Starting phenix.real_space_refine on Thu Mar 13 09:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e32_30974/03_2025/7e32_30974.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e32_30974/03_2025/7e32_30974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2025/7e32_30974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2025/7e32_30974.map" model { file = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2025/7e32_30974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e32_30974/03_2025/7e32_30974.cif" } resolution = 2.9 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= 0.015 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 5615 2.51 5 N 1493 2.21 5 O 1631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 8797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2558 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "G" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2273 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Chain: "R" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CLR': 1, 'SRO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.55, per 1000 atoms: 0.63 Number of scatterers: 8797 At special positions: 0 Unit cell: (108.68, 117.04, 109.725, 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 1631 8.00 N 1493 7.00 C 5615 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 188 " distance=2.03 Simple disulfide: pdb=" SG CYS R 327 " - pdb=" SG CYS R 331 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 41.2% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.612A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.059A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 260 removed outlier: 3.859A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.844A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.028A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.911A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.880A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 35 through 66 removed outlier: 3.939A pdb=" N ILE R 39 " --> pdb=" O GLN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 70 Processing helix chain 'R' and resid 71 through 91 Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.745A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 142 removed outlier: 4.268A pdb=" N LEU R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 150 removed outlier: 4.045A pdb=" N LYS R 148 " --> pdb=" O LEU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 171 Processing helix chain 'R' and resid 171 through 177 removed outlier: 4.150A pdb=" N PHE R 175 " --> pdb=" O ILE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 206 removed outlier: 3.718A pdb=" N THR R 198 " --> pdb=" O GLN R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 230 Processing helix chain 'R' and resid 285 through 327 removed outlier: 3.652A pdb=" N PHE R 310 " --> pdb=" O ILE R 306 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS R 313 " --> pdb=" O ALA R 309 " (cutoff:3.500A) Proline residue: R 316 - end of helix removed outlier: 3.653A pdb=" N VAL R 320 " --> pdb=" O PRO R 316 " (cutoff:3.500A) Proline residue: R 325 - end of helix Processing helix chain 'R' and resid 334 through 359 removed outlier: 3.658A pdb=" N ASN R 348 " --> pdb=" O LEU R 344 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER R 349 " --> pdb=" O GLY R 345 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU R 350 " --> pdb=" O TYR R 346 " (cutoff:3.500A) Proline residue: R 353 - end of helix removed outlier: 3.953A pdb=" N PHE R 359 " --> pdb=" O ILE R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 360 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.838A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.524A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.905A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.120A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.866A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.488A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.605A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.230A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.645A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET E 83 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.641A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.641A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.527A pdb=" N SER E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.721A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.721A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1275 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: 2.72 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2812 1.35 - 1.46: 2162 1.46 - 1.58: 3928 1.58 - 1.70: 2 1.70 - 1.81: 80 Bond restraints: 8984 Sorted by residual: bond pdb=" C17 CLR R 402 " pdb=" C20 CLR R 402 " ideal model delta sigma weight residual 1.535 1.596 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" N PHE R 317 " pdb=" CA PHE R 317 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.30e-02 5.92e+03 4.94e+00 bond pdb=" C23 