Starting phenix.real_space_refine on Wed Aug 5 02:24:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w36_65592/08_2026/9w36_65592.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w36_65592/08_2026/9w36_65592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w36_65592/08_2026/9w36_65592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w36_65592/08_2026/9w36_65592.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w36_65592/08_2026/9w36_65592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w36_65592/08_2026/9w36_65592.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 5107 2.51 5 N 1411 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8044 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1473 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 6, 'TRANS': 215} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 332 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TYR:plan': 3, 'HIS:plan': 4, 'ASP:plan': 7, 'GLU:plan': 5, 'PHE:plan': 4, 'GLN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2534 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 8, 'HIS:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 10, 'ASP:plan': 11, 'GLU:plan': 6, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 229 Chain: "B" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2534 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 15, 'TRANS': 372} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 5, 'GLN:plan1': 9, 'ASP:plan': 10, 'TRP:plan': 1, 'GLU:plan': 5, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 227 Chain: "D" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1503 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 6, 'TRANS': 215} Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 287 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 8, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 109 Time building chain proxies: 1.45, per 1000 atoms: 0.18 Number of scatterers: 8044 At special positions: 0 Unit cell: (79.392, 66.16, 148.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1505 8.00 N 1411 7.00 C 5107 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: 0.55 Conformation dependent library (CDL) restraints added in 363.5 milliseconds 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 55.6% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 47 through 57 Processing helix chain 'C' and resid 72 through 76 removed outlier: 4.188A pdb=" N LEU C 76 " --> pdb=" O PHE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 103 through 114 Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 119 through 134 Processing helix chain 'C' and resid 148 through 162 Processing helix chain 'C' and resid 178 through 197 removed outlier: 4.031A pdb=" N GLY C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.385A pdb=" N ALA C 210 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 26 through 57 Processing helix chain 'A' and resid 76 through 86 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.526A pdb=" N LEU A 140 " --> pdb=" O LEU A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 232 through 244 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 289 Processing helix chain 'A' and resid 289 through 297 removed outlier: 4.036A pdb=" N LYS A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'A' and resid 310 through 351 removed outlier: 4.668A pdb=" N SER A 345 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASP A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 401 removed outlier: 4.173A pdb=" N TYR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.739A pdb=" N ALA A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 16 removed outlier: 3.628A pdb=" N TYR B 8 " --> pdb=" O PRO B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 57 Processing helix chain 'B' and resid 57 through 62 removed outlier: 4.121A pdb=" N MET B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.647A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 127 through 130 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.881A pdb=" N LEU B 140 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 288 Processing helix chain 'B' and resid 288 through 297 removed outlier: 4.417A pdb=" N MET B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.751A pdb=" N ILE B 301 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 351 removed outlier: 4.837A pdb=" N SER B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 351 " --> pdb=" O ILE B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 392 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.955A pdb=" N ALA B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.884A pdb=" N LEU D 76 " --> pdb=" O PHE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 103 through 114 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 119 through 134 Processing helix chain 'D' and resid 148 through 162 Processing helix chain 'D' and resid 178 through 197 Processing helix chain 'D' and resid 207 through 213 Processing sheet with id=AA1, first strand: chain 'C' and resid 21 through 32 removed outlier: 3.958A pdb=" N VAL C 24 " --> pdb=" O LYS C 13 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS C 13 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS C 26 " --> pdb=" O ILE C 11 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 11 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU C 28 " --> pdb=" O LYS C 9 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS C 9 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C 30 " --> pdb=" O GLU C 7 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU C 7 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE C 11 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LYS C 63 " --> pdb=" O ILE C 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 91 removed outlier: 5.478A pdb=" N VAL C 168 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL C 203 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 170 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.547A pdb=" N ALA A 134 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 149 