Starting phenix.real_space_refine on Fri Jul 19 03:52:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/07_2024/8unz_42422.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/07_2024/8unz_42422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/07_2024/8unz_42422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/07_2024/8unz_42422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/07_2024/8unz_42422.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unz_42422/07_2024/8unz_42422.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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 P 3 5.49 5 S 38 5.16 5 C 4059 2.51 5 N 1097 2.21 5 O 1132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6329 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1554 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 394 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 228 Chain: "B" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2376 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 154 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 146 Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 348 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 2004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2004 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 7, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 351 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 163 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.71, per 1000 atoms: 0.74 Number of scatterers: 6329 At special positions: 0 Unit cell: (85.0346, 136.229, 98.9178, 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 38 16.00 P 3 15.00 O 1132 8.00 N 1097 7.00 C 4059 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 47.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 11 through 40 removed outlier: 3.614A pdb=" N ASN A 23 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.832A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 removed outlier: 4.509A pdb=" N ASN A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 254' Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.583A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.541A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 331 through 354 removed outlier: 3.671A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASP A 354 " --> pdb=" O THR A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.715A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.527A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 22 removed outlier: 3.774A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.562A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 61 removed outlier: 3.695A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.701A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 4.158A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.930A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.894A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.541A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 237 removed outlier: 3.833A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 4.768A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.842A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.693A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 removed outlier: 3.828A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.584A pdb=" N ALA R 335 " --> pdb=" O ASP R 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.795A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.964A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.207A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.690A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.006A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.885A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.632A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 252 removed outlier: 3.627A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.002A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2039 1.34 - 1.46: 1305 1.46 - 1.58: 3065 1.58 - 1.70: 5 1.70 - 1.82: 50 Bond restraints: 6464 Sorted by residual: bond pdb=" N VAL R 39 " pdb=" CA VAL R 39 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.18e+00 bond pdb=" N THR R 66 " pdb=" CA THR R 66 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.16e-02 7.43e+03 7.96e+00 bond pdb=" N VAL R 48 " pdb=" CA VAL R 48 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.86e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.451 -0.054 2.00e-02 2.50e+03 7.22e+00 bond pdb=" N ASN A 254 " pdb=" CA ASN A 254 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.33e-02 5.65e+03 7.15e+00 ... (remaining 6459 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.07: 156 107.07 - 113.82: 3704 113.82 - 120.56: 2595 120.56 - 127.31: 2334 127.31 - 134.05: 79 Bond angle restraints: 8868 Sorted by residual: angle pdb=" N SER G 8 " pdb=" CA SER G 8 " pdb=" C SER G 8 " ideal model delta sigma weight residual 111.28 105.00 6.28 1.09e+00 8.42e-01 3.32e+01 angle pdb=" N MET R 40 " pdb=" CA MET R 40 " pdb=" C MET R 40 " ideal model delta sigma weight residual 111.28 105.47 5.81 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N GLN A 19 " pdb=" CA GLN A 19 " pdb=" C GLN A 19 " ideal model delta sigma weight residual 111.71 105.92 5.79 1.15e+00 7.56e-01 2.54e+01 angle pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" C ASN A 371 " ideal model delta sigma weight residual 113.72 107.41 6.31 1.30e+00 5.92e-01 2.36e+01 angle pdb=" N ARG G 13 " pdb=" CA ARG G 13 " pdb=" C ARG G 13 " ideal model delta sigma weight residual 111.28 106.44 4.84 1.09e+00 8.42e-01 1.97e+01 ... (remaining 8863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.04: 3641 34.04 - 68.08: 64 68.08 - 102.11: 3 102.11 - 136.15: 1 136.15 - 170.19: 2 Dihedral angle restraints: 3711 sinusoidal: 1094 harmonic: 2617 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 191 " pdb=" CB CYS R 191 " ideal model delta sinusoidal sigma weight residual -86.00 -157.05 71.05 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 