CLR R 402 " pdb=" C24 CLR R 402 " ideal model delta sigma weight residual 1.525 1.569 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" C24 CLR R 402 " pdb=" C25 CLR R 402 " ideal model delta sigma weight residual 1.530 1.573 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C22 CLR R 402 " pdb=" C23 CLR R 402 " ideal model delta sigma weight residual 1.525 1.567 -0.042 2.00e-02 2.50e+03 4.50e+00 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 12011 1.40 - 2.79: 107 2.79 - 4.19: 54 4.19 - 5.58: 6 5.58 - 6.98: 4 Bond angle restraints: 12182 Sorted by residual: angle pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " pdb=" CG PHE A 354 " ideal model delta sigma weight residual 113.80 117.02 -3.22 1.00e+00 1.00e+00 1.04e+01 angle pdb=" C12 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C18 CLR R 402 " ideal model delta sigma weight residual 111.01 104.03 6.98 3.00e+00 1.11e-01 5.41e+00 angle pdb=" N ILE R 312 " pdb=" CA ILE R 312 " pdb=" C ILE R 312 " ideal model delta sigma weight residual 112.98 110.13 2.85 1.25e+00 6.40e-01 5.20e+00 angle pdb=" C PHE A 354 " pdb=" CA PHE A 354 " pdb=" CB PHE A 354 " ideal model delta sigma weight residual 110.10 114.40 -4.30 1.90e+00 2.77e-01 5.13e+00 angle pdb=" C14 CLR R 402 " pdb=" C8 CLR R 402 " pdb=" C7 CLR R 402 " ideal model delta sigma weight residual 110.19 116.91 -6.72 3.00e+00 1.11e-01 5.01e+00 ... (remaining 12177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.45: 4990 18.45 - 36.90: 319 36.90 - 55.35: 47 55.35 - 73.80: 9 73.80 - 92.25: 11 Dihedral angle restraints: 5376 sinusoidal: 2132 harmonic: 3244 Sorted by residual: dihedral pdb=" CB CYS R 327 " pdb=" SG CYS R 327 " pdb=" SG CYS R 331 " pdb=" CB CYS R 331 " ideal model delta sinusoidal sigma weight residual 93.00 46.74 46.26 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " pdb=" C5 CLR R 402 " ideal model delta sinusoidal sigma weight residual -55.03 37.22 -92.25 1 3.00e+01 1.11e-03 1.11e+01 dihedral pdb=" C5 CLR R 402 " pdb=" C3 CLR R 402 " pdb=" C4 CLR R 402 " pdb=" O1 CLR R 402 " ideal model delta sinusoidal sigma weight residual 175.64 83.89 91.75 1 3.00e+01 1.11e-03 1.10e+01 ... (remaining 5373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1237 0.060 - 0.119: 147 0.119 - 0.179: 8 0.179 - 0.239: 1 0.239 - 0.299: 2 Chirality restraints: 1395 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C17 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C16 CLR R 402 " pdb=" C20 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.55 2.85 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C20 CLR R 402 " pdb=" C17 CLR R 402 " pdb=" C21 CLR R 402 " pdb=" C22 CLR R 402 " both_signs ideal model delta sigma weight residual False 2.59 2.79 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 1392 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 353 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C LEU A 353 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 353 " 0.031 2.00e-02 2.50e+03 pdb=" N PHE A 354 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR R 71 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO R 72 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 72 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 72 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 316 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.58e+00 pdb=" C PRO R 316 " -0.022 2.00e-02 2.50e+03 pdb=" O PRO R 316 " 0.008 2.00e-02 2.50e+03 pdb=" N PHE R 317 " 0.007 2.00e-02 2.50e+03 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 58 2.56 - 3.14: 7225 3.14 - 3.73: 13898 3.73 - 4.31: 19809 4.31 - 4.90: 33277 Nonbonded interactions: 74267 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 1.970 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.013 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.037 3.040 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.122 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.124 3.040 ... (remaining 74262 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: 0.590 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.390 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8984 Z= 0.166 Angle : 0.454 6.979 12182 Z= 0.244 Chirality : 0.040 0.299 1395 Planarity : 0.002 0.047 1520 Dihedral : 12.894 92.246 3268 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 2.17 (0.27), residues: 1097 helix: 2.80 (0.27), residues: 389 sheet: 1.22 (0.32), residues: 265 loop : 0.40 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 343 HIS 0.002 0.000 HIS B 91 PHE 0.011 0.001 PHE A 354 TYR 0.009 0.001 TYR R 197 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.867 Fit side-chains REVERT: A 354 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.4824 (m-80) outliers start: 1 outliers final: 1 residues processed: 158 average time/residue: 0.9564 time to fit residues: 163.4873 Evaluate side-chains 128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 18 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 28 optimal weight: 0.0170 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.115352 