Starting phenix.real_space_refine on Thu Jul 2 08:29:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cx2_30489/07_2026/7cx2_30489.cif" } resolution = 2.8 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= 0.009 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 52 5.16 5 C 5027 2.51 5 N 1374 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7930 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2027 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 7930 At special positions: 0 Unit cell: (77.064, 110.526, 125.736, 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 52 16.00 O 1477 8.00 N 1374 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 348.5 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 40.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 26 through 46 removed outlier: 3.910A pdb=" N VAL R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY R 35 " --> pdb=" O MET R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 83 removed outlier: 3.859A pdb=" N GLU R 73 " --> pdb=" O VAL R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 94 removed outlier: 3.933A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 140 Processing helix chain 'R' and resid 140 through 148 removed outlier: 3.685A pdb=" N VAL R 148 " --> pdb=" O TYR R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 170 Processing helix chain 'R' and resid 171 through 174 Processing helix chain 'R' and resid 195 through 228 Processing helix chain 'R' and resid 258 through 277 removed outlier: 3.661A pdb=" N SER R 277 " --> pdb=" O PHE R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 284 removed outlier: 4.037A pdb=" N THR R 281 " --> pdb=" O SER R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 317 removed outlier: 3.821A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER R 305 " --> pdb=" O LEU R 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN R 307 " --> pdb=" O PHE R 303 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 319 through 330 Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.663A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 4.296A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.549A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.339A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.902A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.899A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.001A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.681A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 4.056A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.982A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.591A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.675A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.733A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.630A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.873A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.929A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.590A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.997A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.623A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.874A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.822A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1125 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: 1.09 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1293 1.31 - 1.44: 2222 1.44 - 1.57: 4495 1.57 - 1.70: 2 1.70 - 1.83: 74 Bond restraints: 8086 Sorted by residual: bond pdb=" C8 P2E R 401 " pdb=" C9 P2E R 401 " ideal model delta sigma weight residual 1.515 1.436 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C11 P2E R 401 " pdb=" O4 P2E R 401 " ideal model delta sigma weight residual 1.402 1.330 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" C10 P2E R 401 " pdb=" C11 P2E R 401 " ideal model delta sigma weight residual 1.529 1.598 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C7 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.529 1.576 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C12 P2E R 401 " pdb=" C8 P2E R 401 " ideal model delta sigma weight residual 1.538 1.498 0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 8081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 10881 2.97 - 5.95: 70 5.95 - 8.92: 7 8.92 - 11.89: 1 11.89 - 14.87: 4 Bond angle restraints: 10963 Sorted by residual: angle pdb=" N VAL R 156 " pdb=" CA VAL R 156 " pdb=" C VAL R 156 " ideal model delta sigma weight residual 110.62 116.74 -6.12 1.02e+00 9.61e-01 3.59e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 116.79 -5.51 1.09e+00 8.42e-01 2.56e+01 angle pdb=" C4 P2E R 401 " pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " ideal model delta sigma weight residual 127.52 112.65 14.87 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C5 P2E R 401 " pdb=" C6 P2E R 401 " pdb=" C7 P2E R 401 " ideal model delta sigma weight residual 125.83 111.98 13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N GLN A 390 " pdb=" CA GLN A 390 " pdb=" C GLN A 390 " ideal model delta sigma weight residual 111.71 116.83 -5.12 1.15e+00 7.56e-01 1.98e+01 ... (remaining 10958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 4325 16.25 - 32.49: 386 32.49 - 48.74: 82 48.74 - 64.98: 17 64.98 - 81.23: 9 Dihedral angle restraints: 4819 sinusoidal: 1848 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -4.97 -81.03 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 4816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.119: 206 0.119 - 0.178: 19 0.178 - 0.238: 1 0.238 - 0.297: 2 Chirality restraints: 1252 Sorted by residual: chirality pdb=" C15 P2E R 401 " pdb=" C14 P2E R 401 " pdb=" C16 P2E R 401 " pdb=" O5 P2E R 401 " both_signs ideal model delta sigma weight residual False 2.23 2.52 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C8 P2E R 401 " pdb=" C12 P2E R 401 " pdb=" C7 P2E R 401 " pdb=" C9 P2E R 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA GLN A 390 " pdb=" N GLN A 390 " pdb=" C GLN A 390 " pdb=" CB GLN A 390 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1249 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " -0.269 2.00e-02 2.50e+03 2.73e-01 7.46e+02 pdb=" C13 P2E R 401 " 0.249 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " 0.296 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " -0.277 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 388 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C LEU A 388 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU A 388 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG A 389 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.028 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C5 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " 0.028 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " -0.028 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 93 2.65 - 3.21: 7115 3.21 - 3.78: 11836 3.78 - 4.34: 17133 4.34 - 4.90: 28054 Nonbonded interactions: 64231 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR R 82 " pdb=" O HOH R 501 " model vdw 2.133 3.040 nonbonded pdb=" O SER N 52 " pdb=" NH1 ARG N 72 " model vdw 2.247 3.120 nonbonded pdb=" O GLU A 50 " pdb=" NH2 ARG A 265 " model vdw 2.276 3.120 nonbonded pdb=" O LEU R 304 " pdb=" ND2 ASN R 307 " model vdw 2.280 3.120 ... (remaining 64226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.740 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:5.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.004 0.079 8089 Z= 0.206 Angle : 0.713 14.865 10969 Z= 0.397 Chirality : 0.047 0.297 1252 Planarity : 0.009 0.273 1402 Dihedral : 13.588 81.229 2886 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.71 % 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: -2.13 (0.23), residues: 1002 helix: -0.55 (0.24), residues: 371 sheet: -0.79 (0.32), residues: 210 loop : -2.51 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 228 TYR 0.024 0.002 TYR B 59 PHE 0.015 0.002 PHE A 212 TRP 0.018 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.21 ( 8086) covalent geometry : angle 0.71159 / 0.40 (10963) SS BOND : bond 0.00171 / 0.08 ( 3) SS BOND : angle 1.93365 / 0.87 ( 6) hydrogen bonds : bond 0.14524 / 10.00 ( 394) hydrogen bonds : angle 5.49290 / 3.98 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7395 (t80) cc_final: 0.6912 (t80) REVERT: R 116 MET cc_start: 0.7244 (tpp) cc_final: 0.6897 (tpp) REVERT: R 124 MET cc_start: 0.8306 (tpp) cc_final: 0.8033 (tpt) REVERT: R 126 MET cc_start: 0.8307 (tpt) cc_final: 0.8107 (tpt) REVERT: R 282 ILE cc_start: 0.8561 (tt) cc_final: 0.8311 (pt) REVERT: A 20 ARG cc_start: 0.7012 (mtp85) cc_final: 0.6757 (tpp80) REVERT: A 24 LYS cc_start: 0.7859 (ttpp) cc_final: 0.7567 (ttmm) REVERT: B 23 LYS cc_start: 0.8989 (tttp) cc_final: 0.8746 (ttpp) REVERT: B 32 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8284 (tp-100) REVERT: N 12 VAL cc_start: 0.9235 (p) cc_final: 0.9015 (m) REVERT: N 105 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7787 (mtm-85) outliers start: 1 outliers final: 0 residues processed: 172 average time/residue: 0.5633 time to fit residues: 101.9076 Evaluate side-chains 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 213 GLN A 390 GLN B 17 GLN B 175 GLN B 176 GLN N 35 ASN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105519 restraints weight = 9783.051| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.62 r_work: 0.3111 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8089 Z= 0.122 Angle : 0.547 7.586 10969 Z= 0.283 Chirality : 0.042 0.140 1252 Planarity : 0.004 0.054 1402 Dihedral : 4.769 55.584 1118 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.03 % Allowed : 12.99 % Favored : 84.98 % 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: -0.71 (0.25), residues: 1002 helix: 1.05 (0.27), residues: 382 sheet: -0.41 (0.33), residues: 217 loop : -2.02 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.010 0.001 TYR B 124 PHE 0.019 0.001 PHE R 119 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8086) covalent geometry : angle 0.54623 / 0.28 (10963) SS BOND : bond 0.00117 / 0.06 ( 3) SS BOND : angle 1.46780 / 0.65 ( 6) hydrogen bonds : bond 0.03814 / 2.54 ( 394) hydrogen bonds : angle 4.17966 / 2.97 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: R 228 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6723 (mtp85) REVERT: R 278 LEU cc_start: 0.7827 (mt) cc_final: 0.7568 (mt) REVERT: R 282 ILE