Starting phenix.real_space_refine on Thu Mar 13 19:10:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y36_33590/03_2025/7y36_33590.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y36_33590/03_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_33590/03_2025/7y36_33590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2025/7y36_33590.map" model { file = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2025/7y36_33590.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y36_33590/03_2025/7y36_33590.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.88, per 1000 atoms: 0.64 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: 2.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.74 Time building geometry restraints manager: 3.03 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.090 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.110 ------------------------------------------------------------------------------- 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 0.072 9407 Z= 0.421 Angle : 0.732 10.207 12732 Z= 0.445 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.024 0.002 TRP B 99 HIS 0.008 0.001 HIS A 357 PHE 0.021 0.002 PHE R 335 TYR 0.038 0.002 TYR B 59 ARG 0.009 0.001 ARG N 72 *********************** 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 : 0.971 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: 1.1635 time to fit residues: 386.3273 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 : 1.681 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 140 HIS R 216 HIS R 463 ASN ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 41 HIS B 62 HIS B 75 GLN B 91 HIS B 119 ASN B 176 GLN B 266 HIS B 295 ASN B 313 ASN N 77 ASN N 82 GLN N 84 ASN N 123 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.181956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149734 restraints weight = 15469.644| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.89 r_work: 0.3790 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9407 Z= 0.286 Angle : 0.738 13.282 12732 Z= 0.390 Chirality : 0.046 0.169 1405 Planarity : 0.005 0.071 1621 Dihedral : 5.056 28.990 1261 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.04 % Allowed : 15.76 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.24), residues: 1127 helix: 0.87 (0.24), residues: 448 sheet: -0.14 (0.32), residues: 222 loop : -0.97 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.010 0.002 HIS B 183 PHE 0.036 0.002 PHE R 335 TYR 0.040 0.002 TYR R 191 ARG 0.011 0.001 ARG P 20 *********************** 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: 40 poor density : 271 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 32 MET cc_start: 0.7799 (ttp) cc_final: 0.7296 (tpp) REVERT: R 49 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8088 (mm-30) REVERT: R 182 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7736 (tm-30) REVERT: R 214 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7892 (mtp85) REVERT: R 281 CYS cc_start: 0.6140 (OUTLIER) cc_final: 0.5668 (t) REVERT: R 322 TRP cc_start: 0.5947 (t60) cc_final: 0.5403 (t60) REVERT: R 441 MET cc_start: 0.7815 (mmm) cc_final: 0.7462 (mmm) REVERT: R 469 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8275 (mm-30) REVERT: A 343 ASP cc_start: 0.8571 (m-30) cc_final: 0.8021 (m-30) REVERT: A 347 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7448 (ptp-110) REVERT: A 363 PHE cc_start: 0.8579 (m-80) cc_final: 0.8288 (m-80) REVERT: A 381 ASP cc_start: 0.8560 (t70) cc_final: 0.8284 (t0) REVERT: B 19 ARG cc_start: 0.7830 (ttp-110) cc_final: 0.7326 (ptp-110) REVERT: B 81 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6096 (pt) REVERT: B 187 VAL cc_start: 0.6454 (OUTLIER) cc_final: 0.5875 (p) REVERT: B 188 MET cc_start: 0.8360 (mmm) cc_final: 0.8148 (mmm) REVERT: B 290 ASP cc_start: 0.7478 (m-30) cc_final: 0.7054 (m-30) REVERT: G 62 ARG cc_start: 0.6741 (tpt-90) cc_final: 0.6273 (tpp80) REVERT: N 35 ASN cc_start: 0.6766 (m-40) cc_final: 0.6428 (m-40) REVERT: N 60 TYR cc_start: 0.8429 (m-80) cc_final: 0.8027 (m-80) REVERT: N 76 LYS cc_start: 0.8440 (tptp) cc_final: 0.8218 (tppp) REVERT: N 91 THR cc_start: 0.4684 (t) cc_final: 0.4453 (t) REVERT: N 120 GLN cc_start: 0.7499 (mm110) cc_final: 0.7217 (mm-40) outliers start: 40 outliers final: 10 residues processed: 293 average time/residue: 1.2546 time to fit residues: 395.5365 Evaluate side-chains 208 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 37 GLN 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 A residue 14 ASN Chi-restraints excluded: chain A residue 347 ARG 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 59 SER 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 67 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 P 32 HIS B 266 HIS B 295 ASN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136159 restraints weight = 15465.475| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.91 r_work: 0.3622 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.7359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9407 Z= 0.220 Angle : 0.654 11.257 12732 Z= 0.340 Chirality : 0.044 0.244 1405 Planarity : 0.004 0.057 1621 Dihedral : 4.556 28.497 1259 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.05 % Allowed : 20.91 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1127 helix: 1.62 (0.24), residues: 451 sheet: 0.06 (0.32), residues: 229 loop : -0.72 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 36 HIS 0.003 0.001 HIS R 420 PHE 0.014 0.002 PHE A 315 TYR 0.027 0.001 TYR R 191 ARG 0.007 0.001 ARG A 38 *********************** 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 274 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 214 ARG cc_start: 0.8283 (mtp85) cc_final: 0.7896 (mtp85) REVERT: R 278 TYR cc_start: 0.5794 (p90) cc_final: 0.5241 (m-80) REVERT: R 281 CYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5147 (t) REVERT: R 322 TRP cc_start: 0.5943 (t60) cc_final: 0.5383 (t60) REVERT: R 358 ASN cc_start: 0.7152 (t0) cc_final: 0.6875 (t0) REVERT: R 441 MET cc_start: 0.8042 (mmm) cc_final: 0.7702 (mmm) REVERT: R 469 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8511 (mm-30) REVERT: A 309 GLU cc_start: 0.8090 (pm20) cc_final: 0.7823 (mt-10) REVERT: A 381 ASP cc_start: 0.8479 (t70) cc_final: 0.8234 (t0) REVERT: A 386 MET cc_start: 0.8756 (tmm) cc_final: 0.8469 (OUTLIER) REVERT: A 389 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8364 (ttm110) REVERT: B 19 ARG cc_start: 0.7787 (ttp-110) cc_final: 0.7349 (ptp-110) REVERT: B 138 GLU cc_start: 0.8434 (mp0) cc_final: 0.8217 (mp0) REVERT: B 230 ASN cc_start: 0.8524 (t0) cc_final: 0.8137 (m-40) REVERT: B 297 TRP cc_start: 0.8651 (m100) cc_final: 0.8375 (m100) REVERT: B 312 ASP cc_start: 0.7746 (t0) cc_final: 0.7492 (t0) REVERT: G 36 ASP cc_start: 0.7964 (t0) cc_final: 0.7732 (t0) REVERT: G 62 ARG cc_start: 0.6957 (tpt-90) cc_final: 0.6579 (tpp80) REVERT: N 35 ASN cc_start: 0.8142 (m-40) cc_final: 0.7463 (m-40) REVERT: N 39 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: N 60 TYR cc_start: 0.8598 (m-80) cc_final: 0.8098 (m-80) REVERT: N 94 TYR cc_start: 0.8480 (m-80) cc_final: 0.8175 (m-80) outliers start: 50 outliers final: 17 residues processed: 254 average time/residue: 1.2716 time to fit residues: 345.8925 Evaluate side-chains 208 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 431 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 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 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 201 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 59 SER 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 5 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 33 ASN A 236 GLN B 266 HIS N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.162734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127377 restraints weight = 14834.890| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.67 r_work: 0.3510 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.8634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9407 Z= 0.210 Angle : 0.650 10.458 12732 Z= 0.340 Chirality : 0.043 0.169 1405 Planarity : 0.004 0.046 1621 Dihedral : 4.390 30.718 1259 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.45 % Allowed : 23.03 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1127 helix: 1.83 (0.24), residues: 450 sheet: 0.25 (0.32), residues: 225 loop : -0.63 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS P 9 PHE 0.014 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.010 0.001 ARG B 251 *********************** 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 271 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7910 (mm-30) REVERT: R 214 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7877 (mtp85) REVERT: R 278 TYR cc_start: 0.6052 (p90) cc_final: 0.5659 (m-80) REVERT: R 322 TRP cc_start: 0.6187 (t60) cc_final: 0.5575 (t60) REVERT: R 358 ASN cc_start: 0.7679 (m-40) cc_final: 0.7455 (t0) REVERT: R 469 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8518 (mm-30) REVERT: A 297 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6980 (mt) REVERT: A 309 GLU cc_start: 0.8140 (pm20) cc_final: 0.7895 (mt-10) REVERT: A 347 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7714 (ptp-110) REVERT: A 381 ASP cc_start: 0.8331 (t70) cc_final: 0.7991 (t0) REVERT: A 389 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8321 (ttm110) REVERT: B 19 ARG cc_start: 0.7863 (ttp-110) cc_final: 0.7077 (ptp-110) REVERT: B 146 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7308 (tp) REVERT: B 217 MET cc_start: 0.8514 (mmm) cc_final: 0.8118 (mmm) REVERT: B 230 ASN cc_start: 0.8699 (t0) cc_final: 0.8338 (m-40) REVERT: B 292 PHE cc_start: 0.8706 (m-10) cc_final: 0.8218 (m-80) REVERT: B 312 ASP cc_start: 0.8026 (t0) cc_final: 0.7692 (t0) REVERT: N 35 ASN cc_start: 0.8375 (m-40) cc_final: 0.8022 (m-40) REVERT: N 60 TYR cc_start: 0.8737 (m-80) cc_final: 0.8144 (m-80) REVERT: N 73 ASP cc_start: 0.5561 (p0) cc_final: 0.5248 (p0) REVERT: N 76 LYS cc_start: 0.8944 (tppp) cc_final: 0.8591 (ttmt) REVERT: N 89 GLU cc_start: 0.8936 (tp30) cc_final: 0.8666 (tp30) REVERT: N 94 TYR cc_start: 0.8842 (m-80) cc_final: 0.8492 (m-80) outliers start: 54 outliers final: 25 residues processed: 246 average time/residue: 1.1677 time to fit residues: 307.0212 Evaluate side-chains 214 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR 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 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 221 THR 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 B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU 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 65 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 51 optimal weight: 0.0370 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 6 GLN B 293 ASN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.145289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109189 restraints weight = 14827.101| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.53 r_work: 0.3275 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 1.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9407 Z= 0.277 Angle : 0.703 9.829 12732 Z= 0.370 Chirality : 0.046 0.172 1405 Planarity : 0.004 0.032 1621 Dihedral : 4.712 25.661 1259 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 6.57 % Allowed : 24.24 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1127 helix: 1.78 (0.24), residues: 450 sheet: 0.15 (0.32), residues: 243 loop : -0.56 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 82 HIS 0.007 0.001 HIS R 420 PHE 0.017 0.002 PHE R 173 TYR 0.021 0.002 TYR R 191 ARG 0.008 0.001 ARG G 62 *********************** 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 303 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8022 (mm-30) REVERT: R 203 THR cc_start: 0.8558 (m) cc_final: 0.8327 (p) REVERT: R 214 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7873 (mtp85) REVERT: R 469 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8510 (mm-30) REVERT: A 14 ASN cc_start: 0.5815 (OUTLIER) cc_final: 0.5128 (p0) REVERT: A 31 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8823 (mm110) REVERT: A 33 ASP cc_start: 0.8359 (m-30) cc_final: 0.7674 (t0) REVERT: A 35 GLN cc_start: 0.8603 (mt0) cc_final: 0.8159 (mp10) REVERT: A 213 GLN cc_start: 0.9159 (tt0) cc_final: 0.8934 (tm-30) REVERT: A 297 LEU cc_start: 0.7359 (mt) cc_final: 0.6940 (mt) REVERT: A 309 GLU cc_start: 0.8308 (pm20) cc_final: 0.7990 (mt-10) REVERT: A 370 GLU cc_start: 0.7694 (mp0) cc_final: 0.7448 (mp0) REVERT: A 381 ASP cc_start: 0.8323 (t70) cc_final: 0.7981 (t0) REVERT: A 389 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8263 (ttm110) REVERT: B 19 ARG cc_start: 0.8208 (ttp-110) cc_final: 0.7976 (ttm110) REVERT: B 37 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6613 (tt) REVERT: B 59 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 135 VAL cc_start: 0.8930 (m) cc_final: 0.8720 (t) REVERT: B 138 GLU cc_start: 0.8186 (mp0) cc_final: 0.7921 (mp0) REVERT: B 189 SER cc_start: 0.9021 (t) cc_final: 0.8672 (t) REVERT: B 197 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8025 (mmm-85) REVERT: B 217 MET cc_start: 0.8586 (mmm) cc_final: 0.8226 (mmm) REVERT: B 219 ARG cc_start: 0.8584 (mmm-85) cc_final: 0.7779 (mpt-90) REVERT: B 229 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7903 (mt) REVERT: B 230 ASN cc_start: 0.8864 (t0) cc_final: 0.8514 (m-40) REVERT: B 304 ARG cc_start: 0.8619 (mtp180) cc_final: 0.8184 (ttm-80) REVERT: B 312 ASP cc_start: 0.8367 (t0) cc_final: 0.8096 (t0) REVERT: N 35 ASN cc_start: 0.8545 (m-40) cc_final: 0.7910 (m-40) REVERT: N 73 ASP cc_start: 0.5919 (p0) cc_final: 0.5686 (p0) REVERT: N 76 LYS cc_start: 0.9173 (tppp) cc_final: 0.8520 (ttmm) REVERT: N 89 GLU cc_start: 0.9084 (tp30) cc_final: 0.8791 (tp30) outliers start: 65 outliers final: 29 residues processed: 283 average time/residue: 1.2429 time to fit residues: 376.6588 Evaluate side-chains 230 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 37 GLN 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 381 ILE Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 444 GLU 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 372 ILE 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 81 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 111 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.147162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111759 restraints weight = 14664.810| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.48 r_work: 0.3313 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 1.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9407 Z= 0.195 Angle : 0.634 9.630 12732 Z= 0.330 Chirality : 0.043 0.158 1405 Planarity : 0.004 0.032 1621 Dihedral : 4.420 24.364 1259 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.04 % Allowed : 29.09 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1127 helix: 2.02 (0.25), residues: 449 sheet: 0.50 (0.35), residues: 220 loop : -0.56 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 23 HIS 0.004 0.001 HIS R 420 PHE 0.017 0.001 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.008 0.001 ARG B 96 *********************** 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 266 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8273 (mm-30) REVERT: R 203 THR cc_start: 0.8613 (m) cc_final: 0.8389 (p) REVERT: R 214 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7895 (mtp85) REVERT: R 349 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8918 (p) REVERT: R 358 ASN cc_start: 0.8285 (m-40) cc_final: 0.7712 (t0) REVERT: R 465 GLU cc_start: 0.8221 (mp0) cc_final: 0.8012 (mp0) REVERT: R 469 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8537 (mm-30) REVERT: A 31 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8715 (mm110) REVERT: A 35 GLN cc_start: 0.8563 (mt0) cc_final: 0.7959 (mp10) REVERT: A 213 GLN cc_start: 0.9063 (tt0) cc_final: 0.8801 (tm-30) REVERT: A 297 LEU cc_start: 0.7314 (mt) cc_final: 0.6936 (mt) REVERT: A 309 GLU cc_start: 0.8340 (pm20) cc_final: 0.7914 (mt-10) REVERT: A 310 ASP cc_start: 0.7955 (p0) cc_final: 0.7551 (p0) REVERT: A 378 ASP cc_start: 0.8063 (m-30) cc_final: 0.7843 (m-30) REVERT: A 381 ASP cc_start: 0.8357 (t70) cc_final: 0.8015 (t0) REVERT: B 78 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8056 (tppt) REVERT: B 197 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8047 (mmm-85) REVERT: B 219 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.8431 (mmt90) REVERT: B 229 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7987 (mt) REVERT: B 230 ASN cc_start: 0.8824 (t0) cc_final: 0.8481 (m110) REVERT: B 233 CYS cc_start: 0.9270 (t) cc_final: 0.8867 (t) REVERT: B 234 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: B 262 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7364 (ptm) REVERT: B 304 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8213 (ttm110) REVERT: B 312 ASP cc_start: 0.8394 (t0) cc_final: 0.8147 (t0) REVERT: N 73 ASP cc_start: 0.5890 (p0) cc_final: 0.5486 (p0) REVERT: N 76 LYS cc_start: 0.9223 (tppp) cc_final: 0.8468 (ttmm) REVERT: N 87 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8139 (ptpp) REVERT: N 117 TYR cc_start: 0.8006 (m-80) cc_final: 0.7735 (m-80) outliers start: 40 outliers final: 16 residues processed: 250 average time/residue: 1.2764 time to fit residues: 339.2449 Evaluate side-chains 217 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 P residue 32 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 81 ILE 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 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 65 optimal weight: 0.0670 chunk 89 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 348 ASN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 266 HIS N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112281 restraints weight = 14822.637| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 3.57 r_work: 0.3314 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 1.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9407 Z= 0.183 Angle : 0.633 11.140 12732 Z= 0.329 Chirality : 0.042 0.155 1405 Planarity : 0.004 0.063 1621 Dihedral : 4.292 22.216 1259 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.54 % Allowed : 30.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1127 helix: 2.06 (0.24), residues: 448 sheet: 0.61 (0.35), residues: 225 loop : -0.47 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 23 HIS 0.004 0.001 HIS R 420 PHE 0.024 0.001 PHE R 314 TYR 0.024 0.001 TYR R 191 ARG 0.011 0.001 ARG B 129 *********************** 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 249 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8200 (mm-30) REVERT: R 203 THR cc_start: 0.8603 (m) cc_final: 0.8359 (p) REVERT: R 214 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7888 (mtp85) REVERT: R 349 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8910 (p) REVERT: R 358 ASN cc_start: 0.8267 (m-40) cc_final: 0.7689 (t0) REVERT: R 469 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8508 (mm-30) REVERT: A 31 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8677 (mm110) REVERT: A 35 GLN cc_start: 0.8631 (mt0) cc_final: 0.7995 (mp10) REVERT: A 213 GLN cc_start: 0.9075 (tt0) cc_final: 0.8779 (tm-30) REVERT: A 297 LEU cc_start: 0.7410 (mt) cc_final: 0.7063 (mt) REVERT: A 309 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: A 310 ASP cc_start: 0.8077 (p0) cc_final: 0.7699 (p0) REVERT: A 378 ASP cc_start: 0.8043 (m-30) cc_final: 0.7816 (m-30) REVERT: A 381 ASP cc_start: 0.8372 (t70) cc_final: 0.7973 (t0) REVERT: B 78 LYS cc_start: 0.8242 (ttmm) cc_final: 0.8031 (tppt) REVERT: B 197 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.8059 (mmm-85) REVERT: B 217 MET cc_start: 0.8306 (mmm) cc_final: 0.7993 (mpp) REVERT: B 219 ARG cc_start: 0.8895 (mmm-85) cc_final: 0.8376 (mmm-85) REVERT: B 230 ASN cc_start: 0.8789 (t0) cc_final: 0.8510 (m110) REVERT: B 233 CYS cc_start: 0.9298 (t) cc_final: 0.8880 (t) REVERT: B 234 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8632 (m-80) REVERT: B 304 ARG cc_start: 0.8548 (mtp180) cc_final: 0.8182 (ttm110) REVERT: B 312 ASP cc_start: 0.8449 (t0) cc_final: 0.8156 (t0) REVERT: N 35 ASN cc_start: 0.8575 (m-40) cc_final: 0.8247 (m-40) REVERT: N 73 ASP cc_start: 0.5754 (p0) cc_final: 0.5435 (p0) REVERT: N 76 LYS cc_start: 0.9196 (tppp) cc_final: 0.8520 (ttmt) REVERT: N 89 GLU cc_start: 0.9125 (tp30) cc_final: 0.8809 (pp20) REVERT: N 91 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7734 (t) outliers start: 35 outliers final: 21 residues