0) cc_final: 0.7469 (pm20) REVERT: B 217 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.5994 (pmt) REVERT: B 219 ARG cc_start: 0.8666 (mmm-85) cc_final: 0.8361 (mmt90) REVERT: B 233 CYS cc_start: 0.9279 (t) cc_final: 0.8797 (t) REVERT: B 234 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: B 294 CYS cc_start: 0.7946 (m) cc_final: 0.7709 (t) REVERT: B 312 ASP cc_start: 0.8535 (t0) cc_final: 0.8307 (t0) REVERT: B 314 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8098 (tmm-80) REVERT: G 24 ASN cc_start: 0.8701 (p0) cc_final: 0.8421 (p0) REVERT: G 36 ASP cc_start: 0.8608 (t0) cc_final: 0.8346 (m-30) REVERT: G 49 PRO cc_start: 0.8921 (Cg_exo) cc_final: 0.8677 (Cg_endo) REVERT: G 58 GLU cc_start: 0.8204 (mp0) cc_final: 0.7777 (mm-30) REVERT: G 62 ARG cc_start: 0.6918 (tpt-90) cc_final: 0.6702 (tpp80) REVERT: N 76 LYS cc_start: 0.9218 (tppp) cc_final: 0.8977 (tppp) REVERT: N 90 ASP cc_start: 0.8472 (m-30) cc_final: 0.8150 (m-30) REVERT: N 91 THR cc_start: 0.9096 (t) cc_final: 0.8636 (m) REVERT: N 106 ASP cc_start: 0.8621 (p0) cc_final: 0.8306 (p0) REVERT: N 117 TYR cc_start: 0.8074 (m-80) cc_final: 0.7835 (m-80) REVERT: N 123 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8407 (tm-30) outliers start: 37 outliers final: 26 residues processed: 235 average time/residue: 0.5783 time to fit residues: 144.3546 Evaluate side-chains 240 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 438 GLN Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.0770 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 0.0030 overall best weight: 0.7752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.140128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106596 restraints weight = 14894.051| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.40 r_work: 0.3227 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 1.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9414 Z= 0.143 Angle : 0.704 10.758 12744 Z= 0.366 Chirality : 0.044 0.186 1405 Planarity : 0.004 0.058 1621 Dihedral : 4.248 21.551 1259 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.74 % Allowed : 31.82 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1127 helix: 1.87 (0.24), residues: 448 sheet: 0.44 (0.36), residues: 214 loop : -0.40 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 105 TYR 0.025 0.001 TYR R 191 PHE 0.029 0.001 PHE R 335 TRP 0.030 0.001 TRP P 23 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 9407) covalent geometry : angle 0.70218 (12732) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.59928 ( 12) hydrogen bonds : bond 0.04089 ( 472) hydrogen bonds : angle 4.29546 ( 1359) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4049.15 seconds wall clock time: 69 minutes 34.03 seconds (4174.03 seconds total)