Starting phenix.real_space_refine on Sun May 3 22:33:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyq_42817/05_2026/8uyq_42817_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyq_42817/05_2026/8uyq_42817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uyq_42817/05_2026/8uyq_42817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyq_42817/05_2026/8uyq_42817.map" model { file = "/net/cci-nas-00/data/ceres_data/8uyq_42817/05_2026/8uyq_42817_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyq_42817/05_2026/8uyq_42817_neut_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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: 5 Type Number sf(0) Gaussians S 57 5.16 5 C 5251 2.51 5 N 1426 2.21 5 O 1506 1.98 5 H 8239 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16479 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4974 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain: "N" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1890 Classifications: {'peptide': 126} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "X" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3632 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Chain: "Y" Number of atoms: 5106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5106 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "Z" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'XVT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.53, per 1000 atoms: 0.21 Number of scatterers: 16479 At special positions: 0 Unit cell: (83.888, 99.296, 139.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 57 16.00 O 1506 8.00 N 1426 7.00 C 5251 6.00 H 8239 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.44 Conformation dependent library (CDL) restraints added in 586.6 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 43.6% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 Processing helix chain 'A' and resid 56 through 86 removed outlier: 3.750A pdb=" N PHE A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 71 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 93 through 127 removed outlier: 3.547A pdb=" N TYR A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 136 through 163 removed outlier: 3.618A pdb=" N CYS A 140 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLN A 158 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N PHE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 162 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 187 removed outlier: 4.092A pdb=" N LYS A 185 " --> pdb=" O PRO A 181 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 224 removed outlier: 3.992A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 231 through 258 removed outlier: 3.671A pdb=" N ALA A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 265 through 276 removed outlier: 4.187A pdb=" N PHE A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TYR A 274 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.565A pdb=" N LEU A 281 " --> pdb=" O ILE A 277 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 291 through 304 removed outlier: 3.916A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.623A 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: 3.598A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 40 Processing helix chain 'X' and resid 52 through 60 removed outlier: 3.987A pdb=" N MET X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.808A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 Processing helix chain 'X' and resid 280 through 283 removed outlier: 3.896A pdb=" N ARG X 283 " --> pdb=" O ARG X 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 280 through 283' Processing helix chain 'X' and resid 293 through 303 Processing helix chain 'X' and resid 307 through 312 removed outlier: 4.061A pdb=" N TYR X 311 " --> pdb=" O LYS X 307 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 318 Processing helix chain 'X' and resid 331 through 351 removed outlier: 4.097A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'Y' and resid 4 through 26 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Z' and resid 8 through 24 Processing helix chain 'Z' and resid 29 through 45 Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 7.998A pdb=" N ILE A 173 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 12 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.697A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 207 through 214 removed outlier: 6.287A pdb=" N HIS X 41 " --> pdb=" O HIS X 220 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE X 222 " --> pdb=" O HIS X 41 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU X 43 " --> pdb=" O PHE X 222 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL X 224 " --> pdb=" O LEU X 43 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU X 45 " --> pdb=" O VAL X 224 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG X 42 " --> pdb=" O ALA X 243 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE X 245 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N LEU X 44 " --> pdb=" O ILE X 245 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL X 247 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU X 46 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP X 249 " --> pdb=" O LEU X 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 46 through 51 removed outlier: 5.369A pdb=" N THR Y 47 " --> pdb=" O ASN Y 340 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN Y 340 " --> pdb=" O THR Y 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 58 through 63 Processing sheet with id=AA7, first strand: chain 'Y' and resid 102 through 105 removed outlier: 3.569A pdb=" N GLY Y 115 " --> pdb=" O THR Y 102 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Y' and resid 146 through 151 removed outlier: 4.086A pdb=" N THR Y 165 " --> pdb=" O SER Y 161 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 187 through 192 removed outlier: 4.176A pdb=" N SER Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 229 through 234 removed outlier: 6.587A pdb=" N CYS Y 250 " --> pdb=" O THR Y 263 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR Y 263 " --> pdb=" O CYS Y 250 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU Y 252 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN Y 259 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Y' and resid 273 through 278 removed outlier: 6.643A pdb=" N GLY Y 288 " --> pdb=" O THR Y 274 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL Y 276 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LEU Y 286 " --> pdb=" O VAL Y 276 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE Y 278 " --> pdb=" O LEU Y 284 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU Y 284 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY Y 306 " --> pdb=" O VAL Y 296 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1173 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: 3.70 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6751 1.03 - 1.23: 1640 1.23 - 1.43: 3406 1.43 - 1.62: 4769 1.62 - 1.82: 81 Bond restraints: 16647 Sorted by residual: bond pdb=" C VAL A 75 " pdb=" O VAL A 75 " ideal model delta sigma weight residual 1.236 1.415 -0.178 1.11e-02 8.12e+03 2.58e+02 bond pdb=" C TYR A 72 " pdb=" O TYR A 72 " ideal model delta sigma weight residual 1.236 1.390 -0.153 1.15e-02 7.56e+03 1.78e+02 bond pdb=" C ILE A 81 " pdb=" O ILE A 81 " ideal model delta sigma weight residual 1.237 1.348 -0.111 1.19e-02 7.06e+03 8.66e+01 bond pdb=" C GLU A 21 " pdb=" O GLU A 21 " ideal model delta sigma weight residual 1.237 1.328 -0.092 1.16e-02 7.43e+03 6.26e+01 bond pdb=" CAB XVT A 401 " pdb=" NAC XVT A 401 " ideal model delta sigma weight residual 1.488 1.335 0.153 2.00e-02 2.50e+03 5.87e+01 ... (remaining 16642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.47: 29897 11.47 - 22.94: 33 22.94 - 34.41: 0 34.41 - 45.88: 1 45.88 - 57.35: 51 Bond angle restraints: 29982 Sorted by residual: angle pdb=" C LEU Y 318 " pdb=" N GLY Y 319 " pdb=" H GLY Y 319 " ideal model delta sigma weight residual 124.52 67.16 57.35 3.00e+00 1.11e-01 3.65e+02 angle pdb=" CA GLY Y 319 " pdb=" N GLY Y 319 " pdb=" H GLY Y 319 " ideal model delta sigma weight residual 114.22 58.64 55.57 3.00e+00 1.11e-01 3.43e+02 angle pdb=" C LEU X 46 " pdb=" N GLY X 47 " pdb=" H GLY X 47 " ideal model delta sigma weight residual 124.72 70.95 53.77 3.00e+00 1.11e-01 3.21e+02 angle pdb=" C GLY N 9 " pdb=" N GLY N 10 " pdb=" H GLY N 10 " ideal model delta sigma weight residual 124.87 71.29 53.58 3.00e+00 1.11e-01 3.19e+02 angle pdb=" CA GLY X 47 " pdb=" N GLY X 47 " pdb=" H GLY X 47 " ideal model delta sigma weight residual 114.42 61.40 53.02 3.00e+00 1.11e-01 3.12e+02 ... (remaining 29977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7085 17.76 - 35.51: 505 35.51 - 53.27: 150 53.27 - 71.02: 85 71.02 - 88.78: 16 Dihedral angle restraints: 7841 sinusoidal: 4224 harmonic: 3617 Sorted by residual: dihedral pdb=" N TYR A 72 " pdb=" C TYR A 72 " pdb=" CA TYR A 72 " pdb=" CB TYR A 72 " ideal model delta harmonic sigma weight residual 122.80 111.52 11.28 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" C THR A 76 " pdb=" N THR A 76 " pdb=" CA THR A 76 " pdb=" CB THR A 76 " ideal model delta harmonic sigma weight residual -122.00 -132.52 10.52 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" CA PHE Y 234 " pdb=" C PHE Y 234 " pdb=" N PHE Y 235 " pdb=" CA PHE Y 235 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 