Starting phenix.real_space_refine on Tue Jan 13 22:09:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpb_36474/01_2026/8jpb_36474_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpb_36474/01_2026/8jpb_36474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpb_36474/01_2026/8jpb_36474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpb_36474/01_2026/8jpb_36474.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpb_36474/01_2026/8jpb_36474_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpb_36474/01_2026/8jpb_36474_neut.cif" } resolution = 3.07 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= 0.003 sd= 0.062 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 1 5.21 5 S 55 5.16 5 C 6198 2.51 5 N 1647 2.21 5 O 1741 1.98 5 F 5 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9650 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5163 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 28, 'TRANS': 629} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 128 Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "Q" Number of atoms: 2149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2149 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 119} Link IDs: {'PTRANS': 11, 'TRANS': 305} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 605 Unresolved non-hydrogen dihedrals: 401 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 14, 'ARG:plan': 12, 'PHE:plan': 5, 'GLN:plan1': 9, 'TYR:plan': 6, 'HIS:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 333 Chain: "R" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2178 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 257 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 3, 'PHE:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 123 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'STU': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'SRW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.54, per 1000 atoms: 0.26 Number of scatterers: 9650 At special positions: 0 Unit cell: (109.592, 112.888, 172.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 55 16.00 P 2 15.00 Al 1 13.00 Mg 1 11.99 F 5 9.00 O 1741 8.00 N 1647 7.00 C 6198 6.00 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=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 444.3 milliseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 6 sheets defined 64.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'G' and resid 3 through 19 Processing helix chain 'G' and resid 23 through 28 removed outlier: 3.889A pdb=" N ALA G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 38 No H-bonds generated for 'chain 'G' and resid 36 through 38' Processing helix chain 'G' and resid 39 through 49 removed outlier: 4.313A pdb=" N LYS G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.679A pdb=" N LEU G 76 " --> pdb=" O CYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 93 removed outlier: 4.609A pdb=" N LEU G 82 " --> pdb=" O GLU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 113 removed outlier: 3.842A pdb=" N VAL G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 119 Processing helix chain 'G' and resid 125 through 138 removed outlier: 3.668A pdb=" N ILE G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 Processing helix chain 'G' and resid 159 through 167 removed outlier: 3.506A pdb=" N GLN G 163 " --> pdb=" O GLY G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.790A pdb=" N THR G 172 " --> pdb=" O SER G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 189 No H-bonds generated for 'chain 'G' and resid 187 through 189' Processing helix chain 'G' and resid 224 through 230 Processing helix chain 'G' and resid 232 through 248 Processing helix chain 'G' and resid 278 through 287 removed outlier: 3.580A pdb=" N HIS G 282 " --> pdb=" O ASP G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 311 removed outlier: 4.431A pdb=" N PHE G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR G 297 " --> pdb=" O ASP G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 321 No H-bonds generated for 'chain 'G' and resid 319 through 321' Processing helix chain 'G' and resid 358 through 363 Processing helix chain 'G' and resid 370 through 387 removed outlier: 3.946A pdb=" N TRP G 374 " --> pdb=" O SER G 370 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE G 375 " --> pdb=" O SER G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 404 Processing helix chain 'G' and resid 405 through 408 Processing helix chain 'G' and resid 418 through 429 Processing helix chain 'G' and resid 432 through 436 removed outlier: 3.682A pdb=" N ARG G 435 " --> pdb=" O ASP G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 449 removed outlier: 3.605A pdb=" N VAL G 447 " --> pdb=" O GLY G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 