processed: 235 average time/residue: 1.3416 time to fit residues: 336.7527 Evaluate side-chains 221 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 2.066 ------------------------------------------------------------------------------- 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 438 GLN Chi-restraints excluded: chain P residue 32 HIS 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 372 ILE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 50 THR 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 187 VAL Chi-restraints excluded: chain B residue 234 PHE 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 22 CYS Chi-restraints excluded: chain N residue 91 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 107 optimal weight: 0.0050 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 266 HIS N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107218 restraints weight = 15008.041| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.54 r_work: 0.3246 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 1.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9407 Z= 0.243 Angle : 0.684 11.238 12732 Z= 0.353 Chirality : 0.043 0.170 1405 Planarity : 0.004 0.036 1621 Dihedral : 4.405 22.425 1259 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.74 % Allowed : 29.90 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1127 helix: 1.96 (0.24), residues: 449 sheet: 0.47 (0.34), residues: 233 loop : -0.42 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P 23 HIS 0.006 0.001 HIS R 420 PHE 0.021 0.001 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.009 0.001 ARG B 129 *********************** 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 247 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 210 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8059 (mm-30) REVERT: R 203 THR cc_start: 0.8597 (m) cc_final: 0.8324 (p) REVERT: R 214 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7874 (mtp85) REVERT: R 349 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8975 (p) REVERT: R 358 ASN cc_start: 0.8406 (m-40) cc_final: 0.7763 (t0) REVERT: R 431 GLU cc_start: 0.7744 (pp20) cc_final: 0.7384 (pp20) REVERT: R 469 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8555 (mm-30) REVERT: A 31 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8706 (mm110) REVERT: A 33 ASP cc_start: 0.8446 (m-30) cc_final: 0.7799 (OUTLIER) REVERT: A 35 GLN cc_start: 0.8610 (mt0) cc_final: 0.7974 (mp10) REVERT: A 213 GLN cc_start: 0.9086 (tt0) cc_final: 0.8806 (tm-30) REVERT: A 292 ASN cc_start: 0.8294 (m-40) cc_final: 0.8035 (m110) REVERT: A 309 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: A 381 ASP cc_start: 0.8359 (t70) cc_final: 0.8037 (t0) REVERT: B 59 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: B 197 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: B 219 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8320 (mmt90) REVERT: B 230 ASN cc_start: 0.8872 (t0) cc_final: 0.8583 (m110) REVERT: B 233 CYS cc_start: 0.9234 (t) cc_final: 0.8768 (t) REVERT: B 234 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8766 (m-80) REVERT: B 294 CYS cc_start: 0.8027 (m) cc_final: 0.7736 (t) REVERT: B 304 ARG cc_start: 0.8652 (mtp180) cc_final: 0.8307 (ttm-80) REVERT: B 312 ASP cc_start: 0.8493 (t0) cc_final: 0.8188 (t0) REVERT: G 13 ARG cc_start: 0.7242 (tmm-80) cc_final: 0.6882 (ptp-170) REVERT: N 35 ASN cc_start: 0.8650 (m-40) cc_final: 0.8336 (m-40) REVERT: N 73 ASP cc_start: 0.5879 (p0) cc_final: 0.5579 (p0) REVERT: N 76 LYS cc_start: 0.9225 (tppp) cc_final: 0.8469 (ttmm) outliers start: 37 outliers final: 22 residues processed: 235 average time/residue: 1.3472 time to fit residues: 338.0507 Evaluate side-chains 221 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain P residue 32 HIS 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 372 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 76 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE 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 46 LYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 84 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.107015 restraints weight = 14735.940| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 3.48 r_work: 0.3248 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 1.