7838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.775: 1300 0.775 - 1.549: 0 1.549 - 2.323: 0 2.323 - 3.098: 0 3.098 - 3.872: 2 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CB ILE X 308 " pdb=" CA ILE X 308 " pdb=" CG1 ILE X 308 " pdb=" CG2 ILE X 308 " both_signs ideal model delta sigma weight residual False 2.64 -1.23 3.87 2.00e-01 2.50e+01 3.75e+02 chirality pdb=" CAB XVT A 401 " pdb=" CAA XVT A 401 " pdb=" NAC XVT A 401 " pdb=" SAF XVT A 401 " both_signs ideal model delta sigma weight residual False 3.38 0.28 3.10 2.00e-01 2.50e+01 2.40e+02 chirality pdb=" CA PRO A 181 " pdb=" N PRO A 181 " pdb=" C PRO A 181 " pdb=" CB PRO A 181 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1299 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 23 " 0.116 2.00e-02 2.50e+03 1.25e-01 2.34e+02 pdb=" CD GLN A 23 " -0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN A 23 " -0.113 2.00e-02 2.50e+03 pdb=" NE2 GLN A 23 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN A 23 " -0.184 2.00e-02 2.50e+03 pdb="HE22 GLN A 23 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 41 " -0.081 2.00e-02 2.50e+03 8.89e-02 1.19e+02 pdb=" CG ASN A 41 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 41 " 0.084 2.00e-02 2.50e+03 pdb=" ND2 ASN A 41 " -0.007 2.00e-02 2.50e+03 pdb="HD21 ASN A 41 " 0.132 2.00e-02 2.50e+03 pdb="HD22 ASN A 41 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 282 " -0.079 2.00e-02 2.50e+03 7.19e-02 7.75e+01 pdb=" CG ASN A 282 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 282 " 0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN A 282 " 0.062 2.00e-02 2.50e+03 pdb="HD21 ASN A 282 " 0.062 2.00e-02 2.50e+03 pdb="HD22 ASN A 282 " -0.119 2.00e-02 2.50e+03 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 0.06 - 0.97: 4 0.97 - 1.88: 155 1.88 - 2.78: 32633 2.78 - 3.69: 74243 3.69 - 4.60: 128054 Warning: very small nonbonded interaction distances. Nonbonded interactions: 235089 Sorted by model distance: nonbonded pdb=" CD LYS A 310 " pdb=" HG3 ARG Y 46 " model vdw 0.062 2.920 nonbonded pdb=" HZ2 LYS A 310 " pdb=" HB3 ARG Y 46 " model vdw 0.373 1.816 nonbonded pdb=" HZ1 LYS A 310 " pdb=" CA ARG Y 46 " model vdw 0.435 2.200 nonbonded pdb=" HE2 LYS A 310 " pdb=" HB2 ARG Y 46 " model vdw 0.746 2.440 nonbonded pdb=" CD LYS A 310 " pdb=" CG ARG Y 46 " model vdw 0.971 3.400 ... (remaining 235084 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 group one per residue 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.240 Find NCS groups from input model: 0.050 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4383 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 : 0.013 0.837 8409 Z= 1.113 Angle : 1.373 20.736 11384 Z= 0.909 Chirality : 0.152 3.872 1302 Planarity : 0.009 0.161 1441 Dihedral : 13.772 88.780 3052 Min Nonbonded Distance : 0.971 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.66 % Allowed : 0.66 % Favored : 98.68 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.26), residues: 1024 helix: 1.33 (0.26), residues: 385 sheet: -0.99 (0.34), residues: 204 loop : -0.34 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Y 219 TYR 0.074 0.006 TYR A 72 PHE 0.032 0.004 PHE A 210 TRP 0.047 0.005 TRP A 301 HIS 0.008 0.002 HIS Y 142 Details of bonding type rmsd covalent geometry : bond 0.00928 ( 8408) covalent geometry : angle 1.37342 (11384) hydrogen bonds : bond 0.18402 ( 415) hydrogen bonds : angle 7.04714 ( 1173) Misc. bond : bond 0.83689 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 180 time to evaluate : 0.427 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.6059 (m-80) cc_final: 0.5563 (m-10) REVERT: A 137 ARG cc_start: 0.6762 (ttt90) cc_final: 0.6366 (tpm170) REVERT: N 2 VAL cc_start: 0.7267 (t) cc_final: 0.7058 (m) REVERT: N 112 SER cc_start: 0.6763 (m) cc_final: 0.6501 (t) REVERT: X 239 ASN cc_start: 0.7393 (p0) cc_final: 0.7081 (p0) REVERT: Y 189 SER cc_start: 0.7269 (t) cc_final: 0.6875 (m) outliers start: 6 outliers final: 2 residues processed: 184 average time/residue: 0.2380 time to fit residues: 57.8454 Evaluate side-chains 112 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PRO Chi-restraints excluded: chain A residue 259 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN X 19 GLN ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.258179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.226070 restraints weight = 26880.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.232040 restraints weight = 17655.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.235493 restraints weight = 13274.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.238181 restraints weight = 10946.