454 Processing helix chain 'G' and resid 457 through 464 Processing helix chain 'G' and resid 481 through 486 Processing helix chain 'G' and resid 489 through 494 Processing helix chain 'G' and resid 499 through 504 Processing helix chain 'G' and resid 505 through 507 No H-bonds generated for 'chain 'G' and resid 505 through 507' Processing helix chain 'G' and resid 513 through 525 Processing helix chain 'G' and resid 525 through 548 Processing helix chain 'G' and resid 636 through 659 Processing helix chain 'Q' and resid 51 through 64 Processing helix chain 'Q' and resid 68 through 98 removed outlier: 4.053A pdb=" N LYS Q 77 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU Q 78 " --> pdb=" O GLY Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 3.563A pdb=" N LYS Q 107 " --> pdb=" O TYR Q 103 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA Q 108 " --> pdb=" O GLU Q 104 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS Q 109 " --> pdb=" O HIS Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 138 removed outlier: 3.791A pdb=" N ASP Q 130 " --> pdb=" O ASN Q 126 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA Q 131 " --> pdb=" O PRO Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 147 Processing helix chain 'Q' and resid 148 through 151 Processing helix chain 'Q' and resid 156 through 164 Processing helix chain 'Q' and resid 164 through 169 Processing helix chain 'Q' and resid 175 through 181 Processing helix chain 'Q' and resid 209 through 214 removed outlier: 4.244A pdb=" N ARG Q 214 " --> pdb=" O ARG Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 removed outlier: 3.875A pdb=" N HIS Q 218 " --> pdb=" O LYS Q 215 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE Q 220 " --> pdb=" O ILE Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 236 removed outlier: 3.603A pdb=" N ASP Q 236 " --> pdb=" O SER Q 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 233 through 236' Processing helix chain 'Q' and resid 246 through 261 Processing helix chain 'Q' and resid 262 through 265 Processing helix chain 'Q' and resid 275 through 286 removed outlier: 4.074A pdb=" N GLU Q 281 " --> pdb=" O ASP Q 277 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET Q 284 " --> pdb=" O GLU Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 287 through 292 removed outlier: 4.121A pdb=" N TYR Q 291 " --> pdb=" O HIS Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 316 removed outlier: 3.790A pdb=" N LEU Q 316 " --> pdb=" O MET Q 312 " (cutoff:3.500A) Processing helix chain 'Q' and resid 333 through 352 removed outlier: 3.651A pdb=" N ALA Q 343 " --> pdb=" O PHE Q 339 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP Q 346 " --> pdb=" O ALA Q 342 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 88 removed outlier: 4.232A pdb=" N VAL R 79 " --> pdb=" O VAL R 75 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 127 removed outlier: 3.719A pdb=" N MET R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 4.020A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN R 126 " --> pdb=" O VAL R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.636A pdb=" N ARG R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 181 removed outlier: 4.139A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 removed outlier: 4.089A pdb=" N LYS R 187 " --> pdb=" O SER R 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.882A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 271 removed outlier: 3.534A pdb=" N MET R 266 " --> pdb=" O LYS R 262 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 328 removed outlier: 4.171A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 368 removed outlier: 3.682A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 378 removed outlier: 3.636A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 191 through 200 removed outlier: 4.401A pdb=" N GLY G 207 " --> pdb=" O HIS G 194 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL G 205 " --> pdb=" O ILE G 196 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY G 198 " --> pdb=" O GLY G 203 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY G 203 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR G 259 " --> pdb=" O ILE G 270 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASP G 272 " --> pdb=" O MET G 257 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N MET G 257 " --> pdb=" O ASP G 272 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'G' and resid 323 through 325 Processing sheet with id=AA4, first strand: chain 'G' and resid 597 through 602 removed outlier: 5.250A pdb=" N SER G 599 " --> pdb=" O TRP G 590 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TRP G 590 " --> pdb=" O SER G 599 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 601 " --> pdb=" O