153.49 -60.49 1 1.00e+01 1.00e-02 4.87e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -85.22 -170.19 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 3708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 860 0.060 - 0.120: 166 0.120 - 0.180: 44 0.180 - 0.241: 6 0.241 - 0.301: 5 Chirality restraints: 1081 Sorted by residual: chirality pdb=" CA GLN B 17 " pdb=" N GLN B 17 " pdb=" C GLN B 17 " pdb=" CB GLN B 17 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ILE G 9 " pdb=" N ILE G 9 " pdb=" C ILE G 9 " pdb=" CB ILE G 9 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA LEU B 4 " pdb=" N LEU B 4 " pdb=" C LEU B 4 " pdb=" CB LEU B 4 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1078 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU R 62 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C GLU R 62 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU R 62 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG R 63 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 14 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C ASN A 14 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN A 14 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 15 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 35 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C GLY R 35 " 0.034 2.00e-02 2.50e+03 pdb=" O GLY R 35 " -0.013 2.00e-02 2.50e+03 pdb=" N MET R 36 " -0.012 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1164 2.77 - 3.30: 6045 3.30 - 3.84: 9866 3.84 - 4.37: 10324 4.37 - 4.90: 18661 Nonbonded interactions: 46060 Sorted by model distance: nonbonded pdb=" OG SER R 111 " pdb=" O SER R 165 " model vdw 2.238 2.440 nonbonded pdb=" OG1 THR A 55 " pdb=" O1A GTP A 401 " model vdw 2.267 2.440 nonbonded pdb=" OG SER A 54 " pdb=" O1A GTP A 401 " model vdw 2.319 2.440 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.373 2.520 nonbonded pdb=" OD1 ASP A 223 " pdb=" N VAL A 224 " model vdw 2.396 2.520 ... (remaining 46055 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.680 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.005 0.054 6464 Z= 0.337 Angle : 0.811 10.276 8868 Z= 0.542 Chirality : 0.056 0.301 1081 Planarity : 0.003 0.036 1111 Dihedral : 13.666 170.188 2001 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.29), residues: 878 helix: 2.35 (0.28), residues: 377 sheet: -0.17 (0.44), residues: 145 loop : -0.85 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 109 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.018 0.001 TYR R 185 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.809 Fit side-chains REVERT: B 143 THR cc_start: 0.8413 (p) cc_final: 0.8154 (t) REVERT: B 233 CYS cc_start: 0.9348 (t) cc_final: 0.9011 (t) REVERT: G 38 MET cc_start: 0.7924 (ptp) cc_final: 0.7678 (ptp) REVERT: G 48 ASP cc_start: 0.8558 (t70) cc_final: 0.8130 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1437 time to fit residues: 18.8987 Evaluate side-chains 67 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN B 340 ASN ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6464 Z= 0.252 Angle : 0.519 6.875 8868 Z= 0.282 Chirality : 0.041 0.159 1081 Planarity : 0.003 0.040 1111 Dihedral : 9.656 175.153 969 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.49 % Allowed : 10.43 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 878 helix: 2.18 (0.27), residues: 386 sheet: -0.33 (0.42), residues: 153 loop : -0.78 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 109 HIS 0.006 0.001 HIS R 178 PHE 0.017 0.001 PHE B 151 TYR 0.032 0.002 TYR R 185 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.658 Fit side-chains REVERT: B 143 THR cc_start: 0.8605 (p) cc_final: 0.8352 (t) REVERT: B 292 PHE cc_start: 0.8979 (m-80) cc_final: 0.8739 (m-80) REVERT: G 38 MET cc_start: 0.7923 (ptp) cc_final: 0.7615 (ptp) outliers start: 8 outliers final: 7 residues processed: 78 average time/residue: 0.1226 time to fit residues: 14.2577 Evaluate side-chains 73 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6464 Z= 0.239 Angle : 0.502 5.869 8868 Z= 0.271 Chirality : 0.040 0.151 1081 Planarity : 0.003 0.041 1111 Dihedral : 9.241 179.855 969 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.68 % Allowed : 13.41 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 878 helix: 2.21 (0.26), residues: 391 sheet: -0.42 (0.42), residues: 155 loop : -0.84 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 109 HIS 0.004 0.001 HIS B 183 PHE 0.015 0.001 PHE B 151 TYR 0.026 0.001 TYR R 185 ARG 0.002 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.699 Fit side-chains REVERT: A 347 ARG cc_start: 0.8678 (tpm170) cc_final: 0.8463 (tpm170) REVERT: B 143 THR cc_start: 0.8896 (p) cc_final: 0.8680 (t) REVERT: G 38 MET cc_start: 0.8044 (ptp) cc_final: 0.7683 (ptp) outliers start: 9 outliers final: 7 residues processed: 76 average time/residue: 0.1400 time to fit residues: 15.5612 Evaluate side-chains 73 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6464 Z= 0.216 Angle : 0.481 5.957 8868 Z= 0.259 Chirality : 0.040 0.150 1081 Planarity : 0.003 0.042 1111 Dihedral : 8.992 179.425 969 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.68 % Allowed : 16.01 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 878 helix: 2.35 (0.27), residues: 385 sheet: -0.62 (0.41), residues: 164 loop : -0.82 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 109 HIS 0.008 0.001 HIS R 178 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.705 Fit side-chains REVERT: G 38 MET cc_start: 0.8074 (ptp) cc_final: 0.7678 (ptp) outliers start: 9 outliers final: 6 residues processed: 75 average time/residue: 0.1251 time to fit residues: 14.1549 Evaluate side-chains 69 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 203 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 178 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6464 Z= 0.283 Angle : 0.523 5.877 8868 Z= 0.284 Chirality : 0.041 0.152 1081 Planarity : 0.003 0.044 1111 Dihedral : 8.795 179.506 969 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.79 % Allowed : 16.76 