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.239285 restraints weight = 9540.322| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5630 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8409 Z= 0.213 Angle : 0.976 20.783 11384 Z= 0.568 Chirality : 0.060 1.470 1302 Planarity : 0.006 0.117 1441 Dihedral : 5.002 34.382 1146 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.43 % Allowed : 7.40 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 1024 helix: 1.77 (0.26), residues: 387 sheet: -1.20 (0.32), residues: 214 loop : -0.44 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG Y 46 TYR 0.028 0.002 TYR A 72 PHE 0.026 0.002 PHE A 93 TRP 0.016 0.002 TRP Y 339 HIS 0.007 0.002 HIS Y 183 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8408) covalent geometry : angle 0.97596 (11384) hydrogen bonds : bond 0.06864 ( 415) hydrogen bonds : angle 5.09654 ( 1173) Misc. bond : bond 0.02561 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.330 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 PHE cc_start: 0.6757 (m-80) cc_final: 0.6240 (m-10) REVERT: A 135 MET cc_start: 0.6405 (mmt) cc_final: 0.6127 (mmt) REVERT: N 112 SER cc_start: 0.7649 (m) cc_final: 0.7430 (t) outliers start: 13 outliers final: 6 residues processed: 145 average time/residue: 0.2044 time to fit residues: 40.5711 Evaluate side-chains 118 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain X residue 213 GLN Chi-restraints excluded: chain Y residue 46 ARG Chi-restraints excluded: chain Y residue 294 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 220 GLN Z 18 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.272489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.260762 restraints weight = 24727.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.249561 restraints weight = 31189.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.249998 restraints weight = 19761.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.253412 restraints weight = 16077.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.254265 restraints weight = 12674.173| |-----------------------------------------------------------------------------| r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.6191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8409 Z= 0.174 Angle : 0.915 20.779 11384 Z= 0.531 Chirality : 0.065 1.797 1302 Planarity : 0.005 0.108 1441 Dihedral : 4.339 20.477 1139 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.88 % Allowed : 9.38 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1024 helix: 2.00 (0.26), residues: 404 sheet: -0.90 (0.34), residues: 206 loop : -0.71 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG Y 46 TYR 0.022 0.002 TYR Y 59 PHE 0.018 0.002 PHE A 176 TRP 0.018 0.002 TRP Y 82 HIS 0.006 0.001 HIS Y 62 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8408) covalent geometry : angle 0.91463 (11384) hydrogen bonds : bond 0.05502 ( 415) hydrogen bonds : angle 4.60081 ( 1173) Misc. bond : bond 0.01458 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.410 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 MET cc_start: 0.6543 (mmt) cc_final: 0.6260 (mmt) REVERT: X 386 MET cc_start: 0.7968 (tmm) cc_final: 0.7681 (ttm) REVERT: X 391 TYR cc_start: 0.3939 (m-80) cc_final: 0.3647 (m-80) REVERT: Y 138 GLU cc_start: 0.6230 (pm20) cc_final: 0.5871 (pt0) outliers start: 8 outliers final: 6 residues processed: 131 average time/residue: 0.1621 time to fit residues: 30.8155 Evaluate side-chains 114 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain X residue 213 GLN Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 294 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN X 218 ASN Y 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.234296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.206347 restraints weight = 24200.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.209394 restraints weight = 17793.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.211402 restraints weight = 14424.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.212244 restraints weight = 12523.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.213502 restraints weight = 11543.377| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.7845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8409 Z= 0.162 Angle : 0.913 20.547 11384 Z= 0.530 Chirality : 0.058 1.483 1302 Planarity : 0.006 0.116 1441 Dihedral : 4.278 20.200 1139 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.66 % Allowed : 9.93 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1024 helix: 2.20 (0.26), residues: 397 sheet: -0.88 (0.35), residues: 195 loop : -0.69 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG X 342 TYR 0.021 0.002 TYR Y 59 PHE 0.016 0.002 PHE A 93 TRP 0.013 0.002 TRP X 234 HIS 0.004 0.001 HIS Y 