LEU G 588 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN G 577 " --> pdb=" O LYS G 567 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET G 561 " --> pdb=" O LEU G 583 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 631 " --> pdb=" O MET G 568 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G 608 " --> pdb=" O LYS G 623 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 190 through 192 removed outlier: 5.954A pdb=" N LEU Q 40 " --> pdb=" O ARG Q 202 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL Q 204 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU Q 42 " --> pdb=" O VAL Q 204 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS Q 41 " --> pdb=" O SER Q 225 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET Q 227 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU Q 43 " --> pdb=" O MET Q 227 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LEU Q 229 " --> pdb=" O LEU Q 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU Q 45 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ALA Q 231 " --> pdb=" O LEU Q 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER Q 268 " --> pdb=" O THR Q 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 207 through 211 removed outlier: 3.553A pdb=" N GLY R 208 " --> pdb=" O THR R 225 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1701 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: 1.24 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1558 1.30 - 1.43: 2588 1.43 - 1.56: 5625 1.56 - 1.69: 6 1.69 - 1.81: 91 Bond restraints: 9868 Sorted by residual: bond pdb=" C13 SRW R 501 " pdb=" C16 SRW R 501 " ideal model delta sigma weight residual 1.447 1.289 0.158 2.00e-02 2.50e+03 6.21e+01 bond pdb=" C14 SRW R 501 " pdb=" N3 SRW R 501 " ideal model delta sigma weight residual 1.309 1.453 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C13 SRW R 501 " pdb=" N1 SRW R 501 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C13 SRW R 501 " pdb=" N2 SRW R 501 " ideal model delta sigma weight residual 1.327 1.210 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C ASP Q 165 " pdb=" O ASP Q 165 " ideal model delta sigma weight residual 1.236 1.172 0.064 1.18e-02 7.18e+03 2.96e+01 ... (remaining 9863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.17: 13440 14.17 - 28.34: 4 28.34 - 42.50: 0 42.50 - 56.67: 0 56.67 - 70.84: 2 Bond angle restraints: 13446 Sorted by residual: angle pdb=" F1 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F2 ALF Q 403 " ideal model delta sigma weight residual 108.68 179.52 -70.84 3.00e+00 1.11e-01 5.58e+02 angle pdb=" F3 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F4 ALF Q 403 " ideal model delta sigma weight residual 109.63 179.52 -69.89 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F2 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F4 ALF Q 403 " ideal model delta sigma weight residual 110.21 90.03 20.18 3.00e+00 1.11e-01 4.53e+01 angle pdb=" F1 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F3 ALF Q 403 " ideal model delta sigma weight residual 109.69 90.20 19.49 3.00e+00 1.11e-01 4.22e+01 angle pdb=" F2 ALF Q 403 " pdb="AL ALF Q 403 " pdb=" F3 ALF Q 403 " ideal model delta sigma weight residual 109.59 90.12 19.47 3.00e+00 1.11e-01 4.21e+01 ... (remaining 13441 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.65: 5645 30.65 - 61.30: 194 61.30 - 91.95: 20 91.95 - 122.61: 5 122.61 - 153.26: 2 Dihedral angle restraints: 5866 sinusoidal: 2111 harmonic: 3755 Sorted by residual: dihedral pdb=" O2B GDP Q 401 " pdb=" O3A GDP Q 401 " pdb=" PB GDP Q 401 " pdb=" PA GDP Q 401 " ideal model delta sinusoidal sigma weight residual 180.00 66.49 113.51 1 2.00e+01 2.50e-03 3.36e+01 dihedral pdb=" C25 SRW R 501 " pdb=" C24 SRW R 501 " pdb=" C26 SRW R 501 " pdb=" F1 SRW R 501 " ideal model delta sinusoidal sigma weight residual 106.02 -100.72 -153.26 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CA LYS G 266 " pdb=" C LYS G 266 " pdb=" N LEU G 267 " pdb=" CA LEU G 267 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1440 0.079 - 0.158: 102 0.158 - 0.237: 4 0.237 - 0.316: 0 0.316 - 0.395: 3 Chirality restraints: 1549 Sorted by residual: chirality pdb=" CA GLU G 5 " pdb=" N GLU G 5 " pdb=" C GLU G 5 " pdb=" CB GLU G 5 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C24 SRW R 501 " pdb=" C14 SRW R 501 " pdb=" C25 SRW R 501 " pdb=" F1 SRW R 501 " both_signs ideal model delta sigma weight residual True 1.45 1.83 -0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA HIS R 132 " pdb=" N HIS R 132 " pdb=" C HIS R 132 " pdb=" CB HIS R 132 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1546 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU R 291 " -0.061 5.00e-02 4.00e+02 9.10e-02 1.32e+01 pdb=" N PRO R 292 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO R 292 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 292 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 203 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C GLY G 203 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY G 203 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU G 204 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 539 " -0.194 9.50e-02 1.11e+02 8.72e-02 5.19e+00 pdb=" NE ARG G 539 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 539 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG G 539 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG G 539 " -0.003 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 32 2.47 - 3.08: 7066 3.08 - 3.69: 14670 3.69 - 4.29: 21378 4.29 - 4.90: 35676 Nonbonded interactions: 78822 Sorted by model distance: nonbonded pdb=" O3B GDP Q 401 " pdb="MG MG Q 402 " model vdw 1.864 2.170 nonbonded pdb=" OG SER Q 53 " pdb="MG MG Q 402 " model vdw 1.897 2.170 nonbonded pdb=" OE2 GLU G 181 " pdb=" OG SER G 514 " model vdw 2.250 3.040 nonbonded pdb=" OG SER G 125 " pdb=" OE2 GLU G 152 " model vdw 2.253 3.040 nonbonded pdb=" O2A GDP Q 401 " pdb=" F1 ALF Q 403 " model vdw 2.269 2.990 ... (remaining 78817 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.060 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 0.158 9868 Z= 0.271 Angle : 1.145 70.840 13446 Z= 0.467 Chirality : 0.043 0.395 1549 Planarity : 0.004 0.091 1703 Dihedral : 16.039 153.257 3430 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.65 % Allowed : 12.68 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1267 helix: 1.38 (0.20), residues: 712 sheet: -0.81 (0.47), residues: 114 loop : -0.38 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 539 TYR 0.012 0.001 TYR R 339 PHE 0.015 0.001 PHE G 391 TRP 0.014 0.001 TRP G 590 HIS 0.007 0.001 HIS R 132 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9868) covalent geometry : angle 1.14510 (13446) hydrogen bonds : bond 0.13876 ( 584) hydrogen bonds : angle 6.29507 ( 1701) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 516 ARG cc_start: 0.8283 (mmm160) cc_final: 0.8006 (mmm160) REVERT: G 639 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: Q 90 MET cc_start: 0.4519 (ptm) cc_final: 0.4228 (ttp) REVERT: Q 186 THR cc_start: 0.7221 (m) cc_final: 0.6992 (m) REVERT: Q 277 ASP cc_start: 0.4399 (p0) cc_final: 0.3647 (p0) REVERT: Q 278 LEU cc_start: 0.6299 (mm) cc_final: 0.6052 (tp) REVERT: Q 279 LEU cc_start: 0.5739 (tp) cc_final: 0.5282 (tp) REVERT: Q 292 PHE cc_start: 0.4839 (m-10) cc_final: 0.4537 (m-10) REVERT: R 240 ASN cc_start: 0.7023 (OUTLIER) cc_final: 0.6770 (t0) REVERT: R 306 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6749 (mtt90) outliers start: 6 outliers final: 2 residues processed: 199 average time/residue: 0.1072 time to fit residues: 29.1994 Evaluate side-chains 155 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 456 LEU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain R residue 240 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 82 ASN R 261 ASN R 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.200721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.162829 restraints weight = 12949.297| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.56 r_work: 0.3418 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9868 Z= 0.196 Angle : 0.847 30.096 13446 Z= 0.373 Chirality : 0.044 0.210 1549 Planarity : 0.004 0.053 1703 Dihedral : 11.722 147.680 1436 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.73 % Allowed : 13.65 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1267 helix: 1.27 (0.20), residues: 730 sheet: -0.52 (0.47), residues: 115 loop : -0.58 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 539 TYR 0.016 0.002 TYR Q 159 PHE 0.018 0.002 PHE G 391 TRP 0.007 0.001 TRP G 590 HIS 0.006 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 9868) covalent geometry : angle 0.84653 (13446) hydrogen bonds : bond 0.04418 ( 584) hydrogen bonds : angle 5.22530 ( 1701) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.375 Fit side-chains REVERT: G 20 SER cc_start: 0.8759 (t) cc_final: 0.8463 (p) REVERT: G 33 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8851 (tp) REVERT: G 136 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7934 (mm) REVERT: G 516 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8205 (mmm160) REVERT: G 536 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8217 (mp) REVERT: G 604 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: G 639 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: Q 80 TYR cc_start: 0.6143 (m-10) cc_final: 0.5908 (m-10) REVERT: Q 90 MET cc_start: 0.4960 (ptm) cc_final: 0.4702 (ptm) REVERT: Q 128 TYR cc_start: 0.4583 (m-80) cc_final: 0.3897 (m-80) REVERT: Q 177 GLN cc_start: 0.7033 (tp-100) cc_final: 0.6793 (tp-100) REVERT: Q 186 THR cc_start: 0.7191 (m) cc_final: 0.6974 (m) REVERT: Q 235 TYR cc_start: 0.5470 (p90) cc_final: 0.4635 (p90) REVERT: R 170 ILE cc_start: 0.7613 (mt) cc_final: 0.7335 (mm) REVERT: R 333 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.5710 (mp10) outliers start: 16 outliers final: 8 residues processed: 173 average time/residue: 0.1059 time to fit residues: 24.8639 Evaluate side-chains 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 219 CYS Chi-restraints excluded: chain Q residue 266 ASN Chi-restraints excluded: chain R residue 333 GLN Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 140 GLN G 629 GLN Q 82 ASN R 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.202075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.164068 restraints weight = 13008.331| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.31 r_work: 0.3414 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9868 Z= 0.141 Angle : 0.807 29.745 13446 Z= 0.347 Chirality : 0.042 0.205 1549 Planarity : 0.004 0.041 1703 Dihedral : 11.375 148.372 1432 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.38 % Allowed : 13.65 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1267 helix: 1.40 (0.20), residues: 723 sheet: -0.62 (0.46), residues: 115 loop : -0.60 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 625 TYR 0.035 0.002 TYR Q 160 PHE 0.014 0.001 PHE G 391 TRP 0.008 0.001 TRP R 134 HIS 0.005 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9868) covalent geometry : angle 0.80662 (13446) hydrogen bonds : bond 0.03912 ( 584) hydrogen bonds : angle 4.95674 ( 1701) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.368 Fit side-chains REVERT: G 33 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8834 (tp) REVERT: G 136 LEU cc_start: 0.8371 (mm) cc_final: 0.7834 (mm) REVERT: G 516 ARG cc_start: 0.8442 (mmm160) cc_final: 0.8172 (mmm160) REVERT: G 536 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8387 (mp) REVERT: G 539 ARG cc_start: 0.7542 (mtm110) cc_final: 0.7209 (mtm-85) REVERT: G 604 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6358 (tt0) REVERT: G 639 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: Q 80 TYR cc_start: 0.6053 (m-10) cc_final: 0.5797 (m-10) REVERT: Q 81 GLN cc_start: 0.7227 (mt0) cc_final: 0.6861 (pp30) REVERT: Q 128 TYR cc_start: 0.4466 (m-80) cc_final: 0.3710 (m-80) REVERT: Q 177 GLN cc_start: 0.7321 (tp-100) cc_final: 0.7095 (tp-100) REVERT: Q 232 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.4728 (mp) REVERT: Q 235 TYR cc_start: 0.5508 (p90) cc_final: 0.4445 (p90) REVERT: Q 248 MET cc_start: 0.7259 (ttt) cc_final: 0.6927 (ttm) REVERT: Q 263 TRP cc_start: 0.7733 (m-90) cc_final: 0.7273 (m-90) REVERT: Q 279 LEU cc_start: 0.6466 (tp) cc_final: 0.6141 (tp) REVERT: R 170 ILE cc_start: 0.7579 (mt) cc_final: 0.7373 (mm) REVERT: R 333 GLN cc_start: 0.6694 (OUTLIER) cc_final: 0.5692 (mp10) outliers start: 22 outliers final: 10 residues processed: 170 average time/residue: 0.1029 time to fit residues: 23.8948 Evaluate side-chains 162 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 219 CYS Chi-restraints excluded: chain Q residue 232 LEU Chi-restraints excluded: chain Q residue 266 ASN Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain R residue 333 GLN Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 122 HIS Q 58 GLN R 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.201997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.165083 restraints weight = 12987.265| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.75 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9868 Z= 0.135 Angle : 0.792 29.620 13446 Z= 0.337 Chirality : 0.041 0.211 1549 Planarity : 0.004 0.042 1703 Dihedral : 11.057 148.490 1432 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.14 % Allowed : 14.08 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1267 helix: 1.39 (0.20), residues: 730 sheet: -0.65 (0.45), residues: 115 loop : -0.45 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 92 TYR 0.013 0.002 TYR R 344 PHE 0.018 0.001 PHE Q 339 TRP 0.010 0.001 TRP R 134 HIS 0.005 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9868) covalent geometry : angle 0.79210 (13446) hydrogen bonds : bond 0.03699 ( 584) hydrogen bonds : angle 4.73683 ( 1701) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.366 Fit side-chains REVERT: G 136 LEU cc_start: 0.8582 (mm) cc_final: 0.8342 (mm) REVERT: G 516 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7375 (mmm160) REVERT: G 536 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8211 (mp) REVERT: G 604 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5888 (tt0) REVERT: G 625 ARG cc_start: 0.7719 (ttp80) cc_final: 0.7453 (ttp80) REVERT: G 