restraints weight = 9857.716| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.31 r_work: 0.3216 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8984 Z= 0.237 Angle : 0.555 7.670 12182 Z= 0.293 Chirality : 0.043 0.158 1395 Planarity : 0.004 0.046 1520 Dihedral : 5.027 77.055 1281 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.51 % Allowed : 9.08 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.60 (0.26), residues: 1097 helix: 2.13 (0.26), residues: 399 sheet: 0.79 (0.31), residues: 272 loop : 0.31 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.004 0.001 HIS B 62 PHE 0.017 0.002 PHE B 151 TYR 0.014 0.001 TYR B 59 ARG 0.008 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.967 Fit side-chains REVERT: A 198 MET cc_start: 0.8347 (ttm) cc_final: 0.7858 (ttm) REVERT: A 354 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.4742 (m-80) REVERT: B 19 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7643 (ttp80) REVERT: B 119 ASN cc_start: 0.8272 (m110) cc_final: 0.7808 (m-40) REVERT: B 163 ASP cc_start: 0.7202 (t0) cc_final: 0.6869 (t0) REVERT: B 164 THR cc_start: 0.8530 (m) cc_final: 0.8262 (m) REVERT: B 184 THR cc_start: 0.8165 (p) cc_final: 0.7952 (p) REVERT: B 197 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.7899 (mtp85) outliers start: 24 outliers final: 8 residues processed: 144 average time/residue: 0.9943 time to fit residues: 154.8869 Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 67 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 16 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.113983 restraints weight = 10041.501| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.36 r_work: 0.3203 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8984 Z= 0.178 Angle : 0.492 5.387 12182 Z= 0.263 Chirality : 0.041 0.149 1395 Planarity : 0.004 0.050 1520 Dihedral : 4.721 74.996 1281 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.77 % Allowed : 12.84 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.49 (0.26), residues: 1097 helix: 2.08 (0.26), residues: 403 sheet: 0.66 (0.31), residues: 272 loop : 0.25 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.013 0.001 PHE B 151 TYR 0.016 0.001 TYR R 197 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.089 Fit side-chains REVERT: A 198 MET cc_start: 0.8295 (ttm) cc_final: 0.7824 (ttm) REVERT: A 261 ASP cc_start: 0.6826 (p0) cc_final: 0.6299 (t0) REVERT: A 354 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.4759 (m-80) REVERT: B 19 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7624 (ttp80) REVERT: B 44 GLN cc_start: 0.7222 (tt0) cc_final: 0.6983 (tt0) REVERT: B 120 ILE cc_start: 0.8095 (pt) cc_final: 0.7873 (mp) REVERT: B 164 THR cc_start: 0.8414 (m) cc_final: 0.8180 (m) REVERT: B 197 ARG cc_start: 0.8247 (ttm-80) cc_final: 0.7856 (mtp85) REVERT: E 83 MET cc_start: 0.8274 (mtm) cc_final: 0.7938 (mtp) outliers start: 17 outliers final: 4 residues processed: 144 average time/residue: 1.0524 time to fit residues: 164.8359 Evaluate side-chains 131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.156082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109334 restraints weight = 9955.680| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.39 r_work: 0.3188 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8984 Z= 0.210 Angle : 0.508 6.234 12182 Z= 0.272 Chirality : 0.041 0.153 1395 Planarity : 0.004 0.055 1520 Dihedral : 4.733 74.019 1281 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 13.99 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.26), residues: 1097 helix: 1.91 (0.26), residues: 404 sheet: 0.36 (0.31), residues: 278 loop : 0.23 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 PHE 0.016 0.001 PHE R 175 TYR 0.016 0.001 TYR R 197 ARG 0.008 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.864 Fit side-chains REVERT: A 198 MET cc_start: 0.8386 (ttm) cc_final: 0.7954 (ttm) REVERT: A 354 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.5164 (m-80) REVERT: B 19 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7647 (ttp80) REVERT: B 44 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: B 119 ASN cc_start: 0.8737 (m-40) cc_final: 0.8356 (m-40) REVERT: B 120 ILE cc_start: 0.8282 (pt) cc_final: 0.8054 (mp) REVERT: B 267 ASP cc_start: 0.8139 (m-30) cc_final: 0.7841 (m-30) REVERT: E 140 MET cc_start: 0.8955 (mmm) cc_final: 0.8266 (mmm) REVERT: G 19 LEU cc_start: 0.7728 (mt) cc_final: 0.7472 (mt) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 1.0571 time to fit residues: 159.4152 Evaluate side-chains 137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.155470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108710 restraints weight = 9981.146| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.39 r_work: 0.3100 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8984 Z= 0.206 Angle : 0.508 5.349 12182 Z= 0.274 Chirality : 0.041 0.149 1395 Planarity : 0.004 0.056 1520 Dihedral : 4.667 73.978 1279 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.19 % Allowed : 15.14 