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 191 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY A 150 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL A 202 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE A 205 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 114 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLN A 98 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N ALA A 220 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN A 221 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.547A pdb=" N ALA A 134 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 169 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS A 184 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N GLN A 100 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLN A 98 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 10.135A pdb=" N ALA A 220 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLN A 221 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA6, first strand: chain 'B' and resid 132 through 134 removed outlier: 7.406A pdb=" N LEU B 149 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE B 191 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLY B 146 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 206 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 150 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 202 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 115 " --> pdb=" O GLY B 203 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 205 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 112 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY B 101 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL B 114 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLN B 98 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N ALA B 220 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN B 221 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.734A pdb=" N LYS B 184 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR B 166 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLN B 100 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLN B 98 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N ALA B 220 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN B 221 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.967A pdb=" N LEU D 6 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE D 11 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS D 63 " --> pdb=" O ILE D 11 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 41 Processing sheet with id=AB1, first strand: chain 'D' and resid 167 through 169 554 hydrogen bonds defined for protein. 1626 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: 1.46 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2759 1.34 - 1.46: 1409 1.46 - 1.58: 3947 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 8157 Sorted by residual: bond pdb=" CB GLN C 94 " pdb=" CG GLN C 94 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB ASN A 243 " pdb=" CG ASN A 243 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.11e+00 bond pdb=" CB ASN B 243 " pdb=" CG ASN B 243 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.09e+00 bond pdb=" CA VAL A 109 " pdb=" CB VAL A 109 " ideal model delta sigma weight residual 1.527 1.540 -0.013 1.31e-02 5.83e+03 9.41e-01 bond pdb=" CB ILE A 278 " pdb=" CG2 ILE A 278 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.25e-01 ... (remaining 8152 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 11009 2.14 - 4.27: 152 4.27 - 6.41: 18 6.41 - 8.54: 6 8.54 - 10.68: 3 Bond angle restraints: 11188 Sorted by residual: angle pdb=" CA LEU C 196 " pdb=" CB LEU C 196 " pdb=" CG LEU C 196 " ideal model delta sigma weight residual 116.30 126.98 -10.68 3.50e+00 8.16e-02 9.30e+00 angle pdb=" CA MET B 292 " pdb=" CB MET B 292 " pdb=" CG MET B 292 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.25e+00 angle pdb=" CA LEU C 201 " pdb=" CB LEU C 201 " pdb=" CG LEU C 201 " ideal model delta sigma weight residual 116.30 125.39 -9.09 3.50e+00 8.16e-02 6.74e+00 angle pdb=" CB MET B 292 " pdb=" CG MET B 292 " pdb=" SD MET B 292 " ideal model delta sigma weight residual 112.70 104.91 7.79 3.00e+00 1.11e-01 6.74e+00 angle pdb=" CA LEU B 214 " pdb=" CB LEU B 214 " pdb=" CG LEU B 214 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.39e+00 ... (remaining 11183 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.27: 4236 18.27 - 36.53: 424 36.53 - 54.79: 108 54.79 - 73.06: 16 73.06 - 91.32: 9 Dihedral angle restraints: 4793 sinusoidal: 1320 harmonic: 3473 Sorted by residual: dihedral pdb=" CA PRO B 4 " pdb=" C PRO B 4 " pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CB GLU B 54 " pdb=" CG GLU B 54 " pdb=" CD GLU B 54 " pdb=" OE1 GLU B 54 " ideal model delta sinusoidal sigma weight residual 0.00 91.32 -91.32 1 3.00e+01 1.11e-03 1.09e+01 dihedral pdb=" CA ASN C 75 " pdb=" C ASN C 75 " pdb=" N LEU C 76 " pdb=" CA LEU C 76 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 4790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1000 0.040 - 0.079: 312 0.079 - 0.119: 103 0.119 - 0.158: 8 0.158 - 0.198: 2 Chirality restraints: 1425 Sorted by residual: chirality pdb=" CG LEU C 76 " pdb=" CB LEU C 76 " pdb=" CD1 LEU C 76 " pdb=" CD2 LEU C 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CG LEU D 76 " pdb=" CB LEU D 76 " pdb=" CD1 LEU D 76 " pdb=" CD2 LEU D 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA TRP A 77 " pdb=" N TRP A 77 " pdb=" C TRP A 77 " pdb=" CB TRP A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1422 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 220 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" CD GLU C 220 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU C 220 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU C 220 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 3 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 4 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 340 " 0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C LEU B 340 " -0.027 2.00e-02 2.50e+03 pdb=" O