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9407 Z= 0.231 Angle : 0.695 11.734 12732 Z= 0.360 Chirality : 0.043 0.155 1405 Planarity : 0.004 0.031 1621 Dihedral : 4.418 22.138 1259 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.13 % Allowed : 30.51 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1127 helix: 2.01 (0.24), residues: 449 sheet: 0.67 (0.36), residues: 226 loop : -0.46 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP P 23 HIS 0.005 0.001 HIS R 420 PHE 0.023 0.001 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.008 0.001 ARG B 129 *********************** 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 250 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 49 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8021 (mm-30) REVERT: R 203 THR cc_start: 0.8593 (m) cc_final: 0.8310 (p) REVERT: R 214 ARG cc_start: 0.8391 (mtp85) cc_final: 0.7892 (mtp85) REVERT: R 349 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9015 (p) REVERT: R 431 GLU cc_start: 0.7693 (pp20) cc_final: 0.7305 (pp20) REVERT: R 469 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 31 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8698 (mm110) REVERT: A 35 GLN cc_start: 0.8619 (mt0) cc_final: 0.7963 (mp10) REVERT: A 213 GLN cc_start: 0.9148 (tt0) cc_final: 0.8896 (tm-30) REVERT: A 229 ASP cc_start: 0.7840 (p0) cc_final: 0.7558 (p0) REVERT: A 230 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 250 SER cc_start: 0.8627 (t) cc_final: 0.8266 (t) REVERT: A 292 ASN cc_start: 0.8354 (m-40) cc_final: 0.8011 (m110) REVERT: A 299 GLU cc_start: 0.8462 (pp20) cc_final: 0.8155 (pm20) REVERT: A 309 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: A 381 ASP cc_start: 0.8394 (t70) cc_final: 0.8061 (t0) REVERT: A 389 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8007 (ttm110) REVERT: B 59 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: B 197 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.8091 (mmm-85) REVERT: B 211 TRP cc_start: 0.8140 (m-90) cc_final: 0.7792 (m100) REVERT: B 212 ASP cc_start: 0.8140 (t0) cc_final: 0.7609 (t0) REVERT: B 230 ASN cc_start: 0.8883 (t0) cc_final: 0.8654 (m110) REVERT: B 233 CYS cc_start: 0.9248 (t) cc_final: 0.8764 (t) REVERT: B 234 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8782 (m-80) REVERT: B 255 LEU cc_start: 0.8751 (mp) cc_final: 0.8532 (mt) REVERT: B 294 CYS cc_start: 0.8112 (m) cc_final: 0.7837 (t) REVERT: B 304 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8286 (ttm-80) REVERT: B 312 ASP cc_start: 0.8519 (t0) cc_final: 0.8218 (t0) REVERT: G 13 ARG cc_start: 0.7380 (tmm-80) cc_final: 0.7163 (ptp-170) REVERT: N 73 ASP cc_start: 0.5844 (p0) cc_final: 0.5581 (p0) REVERT: N 76 LYS cc_start: 0.9217 (tppp) cc_final: 0.8404 (ttmm) REVERT: N 87 LYS cc_start: 0.8498 (ptmt) cc_final: 0.8250 (ptpt) outliers start: 31 outliers final: 20 residues processed: 239 average time/residue: 1.6319 time to fit residues: 415.2906 Evaluate side-chains 222 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 CYS Chi-restraints excluded: chain R residue 349 THR Chi-restraints excluded: chain R residue 412 VAL Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS 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 372 ILE Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR 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 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS B 266 HIS N 84 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.140492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105757 restraints weight = 14906.387| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.46 r_work: 0.3232 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9407 Z= 0.245 Angle : 0.718 10.611 12732 Z= 0.373 Chirality : 0.044 0.163 1405 Planarity : 0.004 0.038 1621 Dihedral : 4.512 22.622 1259 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.33 % Allowed : 31.