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1097 helix: 1.77 (0.26), residues: 408 sheet: 0.21 (0.31), residues: 276 loop : 0.14 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS B 183 PHE 0.017 0.001 PHE E 68 TYR 0.016 0.001 TYR R 197 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.974 Fit side-chains REVERT: A 313 ARG cc_start: 0.7067 (ptp-170) cc_final: 0.6629 (ptm160) REVERT: A 318 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7709 (tp30) REVERT: A 354 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: B 19 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7703 (ttp80) REVERT: B 44 GLN cc_start: 0.7342 (tt0) cc_final: 0.7140 (tt0) REVERT: B 120 ILE cc_start: 0.8253 (pt) cc_final: 0.8038 (mp) REVERT: B 267 ASP cc_start: 0.8300 (m-30) cc_final: 0.8017 (m-30) REVERT: B 325 MET cc_start: 0.8775 (tpp) cc_final: 0.8569 (mmm) REVERT: E 83 MET cc_start: 0.8459 (mtm) cc_final: 0.8091 (mtp) REVERT: E 140 MET cc_start: 0.8999 (mmm) cc_final: 0.8129 (mmm) REVERT: G 19 LEU cc_start: 0.7777 (mt) cc_final: 0.7537 (mt) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 0.9837 time to fit residues: 149.3568 Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 5.9990 chunk 78 optimal weight: 0.0000 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.109518 restraints weight = 9933.115| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.34 r_work: 0.3093 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8984 Z= 0.188 Angle : 0.496 5.271 12182 Z= 0.268 Chirality : 0.041 0.148 1395 Planarity : 0.004 0.056 1520 Dihedral : 4.594 74.409 1279 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.40 % Allowed : 16.39 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.06 (0.26), residues: 1097 helix: 1.81 (0.26), residues: 408 sheet: 0.11 (0.31), residues: 277 loop : 0.15 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.015 0.001 PHE E 68 TYR 0.017 0.001 TYR R 197 ARG 0.009 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.894 Fit side-chains REVERT: A 198 MET cc_start: 0.8037 (mtp) cc_final: 0.7808 (ttm) REVERT: A 318 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7703 (tt0) REVERT: B 19 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7735 (ttp80) REVERT: B 120 ILE cc_start: 0.8250 (pt) cc_final: 0.8038 (mp) REVERT: B 163 ASP cc_start: 0.7405 (t0) cc_final: 0.7183 (t0) REVERT: B 197 ARG cc_start: 0.8208 (ttm-80) cc_final: 0.7909 (mtp85) REVERT: B 267 ASP cc_start: 0.8304 (m-30) cc_final: 0.8032 (m-30) REVERT: B 325 MET cc_start: 0.8760 (tpp) cc_final: 0.8509 (mmm) REVERT: E 83 MET cc_start: 0.8459 (mtm) cc_final: 0.8064 (mtp) REVERT: E 140 MET cc_start: 0.8980 (mmm) cc_final: 0.8079 (mmm) REVERT: G 19 LEU cc_start: 0.7744 (mt) cc_final: 0.7498 (mt) outliers start: 23 outliers final: 13 residues processed: 141 average time/residue: 0.8886 time to fit residues: 136.3574 Evaluate side-chains 139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 67 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 95 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.171206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132702 restraints weight = 9550.007| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.21 r_work: 0.3359 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8984 Z= 0.181 Angle : 0.492 5.341 12182 Z= 0.265 Chirality : 0.040 0.148 1395 Planarity : 0.004 0.058 1520 Dihedral : 4.397 74.691 1277 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.40 % Allowed : 17.22 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1097 helix: 1.85 (0.26), residues: 408 sheet: 0.12 (0.31), residues: 276 loop : 0.12 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.014 0.001 PHE E 68 TYR 0.017 0.001 TYR R 197 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.902 Fit side-chains REVERT: A 318 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 19 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7846 (ttp80) REVERT: B 163 ASP cc_start: 0.7445 (t0) cc_final: 0.7231 (t0) REVERT: B 197 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.8113 (mtp85) REVERT: B 267 ASP cc_start: 0.8268 (m-30) cc_final: 0.7986 (m-30) REVERT: B 325 MET cc_start: 0.8819 (tpp) cc_final: 0.8584 (mmm) REVERT: E 83 MET cc_start: 0.8649 (mtm) cc_final: 0.8237 (mtp) REVERT: E 140 MET cc_start: 0.9007 (mmm) cc_final: 0.8106 (mmm) REVERT: G 19 LEU cc_start: 0.8130 (mt) cc_final: 0.7851 (mt) outliers start: 23 outliers final: 16 residues processed: 141 average time/residue: 0.9216 time to fit residues: 141.4308 Evaluate side-chains 140 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132453 restraints weight = 9624.068| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.20 r_work: 0.3361 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8984 Z= 0.185 Angle : 0.505 9.833 12182 Z= 0.269 Chirality : 0.041 0.148 1395 Planarity : 0.004 0.059 1520 Dihedral : 4.398 74.419 1277 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.98 % Allowed : 18.16 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1097 helix: 1.88 (0.26), residues: 409 sheet: 0.10 (0.31), residues: 