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.29), residues: 878 helix: 2.27 (0.27), residues: 385 sheet: -0.88 (0.42), residues: 158 loop : -0.92 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 109 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE B 151 TYR 0.017 0.001 TYR R 185 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.722 Fit side-chains REVERT: G 38 MET cc_start: 0.8174 (ptp) cc_final: 0.7751 (ptp) outliers start: 15 outliers final: 12 residues processed: 79 average time/residue: 0.1203 time to fit residues: 14.5789 Evaluate side-chains 76 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 0.0470 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6464 Z= 0.145 Angle : 0.449 6.486 8868 Z= 0.242 Chirality : 0.039 0.149 1081 Planarity : 0.003 0.042 1111 Dihedral : 8.365 178.637 969 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.86 % Allowed : 17.32 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.30), residues: 878 helix: 2.48 (0.27), residues: 384 sheet: -0.76 (0.42), residues: 157 loop : -0.84 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR R 316 ARG 0.001 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.709 Fit side-chains REVERT: G 38 MET cc_start: 0.8153 (ptp) cc_final: 0.7682 (ptp) outliers start: 10 outliers final: 9 residues processed: 83 average time/residue: 0.1171 time to fit residues: 14.9259 Evaluate side-chains 77 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 307 VAL Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6464 Z= 0.255 Angle : 0.518 6.582 8868 Z= 0.277 Chirality : 0.041 0.149 1081 Planarity : 0.003 0.044 1111 Dihedral : 8.357 178.364 969 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.79 % Allowed : 18.62 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.29), residues: 878 helix: 2.38 (0.27), residues: 385 sheet: -0.84 (0.42), residues: 156 loop : -0.89 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 109 HIS 0.004 0.001 HIS A 220 PHE 0.036 0.001 PHE R 289 TYR 0.016 0.001 TYR R 316 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.691 Fit side-chains REVERT: G 38 MET cc_start: 0.8211 (ptp) cc_final: 0.7748 (ptp) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.1129 time to fit residues: 14.0778 Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 312 ASN Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6464 Z= 0.310 Angle : 0.551 8.286 8868 Z= 0.295 Chirality : 0.042 0.152 1081 Planarity : 0.003 0.045 1111 Dihedral : 8.338 178.523 969 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.42 % Allowed : 20.11 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 878 helix: 2.23 (0.27), residues: 385 sheet: -1.07 (0.42), residues: 157 loop : -0.94 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 109 HIS 0.007 0.001 HIS A 362 PHE 0.014 0.002 PHE B 235 TYR 0.022 0.002 TYR R 185 ARG 0.002 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.647 Fit side-chains REVERT: G 38 MET cc_start: 0.8230 (ptp) cc_final: 0.7786 (ptp) outliers start: 13 outliers final: 12 residues processed: 78 average time/residue: 0.1164 time to fit residues: 14.0226 Evaluate side-chains 77 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 93 HIS Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 203 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6464 Z= 0.155 Angle : 0.489 8.168 8868 Z= 0.259 Chirality : 0.040 0.157 1081 Planarity : 0.003 0.042 1111 Dihedral : 8.144 178.028 969 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.86 % Allowed : 21.42 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.30), residues: 878 helix: 2.38 (0.27), residues: 385 sheet: -0.88 (0.43), residues: 156 loop : -0.86 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 109 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 289 TYR 0.029 0.002 TYR R 185 ARG 0.001 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.714 Fit side-chains REVERT: G 38 MET cc_start: 0.8196 (ptp) cc_final: 0.7693 (ptp) outliers start: 10 outliers final: 9 residues processed: 79 average time/residue: 0.1174 time to fit residues: 14.3431 Evaluate side-chains 75 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.1980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6464 Z= 0.141 Angle : 0.474 9.068 8868 Z= 0.249 Chirality : 0.040 0.151 1081 Planarity : 0.003 0.042 1111 Dihedral : 7.945 176.956 969 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.68 % Allowed : 21.42 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 878 helix: 2.46 (0.27), residues: 386 sheet: -0.85 (0.43), residues: 157 loop : -0.83 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 109 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE R 336 TYR 0.028 0.001 TYR R 185 ARG 0.001 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.664 Fit side-chains REVERT: G 38 MET cc_start: 0.8198 (ptp) cc_final: 0.7704 (ptp) REVERT: R 233 ILE cc_start: 0.5491 (tt) cc_final: 0.5272 (tt) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.1360 time to fit residues: 15.6796 Evaluate side-chains 76 residues out of total 776 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.119373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093701 restraints weight = 13195.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.096093 restraints weight = 7817.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.097752 restraints weight = 5538.177| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6464 Z= 0.152 Angle : 0.474 9.167 8868 Z= 0.249 Chirality : 0.039 0.149 1081 Planarity : 0.003 0.041 1111 Dihedral : 7.867 176.269 969 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.68 % Allowed : 21.60 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.30), residues: 878 helix: 2.45 (0.27), residues: 387 sheet: -0.83 (0.43), residues: 157 loop : -0.83 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 109 HIS 0.003 0.001 HIS A 362 PHE 0.017 0.001 PHE R 289 TYR 0.028 0.001 TYR R 185 ARG 0.001 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.10 seconds wall clock time: 27 minutes 11.26 seconds (1631.26 seconds total)