142 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8408) covalent geometry : angle 0.91309 (11384) hydrogen bonds : bond 0.05354 ( 415) hydrogen bonds : angle 4.51083 ( 1173) Misc. bond : bond 0.01686 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.414 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: 15 outliers final: 9 residues processed: 128 average time/residue: 0.1915 time to fit residues: 34.0005 Evaluate side-chains 109 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 213 GLN Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Y residue 294 CYS Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.221492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.205383 restraints weight = 24261.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.204488 restraints weight = 33973.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.205092 restraints weight = 29433.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.205237 restraints weight = 22100.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.205277 restraints weight = 21206.539| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.8908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8409 Z= 0.145 Angle : 0.878 20.902 11384 Z= 0.514 Chirality : 0.060 1.606 1302 Planarity : 0.004 0.054 1441 Dihedral : 4.058 19.971 1139 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.88 % Allowed : 12.47 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1024 helix: 2.29 (0.26), residues: 402 sheet: -1.01 (0.35), residues: 200 loop : -0.75 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 67 TYR 0.022 0.001 TYR Y 59 PHE 0.017 0.002 PHE X 312 TRP 0.012 0.001 TRP Y 82 HIS 0.004 0.001 HIS X 41 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8408) covalent geometry : angle 0.87799 (11384) hydrogen bonds : bond 0.05200 ( 415) hydrogen bonds : angle 4.42817 ( 1173) Misc. bond : bond 0.01441 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.412 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: N 70 ILE cc_start: 0.7291 (tt) cc_final: 0.7001 (tp) REVERT: Y 192 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8172 (mp) REVERT: Y 261 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.5925 (mp) outliers start: 17 outliers final: 11 residues processed: 120 average time/residue: 0.1779 time to fit residues: 30.2573 Evaluate side-chains 113 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain X residue 213 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Y residue 201 SER Chi-restraints excluded: chain Y residue 234 PHE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 266 HIS Chi-restraints excluded: chain Y residue 294 CYS Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.217414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195463 restraints weight = 24232.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.194963 restraints weight = 25643.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.195944 restraints weight = 23546.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.196000 restraints weight = 19823.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.196120 restraints weight = 17322.903| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.9508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8409 Z= 0.120 Angle : 0.854 20.326 11384 Z= 0.501 Chirality : 0.059 1.590 1302 Planarity : 0.004 0.039 1441 Dihedral : 3.902 19.633 1139 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.55 % Allowed : 13.69 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.27), residues: 1024 helix: 2.67 (0.26), residues: 389 sheet: -0.97 (0.35), residues: 197 loop : -0.67 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Y 219 TYR 0.007 0.001 TYR X 391 PHE 0.014 0.001 PHE A 93 TRP 0.013 0.001 TRP Y 169 HIS 0.003 0.001 HIS X 41 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8408) covalent geometry : angle 0.85434 (11384) hydrogen bonds : bond 0.04825 ( 415) hydrogen bonds : angle 4.27562 ( 1173) Misc. bond : bond 0.01699 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.440 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.7283 (ttmt) cc_final: 0.7079 (ttmt) REVERT: Y 192 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8198 (mp) REVERT: Y 261 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6103 (mp) outliers start: 14 outliers final: 6 residues processed: 119 average time/residue: 0.1921 time to fit residues: 32.2111 Evaluate side-chains 107 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain X residue 213 GLN Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 179 THR Chi-restraints excluded: chain Y residue 192 LEU Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 266 HIS Chi-restraints excluded: chain Y residue 294 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN X 213 GLN X 239 ASN Y 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.227690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.195684 restraints weight = 25428.