LEU B 340 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA B 341 " 0.009 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2527 2.82 - 3.34: 8266 3.34 - 3.86: 13318 3.86 - 4.38: 13461 4.38 - 4.90: 23752 Nonbonded interactions: 61324 Sorted by model distance: nonbonded pdb=" OH TYR B 13 " pdb=" OD2 ASP B 300 " model vdw 2.299 3.040 nonbonded pdb=" O ILE A 339 " pdb=" OG1 THR A 343 " model vdw 2.321 3.040 nonbonded pdb=" O THR C 174 " pdb=" OG SER D 44 " model vdw 2.354 3.040 nonbonded pdb=" O PHE A 25 " pdb=" N ALA A 27 " model vdw 2.355 3.120 nonbonded pdb=" O PHE C 95 " pdb=" N HIS C 97 " model vdw 2.370 3.120 ... (remaining 61319 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 28 or (resid 29 and (name N or name CA \ or name C or name O or name CB )) or resid 30 through 40 or (resid 41 through 4 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 43 through 6 \ 9 or (resid 70 through 74 and (name N or name CA or name C or name O or name CB \ )) or resid 75 through 76 or (resid 77 and (name N or name CA or name C or name \ O or name CB )) or resid 78 through 92 or (resid 93 through 95 and (name N or na \ me CA or name C or name O or name CB )) or resid 96 through 128 or (resid 129 th \ rough 131 and (name N or name CA or name C or name O or name CB )) or resid 132 \ through 136 or (resid 137 and (name N or name CA or name C or name O or name CB \ )) or resid 138 through 187 or (resid 188 and (name N or name CA or name C or na \ me O or name CB )) or resid 189 through 199 or (resid 200 and (name N or name CA \ or name C or name O or name CB )) or resid 201 through 215 or (resid 216 and (n \ ame N or name CA or name C or name O or name CB )) or resid 217 through 224 or ( \ resid 225 through 229 and (name N or name CA or name C or name O or name CB )) o \ r resid 230 through 275 or (resid 276 and (name N or name CA or name C or name O \ or name CB )) or resid 277 or (resid 278 and (name N or name CA or name C or na \ me O or name CB )) or resid 279 through 294 or (resid 295 and (name N or name CA \ or name C or name O or name CB )) or resid 296 through 306 or (resid 307 and (n \ ame N or name CA or name C or name O or name CB )) or resid 308 through 312 or ( \ resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 408)) selection = (chain 'B' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 23 or (resid 24 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 57 or (resi \ d 58 through 60 and (name N or name CA or name C or name O or name CB )) or resi \ d 61 or (resid 62 and (name N or name CA or name C or name O or name CB )) or re \ sid 63 through 64 or (resid 65 through 66 and (name N or name CA or name C or na \ me O or name CB )) or resid 67 through 98 or (resid 99 through 100 and (name N o \ r name CA or name C or name O or name CB )) or (resid 101 through 106 and (name \ N or name CA or name C or name O or name CB )) or (resid 107 through 110 and (na \ me N or name CA or name C or name O or name CB )) or resid 111 or (resid 112 and \ (name N or name CA or name C or name O or name CB )) or resid 113 through 121 o \ r (resid 122 through 125 and (name N or name CA or name C or name O or name CB ) \ ) or resid 126 through 146 or (resid 147 and (name N or name CA or name C or nam \ e O or name CB )) or resid 148 or (resid 149 and (name N or name CA or name C or \ name O or name CB )) or resid 150 through 178 or (resid 179 and (name N or name \ CA or name C or name O or name CB )) or resid 180 through 197 or (resid 198 and \ (name N or name CA or name C or name O or name CB )) or resid 199 through 251 o \ r (resid 252 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 53 through 274 or (resid 275 through 276 and (name N or name CA or name C or nam \ e O or name CB )) or resid 277 through 285 or (resid 286 and (name N or name CA \ or name C or name O or name CB )) or resid 287 through 293 or (resid 294 through \ 295 and (name N or name CA or name C or name O or name CB )) or resid 296 throu \ gh 299 or (resid 300 through 303 and (name N or name CA or name C or name O or n \ ame CB )) or resid 304 through 315 or (resid 316 and (name N or name CA or name \ C or name O or name CB )) or resid 317 through 320 or (resid 321 and (name N or \ name CA or name C or name O or name CB )) or resid 322 through 369 or (resid 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 4 \ 08)) } ncs_group { reference = (chain 'C' and (resid 4 or (resid 5 and (name N or name CA or name C or name O o \ r name CB )) or resid 6 through 9 or (resid 10 through 12 and (name N or name CA \ or name C or name O or name CB )) or resid 13 through 15 or (resid 16 through 1 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 18 through 2 \ 4 or (resid 25 through 26 and (name N or name CA or name C or name O or name CB \ )) or resid 27 through 57 or (resid 58 through 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 64 or (resid 65 and (name N or na \ me CA or name C or name O or name CB )) or resid 66 through 71 or (resid 72 thro \ ugh 74 and (name N or name CA or name C or name O or name CB )) or resid 75 thro \ ugh 85 or (resid 86 through 89 and (name N or name CA or name C or name O or nam \ e CB )) or resid 90 through 102 or (resid 103 through 104 and (name N or name CA \ or name C or name O or name CB )) or resid 105 or (resid 106 and (name N or nam \ e CA or name C or name O or name CB )) or resid 107 through 112 or (resid 113 th \ rough 117 and (name N or name CA or name C or name O or name CB )) or resid 118 \ through 125 or (resid 126 through 128 and (name N or name CA or name C or name O \ or name CB )) or resid 129 through 142 or (resid 143 and (name N or name CA or \ name C or name O or name CB )) or resid 144 through 150 or (resid 151 and (name \ N or name CA or name C or name O or name CB )) or resid 152 through 153 or (resi \ d 154 through 158 and (name N or name CA or name C or name O or name CB )) or re \ sid 159 through 163 or (resid 164 and (name N or name CA or name C or name O or \ name CB )) or resid 165 through 167 or (resid 168 and (name N or name CA or name \ C or name O or name CB )) or resid 169 through 170 or (resid 171 and (name N or \ name CA or name C or name O or name CB )) or resid 172 through 189 or (resid 19 \ 0 through 195 and (name N or name CA or name C or name O or name CB )) or resid \ 196 through 216 or (resid 217 and (name N or name CA or name C or name O or name \ CB )) or resid 218 or (resid 219 and (name N or name CA or name C or name O or \ name CB )) or resid 220 through 223 or (resid 224 and (name N or name CA or name \ C or name O or name CB )) or resid 225)) selection = (chain 'D' and (resid 4 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 22 or (resid 23 through 26 and (nam \ e N or name CA or name C or name O or name CB )) or resid 27 through 29 or (resi \ d 30 and (name N or name CA or name C or name O or name CB )) or resid 31 or (re \ sid 32 and (name N or name CA or name C or name O or name CB )) or resid 33 thro \ ugh 39 or (resid 40 and (name N or name CA or name C or name O or name CB )) or \ resid 41 through 43 or (resid 44 and (name N or name CA or name C or name O or n \ ame CB )) or resid 45 through 49 or (resid 50 through 52 and (name N or name CA \ or name C or name O or name CB )) or resid 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )) or resid 55 through 59 or (resid 60 and (nam \ e N or name CA or name C or name O or name CB )) or resid 61 through 66 or (resi \ d 67 and (name N or name CA or name C or name O or name CB )) or resid 68 throug \ h 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 84 or (resid 85 through 89 and (name N or name CA or n \ ame C or name O or name CB )) or resid 90 through 95 or (resid 96 and (name N or \ name CA or name C or name O or name CB )) or resid 97 through 114 or (resid 115 \ through 117 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 18 through 120 or (resid 121 through 123 and (name N or name CA or name C or nam \ e O or name CB )) or resid 124 through 127 or (resid 128 and (name N or name CA \ or name C or name O or name CB )) or resid 129 through 136 or (resid 137 through \ 138 and (name N or name CA or name C or name O or name CB )) or resid 139 throu \ gh 141 or (resid 142 through 143 and (name N or name CA or name C or name O or n \ ame CB )) or resid 144 through 156 or (resid 157 through 158 and (name N or name \ CA or name C or name O or name CB )) or resid 159 through 173 or (resid 174 and \ (name N or name CA or name C or name O or name CB )) or resid 175 through 178 o \ r (resid 179 through 180 and (name N or name CA or name C or name O or name CB ) \ ) or resid 181 through 185 or (resid 186 through 195 and (name N or name CA or n \ ame C or name O or name CB )) or resid 196 through 197 or (resid 198 through 200 \ and (name N or name CA or name C or name O or name CB )) or resid 201 through 2 \ 25)) } 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: 0.990 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.002 0.034 8157 Z= 0.132 Angle : 0.630 10.676 11188 Z= 0.334 Chirality : 0.042 0.198 1425 Planarity : 0.004 0.039 1460 Dihedral : 16.744 91.323 2549 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.06 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 43.81 % Favored : 56.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.26), residues: 1204 helix: 2.00 (0.22), residues: 602 sheet: -1.63 (0.51), residues: 98 loop : -1.93 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 12 TYR 0.018 0.002 TYR D 129 PHE 0.020 0.001 PHE C 91 TRP 0.006 0.001 TRP A 77 HIS 0.002 0.000 HIS C 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 8157) covalent geometry : angle 0.63047 / 0.33 (11188) hydrogen bonds : bond 0.13988 / 10.23 ( 531) hydrogen bonds : angle 7.07082 / 5.14 ( 1626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: C 19 LYS cc_start: 0.7232 (mtmm) cc_final: 0.6524 (ptmm) REVERT: C 219 MET cc_start: 0.5099 (tpt) cc_final: 0.4740 (tpp) REVERT: A 15 ARG cc_start: 0.8544 (tmm-80) cc_final: 0.8251 (ttm110) REVERT: A 313 MET cc_start: 0.7878 (tpp) cc_final: 0.7498 (tpp) REVERT: A 371 TYR cc_start: 0.8483 (t80) cc_final: 0.7780 (t80) REVERT: A 389 PHE cc_start: 0.8231 (t80) cc_final: 0.8000 (t80) REVERT: B 15 ARG cc_start: 0.8578 (tmm-80) cc_final: 0.8203 (ttp80) REVERT: B 389 PHE cc_start: 0.8597 (t80) cc_final: 0.8371 (t80) REVERT: D 85 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7160 (ttm170) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0619 time to fit residues: 16.1028 Evaluate side-chains 182 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.0040 chunk 117 optimal weight: 20.0000 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 ASN D 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123810 restraints weight = 14341.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127207 restraints weight = 8048.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129448 restraints weight = 5482.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.130203 restraints weight = 4310.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131329 restraints weight = 3862.765| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8157 Z= 0.145 Angle : 0.596 8.306 11188 Z= 0.309 Chirality : 0.042 0.202 1425 Planarity : 0.004 0.037 1460 Dihedral : 4.184 18.938 1259 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.65 % Favored : 94.10 % Rotamer: Outliers : 10.06 % Allowed : 32.35 % Favored : 57.59 % 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: 0.19 (0.25), residues: 1204 helix: 1.85 (0.22), residues: 614 sheet: -1.61 (0.42), residues: 140 loop : -1.79 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 12 TYR 0.011 0.002 TYR B 371 PHE 0.017 0.001 PHE C 91 TRP 0.011 0.001 TRP A 77 HIS 0.014 0.001 HIS D 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 8157) covalent geometry : angle 0.59609 / 0.31 (11188) hydrogen bonds : bond 0.04107 / 2.93 ( 531) hydrogen bonds : angle 5.28297 / 3.79 ( 1626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: C 19 LYS cc_start: 0.6822 (mtmm) cc_final: 0.6296 (ptmm) REVERT: C 124 LYS cc_start: 0.8933 (tttm) cc_final: 0.8683 (tttt) REVERT: C 172 GLU cc_start: 0.8205 (tp30) cc_final: 