639 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: Q 128 TYR cc_start: 0.3293 (m-80) cc_final: 0.2844 (m-80) REVERT: Q 273 LEU cc_start: 0.4205 (mt) cc_final: 0.3989 (mt) REVERT: Q 313 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7006 (t80) REVERT: R 249 MET cc_start: 0.7129 (tpt) cc_final: 0.6770 (tpt) outliers start: 29 outliers final: 11 residues processed: 182 average time/residue: 0.1081 time to fit residues: 26.7177 Evaluate side-chains 170 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 219 CYS Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 124 optimal weight: 0.0020 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 459 GLN Q 177 GLN R 261 ASN R 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.203458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.166924 restraints weight = 13028.005| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.73 r_work: 0.3434 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9868 Z= 0.115 Angle : 0.784 29.768 13446 Z= 0.331 Chirality : 0.041 0.240 1549 Planarity : 0.004 0.043 1703 Dihedral : 10.713 148.454 1429 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.49 % Allowed : 15.38 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.24), residues: 1267 helix: 1.54 (0.20), residues: 722 sheet: -0.57 (0.45), residues: 115 loop : -0.27 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 338 TYR 0.019 0.001 TYR Q 80 PHE 0.017 0.001 PHE Q 339 TRP 0.030 0.001 TRP Q 263 HIS 0.004 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9868) covalent geometry : angle 0.78436 (13446) hydrogen bonds : bond 0.03515 ( 584) hydrogen bonds : angle 4.64922 ( 1701) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.379 Fit side-chains REVERT: G 136 LEU cc_start: 0.8323 (mm) cc_final: 0.8049 (mm) REVERT: G 459 GLN cc_start: 0.8413 (tp-100) cc_final: 0.8186 (tp40) REVERT: G 516 ARG cc_start: 0.8290 (mmm160) cc_final: 0.8035 (mmm160) REVERT: G 536 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8343 (mp) REVERT: G 578 ARG cc_start: 0.8344 (ttp80) cc_final: 0.7965 (mtp180) REVERT: G 604 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6389 (tt0) REVERT: G 625 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7670 (ttp80) REVERT: Q 128 TYR cc_start: 0.4467 (m-80) cc_final: 0.3696 (m-80) REVERT: Q 313 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6663 (t80) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 0.1151 time to fit residues: 26.6481 Evaluate side-chains 171 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 219 CYS Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 613 GLN Q 177 GLN R 210 GLN R 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.202625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165784 restraints weight = 13012.657| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.60 r_work: 0.3386 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9868 Z= 0.129 Angle : 0.792 29.898 13446 Z= 0.335 Chirality : 0.041 0.218 1549 Planarity : 0.004 0.043 1703 Dihedral : 10.636 148.507 1429 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.49 % Allowed : 15.60 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.06 (0.24), residues: 1267 helix: 1.54 (0.20), residues: 722 sheet: -0.47 (0.46), residues: 115 loop : -0.29 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 539 TYR 0.042 0.002 TYR R 153 PHE 0.015 0.001 PHE G 391 TRP 0.011 0.001 TRP R 316 HIS 0.005 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9868) covalent geometry : angle 0.79177 (13446) hydrogen bonds : bond 0.03580 ( 584) hydrogen bonds : angle 4.63208 ( 1701) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 168 time to evaluate : 0.312 Fit side-chains REVERT: G 136 LEU cc_start: 0.8377 (mm) cc_final: 0.7949 (mt) REVERT: G 516 ARG cc_start: 0.8356 (mmm160) cc_final: 0.8112 (mmm160) REVERT: G 536 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8330 (mp) REVERT: G 604 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6465 (tt0) REVERT: G 613 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6357 (tm130) REVERT: G 625 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7727 (ttp80) REVERT: Q 181 ARG cc_start: 0.6757 (tpp80) cc_final: 0.6362 (tpp80) REVERT: Q 313 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6611 (t80) outliers start: 23 outliers final: 15 residues processed: 180 average time/residue: 0.1104 time to fit residues: 26.6743 Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 219 CYS Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 613 GLN R 261 ASN R 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.202663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163225 restraints weight = 12945.117| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 3.62 r_work: 0.3403 