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.193917 restraints weight = 39803.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.196426 restraints weight = 28303.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.196946 restraints weight = 20452.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.197302 restraints weight = 18130.319| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 1.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8409 Z= 0.229 Angle : 0.984 20.618 11384 Z= 0.571 Chirality : 0.061 1.498 1302 Planarity : 0.005 0.043 1441 Dihedral : 4.691 20.612 1139 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.43 % Allowed : 13.02 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1024 helix: 1.70 (0.26), residues: 394 sheet: -1.31 (0.33), residues: 235 loop : -0.97 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Y 214 TYR 0.022 0.002 TYR Y 59 PHE 0.022 0.002 PHE N 29 TRP 0.017 0.003 TRP N 47 HIS 0.005 0.001 HIS X 387 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 8408) covalent geometry : angle 0.98433 (11384) hydrogen bonds : bond 0.07535 ( 415) hydrogen bonds : angle 4.91387 ( 1173) Misc. bond : bond 0.01308 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.423 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: symmetry clash revert: symmetry clash REVERT: N 73 ASP cc_start: 0.6210 (OUTLIER) cc_final: 0.5985 (t0) REVERT: N 83 MET cc_start: 0.7170 (ptp) cc_final: 0.6753 (ptp) REVERT: Y 49 ARG cc_start: 0.7792 (tpp80) cc_final: 0.7296 (mtp85) REVERT: Y 261 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6874 (mp) REVERT: Y 262 MET cc_start: 0.7254 (mtm) cc_final: 0.7045 (mtp) REVERT: Z 22 GLU cc_start: 0.6150 (pt0) cc_final: 0.5927 (pt0) outliers start: 22 outliers final: 11 residues processed: 125 average time/residue: 0.2374 time to fit residues: 39.6848 Evaluate side-chains 107 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain X residue 213 GLN Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 266 HIS Chi-restraints excluded: chain Y residue 294 CYS Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.228668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.192156 restraints weight = 25633.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.191709 restraints weight = 26389.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.193558 restraints weight = 23512.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.193988 restraints weight = 19431.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.194512 restraints weight = 18533.773| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 1.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 8409 Z= 0.153 Angle : 0.883 20.041 11384 Z= 0.519 Chirality : 0.059 1.561 1302 Planarity : 0.004 0.058 1441 Dihedral : 4.275 20.972 1139 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.10 % Allowed : 14.24 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.26), residues: 1024 helix: 2.24 (0.26), residues: 389 sheet: -1.10 (0.34), residues: 223 loop : -1.00 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 67 TYR 0.009 0.001 TYR Y 59 PHE 0.016 0.002 PHE A 93 TRP 0.016 0.002 TRP Y 169 HIS 0.005 0.001 HIS Y 91 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8408) covalent geometry : angle 0.88329 (11384) hydrogen bonds : bond 0.05904 ( 415) hydrogen bonds : angle 4.58249 ( 1173) Misc. bond : bond 0.01593 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.418 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: symmetry clash REVERT: Y 49 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7343 (mtp85) REVERT: Y 261 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.7010 (mp) REVERT: Y 262 MET cc_start: 0.7234 (mtm) cc_final: 0.7015 (mtp) outliers start: 10 outliers final: 7 residues processed: 106 average time/residue: 0.2392 time to fit residues: 33.8231 Evaluate side-chains 99 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 266 HIS Chi-restraints excluded: chain Y residue 294 CYS Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.228337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.189638 restraints weight = 27161.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.187506 restraints weight = 33201.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.191574 restraints weight = 23892.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.192857 restraints weight = 15171.