0.7917 (tp30) REVERT: C 208 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: C 219 MET cc_start: 0.4701 (tpt) cc_final: 0.4269 (tpp) REVERT: A 15 ARG cc_start: 0.8523 (tmm-80) cc_final: 0.8245 (ttp80) REVERT: A 185 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.8142 (tpp-160) REVERT: A 201 MET cc_start: 0.4926 (ttt) cc_final: 0.4626 (ttt) REVERT: A 221 GLN cc_start: 0.8331 (mt0) cc_final: 0.7871 (mp10) REVERT: A 313 MET cc_start: 0.7834 (tpp) cc_final: 0.7527 (tpp) REVERT: A 371 TYR cc_start: 0.8397 (t80) cc_final: 0.7752 (t80) REVERT: B 15 ARG cc_start: 0.8648 (tmm-80) cc_final: 0.8263 (ttp80) REVERT: B 389 PHE cc_start: 0.8657 (t80) cc_final: 0.8436 (t80) REVERT: D 49 SER cc_start: 0.7872 (p) cc_final: 0.7559 (t) REVERT: D 85 ARG cc_start: 0.8521 (ttp80) cc_final: 0.7925 (ttm170) outliers start: 65 outliers final: 43 residues processed: 228 average time/residue: 0.0594 time to fit residues: 19.4684 Evaluate side-chains 219 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 202 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN C 86 ASN D 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.159968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120786 restraints weight = 14285.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124030 restraints weight = 8289.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126093 restraints weight = 5763.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127075 restraints weight = 4611.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127677 restraints weight = 4093.668| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8157 Z= 0.165 Angle : 0.610 8.815 11188 Z= 0.315 Chirality : 0.042 0.152 1425 Planarity : 0.003 0.035 1460 Dihedral : 4.336 21.366 1259 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 12.23 % Allowed : 29.72 % Favored : 58.05 % 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: 0.01 (0.25), residues: 1204 helix: 1.62 (0.21), residues: 614 sheet: -1.42 (0.43), residues: 140 loop : -1.84 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 12 TYR 0.012 0.002 TYR B 371 PHE 0.011 0.001 PHE D 67 TRP 0.013 0.001 TRP A 77 HIS 0.003 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 8157) covalent geometry : angle 0.61005 / 0.31 (11188) hydrogen bonds : bond 0.04034 / 2.86 ( 531) hydrogen bonds : angle 5.10219 / 3.66 ( 1626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 183 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 19 LYS cc_start: 0.6992 (mtmm) cc_final: 0.6541 (ptmm) REVERT: C 124 LYS cc_start: 0.8938 (tttm) cc_final: 0.8726 (ttmt) REVERT: C 143 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8188 (mmtp) REVERT: C 172 GLU cc_start: 0.8345 (tp30) cc_final: 0.8044 (tp30) REVERT: C 208 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: C 219 MET cc_start: 0.4740 (tpt) cc_final: 0.4030 (tpp) REVERT: A 15 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8246 (ttp80) REVERT: A 271 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.6710 (m) REVERT: A 313 MET cc_start: 0.7755 (tpp) cc_final: 0.7455 (tpp) REVERT: A 371 TYR cc_start: 0.8434 (t80) cc_final: 0.7717 (t80) REVERT: B 15 ARG cc_start: 0.8614 (tmm-80) cc_final: 0.8233 (ttp80) REVERT: B 99 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 218 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 389 PHE cc_start: 0.8677 (t80) cc_final: 0.8426 (t80) REVERT: D 85 ARG cc_start: 0.8550 (ttp80) cc_final: 0.7907 (ttm170) REVERT: D 176 ASN cc_start: 0.6836 (OUTLIER) cc_final: 0.6510 (t0) outliers start: 79 outliers final: 59 residues processed: 236 average time/residue: 0.0613 time to fit residues: 20.6875 Evaluate side-chains 239 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 206 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 2 optimal weight: 0.4980 chunk 37 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.159485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.120689 restraints weight = 14338.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123725 restraints weight = 8473.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125634 restraints weight = 5958.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126543 restraints weight = 4851.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.127569 restraints weight = 4312.868| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8157 Z= 0.157 Angle : 0.604 8.613 11188 Z= 0.309 Chirality : 0.042 0.146 1425 Planarity : 0.003 0.035 1460 Dihedral : 4.342 21.777 1259 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.06 % Favored : 93.69 % Rotamer: Outliers : 11.30 % Allowed : 30.96 % Favored : 57.74 % 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: -0.03 (0.25), residues: 1204 helix: 1.57 (0.21), residues: 614 sheet: -1.37 (0.43), residues: 140 loop : -1.86 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 12 TYR 0.013 0.002 TYR B 371 PHE 0.012 0.001 PHE C 91 TRP 0.012 0.001 TRP A 77 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 8157) covalent geometry : angle 0.60374 / 0.31 (11188) hydrogen bonds : bond 0.03880 / 2.76 ( 531) hydrogen bonds : angle 5.01856 / 3.60 ( 1626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 175 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 95 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5672 (m-10) REVERT: C 124 LYS cc_start: 0.8973 (tttm) cc_final: 0.8760 (ttmt) REVERT: C 143 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8232 (mmtp) REVERT: C 172 GLU cc_start: 0.8362 (tp30) cc_final: 0.8048 (tp30) REVERT: C 207 GLU cc_start: 0.4819 (OUTLIER) cc_final: 0.4187 (tm-30) REVERT: C 208 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6973 (tt0) REVERT: C 219 MET cc_start: 0.4807 (tpt) cc_final: 0.4562 (tpp) REVERT: A 15 ARG cc_start: 0.8537 (tmm-80) cc_final: 0.8217 (ttp80) REVERT: A 271 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.6741 (m) REVERT: A 313 MET cc_start: 0.7732 (tpp) cc_final: 0.7447 (tpp) REVERT: A 371 TYR cc_start: 0.8447 (t80) cc_final: 0.7759 (t80) REVERT: B 15 ARG cc_start: 0.8615 (tmm-80) cc_final: 0.8235 (ttp80) REVERT: B 99 