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1127 helix: 2.03 (0.24), residues: 449 sheet: 0.55 (0.36), residues: 220 loop : -0.43 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P 23 HIS 0.006 0.001 HIS R 420 PHE 0.024 0.002 PHE R 335 TYR 0.023 0.002 TYR R 191 ARG 0.007 0.001 ARG B 129 ********************** 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 245 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 36 GLU cc_start: 0.8478 (pt0) cc_final: 0.8275 (pm20) REVERT: R 49 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7970 (mm-30) REVERT: R 203 THR cc_start: 0.8615 (m) cc_final: 0.8330 (p) REVERT: R 214 ARG cc_start: 0.8393 (mtp85) cc_final: 0.7898 (mtp85) REVERT: R 349 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9011 (p) REVERT: R 431 GLU cc_start: 0.7606 (pp20) cc_final: 0.7194 (pp20) REVERT: R 469 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8549 (mm-30) REVERT: A 31 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8734 (mm-40) REVERT: A 33 ASP cc_start: 0.8409 (m-30) cc_final: 0.7759 (t0) REVERT: A 35 GLN cc_start: 0.8715 (mt0) cc_final: 0.8055 (mp10) REVERT: A 213 GLN cc_start: 0.9144 (tt0) cc_final: 0.8888 (tm-30) REVERT: A 221 MET cc_start: 0.8360 (ttm) cc_final: 0.7997 (ttp) REVERT: A 229 ASP cc_start: 0.7955 (p0) cc_final: 0.7565 (p0) REVERT: A 230 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 267 GLN cc_start: 0.8647 (tp40) cc_final: 0.8440 (mm-40) REVERT: A 299 GLU cc_start: 0.8418 (pp20) cc_final: 0.8032 (pm20) REVERT: A 309 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 344 GLU cc_start: 0.8574 (tp30) cc_final: 0.8332 (tp30) REVERT: A 381 ASP cc_start: 0.8383 (t70) cc_final: 0.8060 (t0) REVERT: A 389 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.8011 (ttm110) REVERT: B 59 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7414 (m-80) REVERT: B 78 LYS cc_start: 0.8184 (ttmm) cc_final: 0.7954 (tppt) REVERT: B 197 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: B 211 TRP cc_start: 0.8192 (m-90) cc_final: 0.7823 (m100) REVERT: B 212 ASP cc_start: 0.8308 (t0) cc_final: 0.7884 (t0) REVERT: B 215 GLU cc_start: 0.8583 (mp0) cc_final: 0.8027 (mp0) REVERT: B 230 ASN cc_start: 0.8868 (t0) cc_final: 0.8651 (m-40) REVERT: B 233 CYS cc_start: 0.9256 (t) cc_final: 0.8774 (t) REVERT: B 234 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: B 255 LEU cc_start: 0.8787 (mp) cc_final: 0.8560 (mt) REVERT: B 294 CYS cc_start: 0.8045 (m) cc_final: 0.7803 (t) REVERT: B 304 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8296 (ttm-80) REVERT: B 312 ASP cc_start: 0.8545 (t0) cc_final: 0.8205 (t0) REVERT: G 24 ASN cc_start: 0.8786 (p0) cc_final: 0.8519 (p0) REVERT: N 76 LYS cc_start: 0.9201 (tppp) cc_final: 0.8944 (tppp) outliers start: 33 outliers final: 23 residues processed: 230 average time/residue: 1.4039 time to fit residues: 344.9506 Evaluate side-chains 225 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain R residue 444 GLU Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 32 HIS 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 372 ILE Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE 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 22 GLU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN N 84 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104353 restraints weight = 14968.129| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.45 r_work: 0.3208 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 1.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9407 Z= 0.247 Angle : 0.717 10.759 12732 Z= 0.376 Chirality : 0.045 0.171 1405 Planarity : 0.004 0.044 1621 Dihedral : 4.524 24.774 1259 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.54 % Allowed : 31.52 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1127 helix: 1.97 (0.24), residues: 449 sheet: 0.63 (0.36), residues: 214 loop : -0.47 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 23 HIS 0.005 0.001 HIS R 420 PHE 0.025 0.002 PHE R 335 TYR 0.023 0.001 TYR R 191 ARG 0.007 0.001 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8744.41 seconds wall clock time: 153 minutes 52.99 seconds (9232.99 seconds total)