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.196486 restraints weight = 12614.507| |-----------------------------------------------------------------------------| r_work (final): 0.4306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 1.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8409 Z= 0.130 Angle : 0.870 20.162 11384 Z= 0.510 Chirality : 0.059 1.589 1302 Planarity : 0.004 0.041 1441 Dihedral : 4.061 19.197 1139 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.10 % Allowed : 15.23 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1024 helix: 2.47 (0.26), residues: 389 sheet: -1.00 (0.35), residues: 221 loop : -1.00 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.009 0.001 TYR X 339 PHE 0.015 0.001 PHE A 27 TRP 0.016 0.002 TRP Y 169 HIS 0.004 0.001 HIS X 41 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8408) covalent geometry : angle 0.86972 (11384) hydrogen bonds : bond 0.05334 ( 415) hydrogen bonds : angle 4.39914 ( 1173) Misc. bond : bond 0.01650 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 261 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6960 (mp) REVERT: Y 262 MET cc_start: 0.7225 (mtm) cc_final: 0.7018 (mtp) REVERT: Z 38 MET cc_start: 0.5649 (ppp) cc_final: 0.4878 (ptm) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.2433 time to fit residues: 34.1788 Evaluate side-chains 100 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 266 HIS Chi-restraints excluded: chain Y residue 294 CYS Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.229179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.189898 restraints weight = 27134.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.189461 restraints weight = 30809.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.193097 restraints weight = 21518.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.194678 restraints weight = 14197.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.195314 restraints weight = 12106.167| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 1.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8409 Z= 0.124 Angle : 0.866 20.117 11384 Z= 0.508 Chirality : 0.059 1.586 1302 Planarity : 0.004 0.051 1441 Dihedral : 3.945 19.610 1139 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.99 % Allowed : 15.56 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.27), residues: 1024 helix: 2.60 (0.26), residues: 389 sheet: -0.75 (0.36), residues: 201 loop : -0.98 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 67 TYR 0.007 0.001 TYR Y 59 PHE 0.011 0.001 PHE A 27 TRP 0.015 0.002 TRP Y 169 HIS 0.004 0.001 HIS X 41 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8408) covalent geometry : angle 0.86564 (11384) hydrogen bonds : bond 0.04990 ( 415) hydrogen bonds : angle 4.26616 ( 1173) Misc. bond : bond 0.01669 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 43 LYS cc_start: 0.7280 (mptt) cc_final: 0.6842 (mptt) outliers start: 9 outliers final: 8 residues processed: 106 average time/residue: 0.2081 time to fit residues: 30.4243 Evaluate side-chains 98 residues out of total 906 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 225 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 266 HIS Chi-restraints excluded: chain Y residue 294 CYS Chi-restraints excluded: chain Z residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.231685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.196002 restraints weight = 27143.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.194907 restraints weight = 37156.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.197049 restraints weight = 24251.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.198152 restraints weight = 16280.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.198618 restraints weight = 13094.644| |-----------------------------------------------------------------------------| r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 1.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 8409 Z= 0.129 Angle : 0.866 20.090 11384 Z= 0.508 Chirality : 0.059 1.568 1302 Planarity : 0.004 0.043 1441 Dihedral : 3.934 18.585 1139 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.21 % Allowed : 14.90 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.27), residues: 1024 helix: 2.60 (0.26), residues: 389 sheet: -0.77 (0.36), residues: 203 loop : -0.97 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 67 TYR 0.010 0.001 TYR N 60 PHE 0.014 0.001 PHE A 27 TRP 0.013 0.002 TRP Y 169 HIS 0.004 0.001 HIS X 41 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8408) covalent geometry : angle 0.86603 (11384) hydrogen bonds : bond 0.05106 ( 415) hydrogen bonds : angle 4.27720 ( 1173) Misc. bond : bond 0.01640 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2920.07 seconds wall clock time: 50 minutes 29.01 seconds (3029.01 seconds total)