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8019 (pp) REVERT: B 218 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7264 (t0) REVERT: B 389 PHE cc_start: 0.8674 (t80) cc_final: 0.8469 (t80) REVERT: D 71 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: D 85 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7938 (ttm170) REVERT: D 207 GLU cc_start: 0.3799 (OUTLIER) cc_final: 0.2929 (tm-30) outliers start: 73 outliers final: 60 residues processed: 227 average time/residue: 0.0635 time to fit residues: 20.6787 Evaluate side-chains 237 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 169 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 PHE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 ASP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 71 GLN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 30.0000 chunk 90 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 ASN D 84 GLN D 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.147974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109177 restraints weight = 14863.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111708 restraints weight = 9145.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113465 restraints weight = 6683.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114277 restraints weight = 5505.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114784 restraints weight = 4941.928| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 8157 Z= 0.406 Angle : 0.928 8.855 11188 Z= 0.490 Chirality : 0.050 0.159 1425 Planarity : 0.005 0.056 1460 Dihedral : 5.708 26.025 1259 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.97 % Favored : 90.70 % Rotamer: Outliers : 15.79 % Allowed : 27.71 % Favored : 56.50 % 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: -1.31 (0.23), residues: 1204 helix: 0.28 (0.20), residues: 612 sheet: -1.56 (0.41), residues: 146 loop : -2.21 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 179 TYR 0.030 0.003 TYR A 8 PHE 0.021 0.002 PHE D 67 TRP 0.020 0.003 TRP A 77 HIS 0.006 0.002 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.41 ( 8157) covalent geometry : angle 0.92823 / 0.49 (11188) hydrogen bonds : bond 0.06038 / 4.17 ( 531) hydrogen bonds : angle 6.07695 / 4.37 ( 1626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 155 time to evaluate : 0.278 Fit side-chains REVERT: C 124 LYS cc_start: 0.9052 (tttm) cc_final: 0.8836 (ttmt) REVERT: C 143 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8502 (mmtp) REVERT: C 208 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: C 219 MET cc_start: 0.4691 (tpt) cc_final: 0.4334 (tpp) REVERT: A 271 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.7342 (m) REVERT: A 313 MET cc_start: 0.7817 (tpp) cc_final: 0.7568 (tpp) REVERT: A 371 TYR cc_start: 0.8732 (t80) cc_final: 0.8151 (t80) REVERT: B 6 SER cc_start: 0.9366 (p) cc_final: 0.9074 (t) REVERT: B 185 ARG cc_start: 0.8380 (tpp-160) cc_final: 0.7927 (tpp-160) REVERT: B 408 LEU cc_start: 0.8186 (tt) cc_final: 0.7772 (tp) REVERT: D 85 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8058 (ttm170) REVERT: D 117 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8155 (p0) REVERT: D 207 GLU cc_start: 0.3633 (OUTLIER) cc_final: 0.3121 (tm-30) outliers start: 102 outliers final: 75 residues processed: 234 average time/residue: 0.0598 time to fit residues: 20.4764 Evaluate side-chains 227 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 148 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 96 HIS Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 ASN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.159918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.124661 restraints weight = 14593.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126570 restraints weight = 8004.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127260 restraints weight = 6321.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127489 restraints weight = 5009.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.127708 restraints weight = 5201.959| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8157 Z= 0.135 Angle : 0.618 9.932 11188 Z= 0.316 Chirality : 0.042 0.143 1425 Planarity : 0.003 0.034 1460 Dihedral : 4.654 22.290 1259 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.73 % Favored : 93.94 % Rotamer: Outliers : 6.81 % Allowed : 35.91 % Favored : 57.28 % 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: -0.31 (0.24), residues: 1204 helix: 1.37 (0.21), residues: 608 sheet: -1.31 (0.43), residues: 132 loop : -2.06 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 159 TYR 0.012 0.001 TYR B 371 PHE 0.008 0.001 PHE A 389 TRP 0.016 0.001 TRP A 77 HIS 0.004 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8157) covalent geometry : angle 0.61789 / 0.32 (11188) hydrogen bonds : bond 0.03839 / 2.77 ( 531) hydrogen bonds : angle 5.19716 / 3.71 ( 1626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.8963 (tttm) cc_final: 0.8728 (ttmt) REVERT: C 143 LYS cc_start: 0.8601 (mmmm) cc_final: 0.8255 (mmtp) REVERT: C 207 GLU cc_start: 0.4558 (OUTLIER) cc_final: 0.4155 (tm-30) REVERT: C 208 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: C 219 MET cc_start: 0.4741 (tpt) cc_final: 0.4267 (tpp) REVERT: C 224 TRP cc_start: 0.5853 (t-100) cc_final: 0.5522 (t-100) REVERT: A 313 MET cc_start: 0.7591 (tpp) cc_final: 0.7372 (tpp) REVERT: A 371 TYR cc_start: 0.8474 (t80) cc_final: 0.7882 (t80) REVERT: B 15 ARG cc_start: 0.8504 (tmm-80) cc_final: 0.8111 (ttp80) REVERT: B 201 MET cc_start: 0.5919 (ttt) cc_final: 0.5009 (ttt) REVERT: B 319 MET cc_start: 0.8526 (mmp) cc_final: 0.8253 (mmp) REVERT: B 389 PHE cc_start: 0.8679 (t80) cc_final: 0.8343 (t80) REVERT: B 408 LEU cc_start: 0.8160 (tt) cc_final: 0.7675 (tp) REVERT: D 76 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7241 (mm) REVERT: D 85 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7696 (ttm170) REVERT: D 117 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7871 (p0) REVERT: D 207 GLU cc_start: 0.3338 (OUTLIER) cc_final: 0.2959 (tm-30) outliers start: 44 outliers final: 27 residues processed: 207 average time/residue: 0.0653 time to fit residues: 19.1927 Evaluate side-chains 199 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 85 ARG Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 26 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 115 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 ASN ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.154614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.120037 restraints weight = 14099.