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9868 Z= 0.132 Angle : 0.800 29.995 13446 Z= 0.338 Chirality : 0.041 0.225 1549 Planarity : 0.004 0.044 1703 Dihedral : 10.529 148.510 1429 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.60 % Allowed : 15.49 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.05 (0.24), residues: 1267 helix: 1.53 (0.20), residues: 719 sheet: -0.40 (0.46), residues: 115 loop : -0.29 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 214 TYR 0.026 0.002 TYR Q 160 PHE 0.021 0.001 PHE Q 339 TRP 0.028 0.002 TRP Q 263 HIS 0.005 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9868) covalent geometry : angle 0.79974 (13446) hydrogen bonds : bond 0.03581 ( 584) hydrogen bonds : angle 4.61960 ( 1701) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.351 Fit side-chains REVERT: G 136 LEU cc_start: 0.8321 (mm) cc_final: 0.7940 (mm) REVERT: G 516 ARG cc_start: 0.8314 (mmm160) cc_final: 0.8070 (mmm160) REVERT: G 536 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8273 (mp) REVERT: G 539 ARG cc_start: 0.7366 (mtm110) cc_final: 0.6989 (mtm-85) REVERT: G 604 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6440 (tt0) REVERT: G 613 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6489 (tm130) REVERT: G 625 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7768 (ttp80) REVERT: G 639 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: Q 266 ASN cc_start: 0.7817 (p0) cc_final: 0.7611 (p0) REVERT: Q 313 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6616 (t80) outliers start: 24 outliers final: 13 residues processed: 173 average time/residue: 0.1074 time to fit residues: 25.0644 Evaluate side-chains 177 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 219 CYS Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 111 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 94 optimal weight: 30.0000 chunk 88 optimal weight: 6.9990 chunk 43 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 613 GLN Q 177 GLN R 210 GLN R 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.203311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.165875 restraints weight = 12929.521| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.17 r_work: 0.3469 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9868 Z= 0.120 Angle : 0.794 30.045 13446 Z= 0.335 Chirality : 0.041 0.236 1549 Planarity : 0.004 0.044 1703 Dihedral : 10.371 148.473 1429 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.28 % Allowed : 16.47 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1267 helix: 1.50 (0.20), residues: 725 sheet: -0.37 (0.48), residues: 111 loop : -0.32 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 539 TYR 0.015 0.001 TYR Q 160 PHE 0.012 0.001 PHE G 391 TRP 0.023 0.002 TRP Q 263 HIS 0.004 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9868) covalent geometry : angle 0.79399 (13446) hydrogen bonds : bond 0.03470 ( 584) hydrogen bonds : angle 4.59676 ( 1701) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.372 Fit side-chains REVERT: G 136 LEU cc_start: 0.8390 (mm) cc_final: 0.8003 (mm) REVERT: G 516 ARG cc_start: 0.8230 (mmm160) cc_final: 0.8007 (mmm160) REVERT: G 536 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8343 (mp) REVERT: G 539 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7087 (mtm-85) REVERT: G 578 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7941 (ttt-90) REVERT: G 604 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6385 (tt0) REVERT: G 639 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: Q 266 ASN cc_start: 0.7851 (p0) cc_final: 0.7614 (p0) REVERT: Q 313 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6744 (t80) REVERT: R 354 TYR cc_start: 0.7309 (m-80) cc_final: 0.6860 (m-80) outliers start: 21 outliers final: 13 residues processed: 180 average time/residue: 0.1097 time to fit residues: 26.6959 Evaluate side-chains 179 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 237 ILE Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 103 optimal weight: 0.0060 chunk 76 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 210 GLN R 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.200842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.161161 restraints weight = 12815.100| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.16 r_work: 0.3437 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9868 Z= 0.178 Angle : 0.827 30.239 13446 Z= 0.356 Chirality : 0.043 0.239 1549 Planarity : 0.004 0.044 1703 Dihedral : 10.498 148.770 1429 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.60 % Allowed : 16.79 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.24), residues: 1267 helix: 1.37 (0.19), residues: 724 sheet: -0.35 (0.46), residues: 115 loop : -0.42 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 