274 loop : 0.08 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.014 0.001 PHE R 175 TYR 0.017 0.001 TYR R 197 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.877 Fit side-chains REVERT: A 318 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: B 163 ASP cc_start: 0.7471 (t0) cc_final: 0.7241 (t0) REVERT: B 197 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8094 (mtp85) REVERT: B 267 ASP cc_start: 0.8267 (m-30) cc_final: 0.7997 (m-30) REVERT: B 325 MET cc_start: 0.8820 (tpp) cc_final: 0.8585 (mmm) REVERT: E 83 MET cc_start: 0.8606 (mtm) cc_final: 0.8232 (mtp) REVERT: E 140 MET cc_start: 0.9017 (mmm) cc_final: 0.8107 (mmm) REVERT: G 19 LEU cc_start: 0.8126 (mt) cc_final: 0.7839 (mt) outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 0.9412 time to fit residues: 136.4403 Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 50 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.0020 chunk 81 optimal weight: 0.0670 chunk 19 optimal weight: 0.0060 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 overall best weight: 0.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.136716 restraints weight = 9533.975| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.21 r_work: 0.3423 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8984 Z= 0.141 Angle : 0.493 8.939 12182 Z= 0.262 Chirality : 0.040 0.145 1395 Planarity : 0.004 0.059 1520 Dihedral : 4.322 75.315 1277 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.77 % Allowed : 18.58 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.16 (0.26), residues: 1097 helix: 2.05 (0.26), residues: 405 sheet: 0.15 (0.31), residues: 271 loop : 0.04 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.000 HIS E 35 PHE 0.011 0.001 PHE B 151 TYR 0.018 0.001 TYR R 197 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.887 Fit side-chains REVERT: A 318 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7371 (tt0) REVERT: B 119 ASN cc_start: 0.8672 (m-40) cc_final: 0.8304 (m-40) REVERT: B 197 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8060 (mtp85) REVERT: B 267 ASP cc_start: 0.8086 (m-30) cc_final: 0.7788 (m-30) REVERT: B 303 ASP cc_start: 0.7355 (m-30) cc_final: 0.6838 (p0) REVERT: E 83 MET cc_start: 0.8631 (mtm) cc_final: 0.8228 (mtp) REVERT: E 140 MET cc_start: 0.8862 (mmm) cc_final: 0.8046 (mmm) REVERT: G 19 LEU cc_start: 0.8140 (mt) cc_final: 0.7868 (mt) REVERT: G 21 MET cc_start: 0.7157 (tmm) cc_final: 0.6779 (tmm) outliers start: 17 outliers final: 13 residues processed: 139 average time/residue: 0.9554 time to fit residues: 143.7863 Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.170680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132117 restraints weight = 9639.866| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.21 r_work: 0.3361 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8984 Z= 0.207 Angle : 0.532 8.961 12182 Z= 0.280 Chirality : 0.041 0.149 1395 Planarity : 0.004 0.059 1520 Dihedral : 4.392 73.704 1277 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.57 % Allowed : 19.10 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1097 helix: 1.95 (0.26), residues: 404 sheet: 0.07 (0.30), residues: 279 loop : 0.04 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE R 175 TYR 0.017 0.001 TYR R 197 ARG 0.010 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 1.012 Fit side-chains REVERT: A 313 ARG cc_start: 0.7055 (ptp-110) cc_final: 0.6712 (ptm160) REVERT: A 318 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: B 163 ASP cc_start: 0.7487 (t0) cc_final: 0.7253 (t0) REVERT: B 197 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8075 (mtp85) REVERT: B 267 ASP cc_start: 0.8311 (m-30) cc_final: 0.8044 (m-30) REVERT: B 303 ASP cc_start: 0.7576 (m-30) cc_final: 0.7014 (p0) REVERT: E 83 MET cc_start: 0.8612 (mtm) cc_final: 0.8178 (mtp) REVERT: E 140 MET cc_start: 0.9032 (mmm) cc_final: 0.8081 (mmm) REVERT: G 19 LEU cc_start: 0.8170 (mt) cc_final: 0.7888 (mt) outliers start: 15 outliers final: 10 residues processed: 134 average time/residue: 1.0384 time to fit residues: 150.6184 Evaluate side-chains 136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 8.9990 chunk 83 optimal weight: 0.0370 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.170313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.132330 restraints weight = 9602.891| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.16 r_work: 0.3366 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8984 Z= 0.206 Angle : 0.546 8.817 12182 Z= 0.286 Chirality : 0.041 0.148 1395 Planarity : 0.004 0.059 1520 Dihedral : 4.448 73.026 1277 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.46 % Allowed : 19.62 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.02 (0.26), residues: 1097 helix: 1.91 (0.26), residues: 408 sheet: -0.04 (0.30), residues: 279 loop : 0.06 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE E 68 TYR 0.017 0.001 TYR R 197 ARG 0.010 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7428.20 seconds wall clock time: 128 minutes 50.01 seconds (7730.01 seconds total)