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.119520 restraints weight = 13506.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121153 restraints weight = 9401.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121489 restraints weight = 7317.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.121794 restraints weight = 6645.310| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8157 Z= 0.147 Angle : 0.644 12.724 11188 Z= 0.325 Chirality : 0.042 0.193 1425 Planarity : 0.003 0.038 1460 Dihedral : 4.510 22.742 1259 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.02 % Rotamer: Outliers : 8.20 % Allowed : 34.98 % Favored : 56.81 % 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: -0.27 (0.25), residues: 1204 helix: 1.42 (0.21), residues: 612 sheet: -1.23 (0.44), residues: 132 loop : -2.12 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 53 TYR 0.015 0.002 TYR D 120 PHE 0.021 0.001 PHE B 261 TRP 0.016 0.001 TRP A 77 HIS 0.004 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8157) covalent geometry : angle 0.64426 / 0.32 (11188) hydrogen bonds : bond 0.03900 / 2.77 ( 531) hydrogen bonds : angle 5.05094 / 3.63 ( 1626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 174 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9009 (tttm) cc_final: 0.8763 (ttmt) REVERT: C 143 LYS cc_start: 0.8596 (mmmm) cc_final: 0.8281 (mmtp) REVERT: C 208 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: C 219 MET cc_start: 0.4698 (tpt) cc_final: 0.4157 (tpp) REVERT: C 224 TRP cc_start: 0.5677 (t-100) cc_final: 0.5332 (t-100) REVERT: A 313 MET cc_start: 0.7761 (tpp) cc_final: 0.7473 (tpp) REVERT: A 371 TYR cc_start: 0.8517 (t80) cc_final: 0.7896 (t80) REVERT: B 15 ARG cc_start: 0.8658 (tmm-80) cc_final: 0.8271 (ttp80) REVERT: B 408 LEU cc_start: 0.8154 (tt) cc_final: 0.7676 (tp) REVERT: D 207 GLU cc_start: 0.3860 (OUTLIER) cc_final: 0.3386 (tm-30) outliers start: 53 outliers final: 39 residues processed: 211 average time/residue: 0.0663 time to fit residues: 19.6920 Evaluate side-chains 209 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 371 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 0.0670 chunk 38 optimal weight: 7.9990 chunk 44 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 97 HIS C 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.159348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.126122 restraints weight = 13697.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127355 restraints weight = 10716.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129095 restraints weight = 7471.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.129115 restraints weight = 5682.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.129224 restraints weight = 5369.234| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8157 Z= 0.118 Angle : 0.612 10.466 11188 Z= 0.306 Chirality : 0.042 0.174 1425 Planarity : 0.003 0.041 1460 Dihedral : 4.254 20.636 1259 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.98 % Favored : 93.77 % Rotamer: Outliers : 5.73 % Allowed : 36.53 % Favored : 57.74 % 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: 0.03 (0.25), residues: 1204 helix: 1.73 (0.22), residues: 592 sheet: -1.09 (0.45), residues: 132 loop : -1.93 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 53 TYR 0.014 0.001 TYR B 371 PHE 0.013 0.001 PHE D 95 TRP 0.013 0.001 TRP A 77 HIS 0.003 0.001 HIS D 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8157) covalent geometry : angle 0.61174 / 0.31 (11188) hydrogen bonds : bond 0.03452 / 2.50 ( 531) hydrogen bonds : angle 4.85364 / 3.48 ( 1626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 124 LYS cc_start: 0.8988 (tttm) cc_final: 0.8730 (ttmt) REVERT: C 143 LYS cc_start: 0.8550 (mmmm) cc_final: 0.8179 (mmtp) REVERT: C 208 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6985 (tt0) REVERT: C 219 MET cc_start: 0.4687 (tpt) cc_final: 0.4122 (tpp) REVERT: C 224 TRP cc_start: 0.5647 (t-100) cc_final: 0.5303 (t-100) REVERT: A 12 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8239 (tpt-90) REVERT: A 313 MET cc_start: 0.7682 (tpp) cc_final: 0.7407 (tpp) REVERT: A 371 TYR cc_start: 0.8454 (t80) cc_final: 0.7965 (t80) REVERT: B 15 ARG cc_start: 0.8571 (tmm-80) cc_final: 0.8185 (ttp80) REVERT: B 113 MET cc_start: 0.8896 (tpp) cc_final: 0.8681 (tpt) REVERT: B 201 MET cc_start: 0.5419 (tpt) cc_final: 0.5038 (tpt) REVERT: B 408 LEU cc_start: 0.8090 (tt) cc_final: 0.7810 (tp) REVERT: D 85 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7710 (ttm170) REVERT: D 121 LYS cc_start: 0.8634 (tppt) cc_final: 0.8403 (tptm) REVERT: D 207 GLU cc_start: 0.3813 (OUTLIER) cc_final: 0.3349 (tt0) outliers start: 37 outliers final: 26 residues processed: 206 average time/residue: 0.0697 time to fit residues: 20.1300 Evaluate side-chains 203 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.150038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115970 restraints weight = 14252.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116164 restraints weight = 11324.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.117291 restraints weight = 8428.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117408 restraints weight = 6844.