214 TYR 0.018 0.002 TYR Q 160 PHE 0.018 0.001 PHE G 391 TRP 0.028 0.002 TRP R 316 HIS 0.007 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 9868) covalent geometry : angle 0.82735 (13446) hydrogen bonds : bond 0.03834 ( 584) hydrogen bonds : angle 4.72618 ( 1701) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: G 136 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7967 (mm) REVERT: G 516 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8062 (mmm160) REVERT: G 536 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8294 (mp) REVERT: G 589 GLU cc_start: 0.7981 (mm-30) cc_final: 0.6845 (mt-10) REVERT: G 604 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6428 (tt0) REVERT: G 639 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: Q 266 ASN cc_start: 0.7885 (p0) cc_final: 0.7669 (p0) REVERT: Q 313 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.6746 (t80) outliers start: 24 outliers final: 11 residues processed: 181 average time/residue: 0.1102 time to fit residues: 26.6871 Evaluate side-chains 174 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 90 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 177 GLN R 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.202959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.164044 restraints weight = 12857.732| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.22 r_work: 0.3455 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9868 Z= 0.171 Angle : 0.830 30.289 13446 Z= 0.356 Chirality : 0.043 0.262 1549 Planarity : 0.004 0.045 1703 Dihedral : 10.366 148.733 1429 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.06 % Allowed : 17.55 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.24), residues: 1267 helix: 1.33 (0.19), residues: 724 sheet: -0.52 (0.45), residues: 117 loop : -0.44 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 539 TYR 0.016 0.002 TYR G 564 PHE 0.019 0.001 PHE G 391 TRP 0.033 0.002 TRP R 316 HIS 0.006 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9868) covalent geometry : angle 0.82981 (13446) hydrogen bonds : bond 0.03848 ( 584) hydrogen bonds : angle 4.74861 ( 1701) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: G 136 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7966 (mm) REVERT: G 536 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8301 (mp) REVERT: G 539 ARG cc_start: 0.7531 (mtm110) cc_final: 0.7110 (mtm-85) REVERT: G 604 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: G 639 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: Q 256 ARG cc_start: 0.6900 (ttm-80) cc_final: 0.6682 (tpp-160) REVERT: Q 313 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6698 (t80) REVERT: Q 324 ILE cc_start: 0.7153 (mt) cc_final: 0.6931 (mm) outliers start: 19 outliers final: 11 residues processed: 173 average time/residue: 0.1212 time to fit residues: 27.6833 Evaluate side-chains 170 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 MET Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 366 VAL Chi-restraints excluded: chain G residue 507 ARG Chi-restraints excluded: chain G residue 511 LEU Chi-restraints excluded: chain G residue 536 LEU Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 604 GLU Chi-restraints excluded: chain G residue 639 GLU Chi-restraints excluded: chain G residue 651 TYR Chi-restraints excluded: chain Q residue 313 PHE Chi-restraints excluded: chain Q residue 341 PHE Chi-restraints excluded: chain R residue 181 SER Chi-restraints excluded: chain R residue 335 THR Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 92 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 0.0040 chunk 50 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 GLN R 365 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.205571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167281 restraints weight = 12897.539| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 3.56 r_work: 0.3438 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9868 Z= 0.114 Angle : 0.806 29.973 13446 Z= 0.339 Chirality : 0.041 0.287 1549 Planarity : 0.004 0.046 1703 Dihedral : 9.973 148.545 1429 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.84 % Allowed : 17.88 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1267 helix: 1.46 (0.19), residues: 725 sheet: -0.47 (0.45), residues: 117 loop : -0.32 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 625 TYR 0.018 0.001 TYR R 153 PHE 0.010 0.001 PHE G 296 TRP 0.031 0.002 TRP R 316 HIS 0.004 0.001 HIS G 286 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9868) covalent geometry : angle 0.80572 (13446) hydrogen bonds : bond 0.03484 ( 584) hydrogen bonds : angle 4.62103 ( 1701) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2833.24 seconds wall clock time: 49 minutes 9.17 seconds (2949.17 seconds total)