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117532 restraints weight = 6077.150| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 8157 Z= 0.283 Angle : 0.779 10.090 11188 Z= 0.402 Chirality : 0.045 0.160 1425 Planarity : 0.004 0.041 1460 Dihedral : 4.913 25.754 1259 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.39 % Favored : 91.36 % Rotamer: Outliers : 7.28 % Allowed : 36.07 % Favored : 56.66 % 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: -0.63 (0.24), residues: 1204 helix: 1.01 (0.21), residues: 608 sheet: -1.10 (0.46), residues: 122 loop : -2.19 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 53 TYR 0.021 0.003 TYR A 8 PHE 0.014 0.002 PHE D 67 TRP 0.019 0.002 TRP A 77 HIS 0.005 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 ( 8157) covalent geometry : angle 0.77902 / 0.40 (11188) hydrogen bonds : bond 0.04829 / 3.36 ( 531) hydrogen bonds : angle 5.36830 / 3.87 ( 1626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.9004 (tttm) cc_final: 0.8776 (ttmt) REVERT: C 143 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8430 (mmtp) REVERT: C 207 GLU cc_start: 0.4727 (OUTLIER) cc_final: 0.4225 (tm-30) REVERT: C 208 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: C 219 MET cc_start: 0.4645 (tpt) cc_final: 0.4178 (tpp) REVERT: A 54 GLU cc_start: 0.7302 (tt0) cc_final: 0.6993 (tt0) REVERT: A 313 MET cc_start: 0.7798 (tpp) cc_final: 0.7533 (tpp) REVERT: A 371 TYR cc_start: 0.8615 (t80) cc_final: 0.8028 (t80) REVERT: B 15 ARG cc_start: 0.8645 (tmm-80) cc_final: 0.8341 (ttm170) REVERT: B 113 MET cc_start: 0.8996 (tpp) cc_final: 0.8793 (tpt) REVERT: B 408 LEU cc_start: 0.8218 (tt) cc_final: 0.7919 (tp) REVERT: D 85 ARG cc_start: 0.8237 (ttp-170) cc_final: 0.7796 (ttm170) REVERT: D 207 GLU cc_start: 0.3966 (OUTLIER) cc_final: 0.3547 (tt0) outliers start: 47 outliers final: 38 residues processed: 197 average time/residue: 0.0703 time to fit residues: 19.5939 Evaluate side-chains 203 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.155204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121561 restraints weight = 13784.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.122306 restraints weight = 11710.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123010 restraints weight = 9017.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.123348 restraints weight = 7793.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.123669 restraints weight = 6371.278| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8157 Z= 0.144 Angle : 0.659 10.550 11188 Z= 0.330 Chirality : 0.043 0.186 1425 Planarity : 0.004 0.036 1460 Dihedral : 4.499 22.640 1259 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.15 % Favored : 93.60 % Rotamer: Outliers : 5.88 % Allowed : 37.15 % Favored : 56.97 % 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: -0.20 (0.25), residues: 1204 helix: 1.47 (0.22), residues: 608 sheet: -1.11 (0.45), residues: 132 loop : -2.07 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 53 TYR 0.012 0.002 TYR B 8 PHE 0.014 0.001 PHE D 95 TRP 0.015 0.001 TRP A 77 HIS 0.003 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8157) covalent geometry : angle 0.65870 / 0.33 (11188) hydrogen bonds : bond 0.03781 / 2.71 ( 531) hydrogen bonds : angle 5.06123 / 3.63 ( 1626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2408 Ramachandran restraints generated. 1204 Oldfield, 0 Emsley, 1204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: C 124 LYS cc_start: 0.8991 (tttm) cc_final: 0.8735 (ttmt) REVERT: C 143 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8308 (mmtp) REVERT: C 207 GLU cc_start: 0.4703 (OUTLIER) cc_final: 0.4336 (tm-30) REVERT: C 208 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.7024 (tt0) REVERT: C 219 MET cc_start: 0.4625 (tpt) cc_final: 0.3927 (tpp) REVERT: C 224 TRP cc_start: 0.5589 (t-100) cc_final: 0.5218 (t-100) REVERT: A 12 ARG cc_start: 0.8659 (tpp80) cc_final: 0.8286 (tpt-90) REVERT: A 54 GLU cc_start: 0.7208 (tt0) cc_final: 0.6868 (tt0) REVERT: A 313 MET cc_start: 0.7761 (tpp) cc_final: 0.7447 (tpp) REVERT: A 371 TYR cc_start: 0.8552 (t80) cc_final: 0.7958 (t80) REVERT: B 15 ARG cc_start: 0.8589 (tmm-80) cc_final: 0.8200 (ttp80) REVERT: B 113 MET cc_start: 0.8911 (tpp) cc_final: 0.8695 (tpt) REVERT: B 185 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7959 (tpp-160) REVERT: B 408 LEU cc_start: 0.8117 (tt) cc_final: 0.7807 (tp) REVERT: D 85 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7753 (ttm170) REVERT: D 88 TYR cc_start: 0.7272 (m-80) cc_final: 0.6848 (m-80) REVERT: D 121 LYS cc_start: 0.8756 (tppt) cc_final: 0.8471 (tptm) REVERT: D 207 GLU cc_start: 0.3858 (OUTLIER) cc_final: 0.3556 (tt0) outliers start: 38 outliers final: 34 residues processed: 201 average time/residue: 0.0683 time to fit residues: 19.4539 Evaluate side-chains 208 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 202 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 208 GLN Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 TRP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 288 SER Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.157727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120865 restraints weight = 14803.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123907 restraints weight = 8466.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125857 restraints weight = 5841.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127151 restraints weight = 4650.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127733 restraints weight = 4066.207| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8157 Z= 0.183 Angle : 0.685 10.452 11188 Z= 0.347 Chirality : 0.043 0.168 1425 Planarity : 0.004 0.037 1460 Dihedral : 4.585 23.517 1259 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.14 % Favored : 92.61 % Rotamer: Outliers : 7.28 % Allowed : 35.91 % Favored : 56.81 % 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: -0.27 (0.25), residues: 1204 helix: 1.36 (0.21), residues: 608 sheet: -1.08 (0.45), residues: 132 loop : -2.05 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 53 TYR 0.017 0.002 TYR D 129 PHE 0.012 0.001 PHE A 145 TRP 0.016 0.001 TRP A 77 HIS 0.003 0.001 HIS D 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 8157) covalent geometry : angle 0.68489 / 0.35 (11188) hydrogen bonds : bond 0.04059 / 2.87 ( 531) hydrogen bonds : angle 5.08689 / 3.66 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.94 seconds wall clock time: 20 minutes 37.20 seconds (1237.20 seconds total)