cc_start: 0.8444 (tt) cc_final: 0.8128 (pt) REVERT: A 20 ARG cc_start: 0.7115 (mtp85) cc_final: 0.6865 (tpp80) REVERT: A 24 LYS cc_start: 0.7753 (ttpp) cc_final: 0.7178 (ttmm) REVERT: A 220 HIS cc_start: 0.8060 (m170) cc_final: 0.7566 (m-70) REVERT: A 318 TYR cc_start: 0.7139 (t80) cc_final: 0.6697 (t80) REVERT: B 23 LYS cc_start: 0.8574 (tttp) cc_final: 0.8249 (ttpp) REVERT: B 32 GLN cc_start: 0.8767 (tp-100) cc_final: 0.8546 (tp-100) REVERT: B 160 SER cc_start: 0.8945 (m) cc_final: 0.8504 (p) REVERT: B 170 ASP cc_start: 0.8067 (t0) cc_final: 0.7804 (t0) REVERT: B 175 GLN cc_start: 0.8786 (mt0) cc_final: 0.8547 (pt0) REVERT: B 217 MET cc_start: 0.8314 (ptm) cc_final: 0.7791 (pp-130) REVERT: N 73 ASP cc_start: 0.7048 (t70) cc_final: 0.6092 (p0) REVERT: N 78 THR cc_start: 0.8785 (m) cc_final: 0.8332 (m) REVERT: N 105 ARG cc_start: 0.8315 (mtp180) cc_final: 0.7737 (mtm-85) outliers start: 17 outliers final: 6 residues processed: 151 average time/residue: 0.5679 time to fit residues: 90.3804 Evaluate side-chains 137 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 307 ASN A 29 GLN B 9 GLN B 13 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.154267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104162 restraints weight = 9669.137| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.58 r_work: 0.3096 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8089 Z= 0.145 Angle : 0.544 7.351 10969 Z= 0.280 Chirality : 0.042 0.143 1252 Planarity : 0.004 0.057 1402 Dihedral : 4.657 58.028 1118 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.86 % Allowed : 15.49 % Favored : 81.64 % 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: -0.12 (0.26), residues: 1002 helix: 1.63 (0.28), residues: 382 sheet: -0.21 (0.33), residues: 211 loop : -1.72 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 19 TYR 0.013 0.001 TYR B 105 PHE 0.016 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8086) covalent geometry : angle 0.54298 / 0.28 (10963) SS BOND : bond 0.00149 / 0.07 ( 3) SS BOND : angle 1.57657 / 0.70 ( 6) hydrogen bonds : bond 0.03704 / 2.48 ( 394) hydrogen bonds : angle 3.97462 / 2.83 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: R 116 MET cc_start: 0.7135 (tpp) cc_final: 0.6609 (tpp) REVERT: R 228 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6866 (mtp85) REVERT: R 282 ILE cc_start: 0.8445 (tt) cc_final: 0.8116 (pt) REVERT: A 20 ARG cc_start: 0.7202 (mtp85) cc_final: 0.6723 (tpp80) REVERT: A 24 LYS cc_start: 0.7778 (ttpp) cc_final: 0.7247 (ttmm) REVERT: A 314 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 19 ARG cc_start: 0.7269 (ttm110) cc_final: 0.6934 (ttm110) REVERT: B 23 LYS cc_start: 0.8674 (tttp) cc_final: 0.8297 (ttpp) REVERT: B 32 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8458 (tp40) REVERT: B 170 ASP cc_start: 0.8137 (t0) cc_final: 0.7858 (t0) REVERT: B 175 GLN cc_start: 0.8768 (mt0) cc_final: 0.8561 (pt0) REVERT: B 260 GLU cc_start: 0.8638 (pt0) cc_final: 0.8095 (pt0) REVERT: B 266 HIS cc_start: 0.8446 (t70) cc_final: 0.8222 (t70) REVERT: G 17 GLU cc_start: 0.8274 (tp30) cc_final: 0.8030 (tp30) REVERT: G 42 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7898 (tm-30) REVERT: N 73 ASP cc_start: 0.7109 (t70) cc_final: 0.6131 (p0) REVERT: N 78 THR cc_start: 0.8807 (m) cc_final: 0.8363 (m) REVERT: N 89 GLU cc_start: 0.9137 (mp0) cc_final: 0.8932 (mp0) REVERT: N 105 ARG cc_start: 0.8376 (mtp180) cc_final: 0.7764 (mtm-85) outliers start: 24 outliers final: 9 residues processed: 145 average time/residue: 0.5804 time to fit residues: 88.4696 Evaluate side-chains 137 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 32 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 17 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.156558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106073 restraints weight = 9856.590| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.63 r_work: 0.3124 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8089 Z= 0.100 Angle : 0.504 10.494 10969 Z= 0.257 Chirality : 0.041 0.172 1252 Planarity : 0.004 0.056 1402 Dihedral : 4.383 53.518 1118 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.50 % Allowed : 16.81 % Favored : 80.69 % 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: 0.24 (0.27), residues: 1002 helix: 1.90 (0.28), residues: 383 sheet: -0.10 (0.33), residues: 213 loop : -1.44 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.009 0.001 TYR B 124 PHE 0.014 0.001 PHE A 212 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 8086) covalent geometry : angle 0.50329 / 0.26 (10963) SS BOND : bond 0.00160 / 0.08 ( 3) SS BOND : angle 1.17827 / 0.52 ( 6) hydrogen bonds : bond 0.03189 / 2.13 ( 394) hydrogen bonds : angle 3.75383 / 2.67 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7125 (t80) cc_final: 0.6789 (t80) REVERT: R 116 MET cc_start: 0.7065 (tpp) cc_final: 0.6447 (tpt) REVERT: R 228 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6770 (mtp85) REVERT: R 282 ILE cc_start: 0.8406 (tt) cc_final: 0.8092 (pt) REVERT: A 20 ARG cc_start: 0.7112 (mtp85) cc_final: 0.6872 (tpp80) REVERT: A 24 LYS cc_start: 0.7701 (ttpp) cc_final: 0.7149 (ttmm) REVERT: A 27 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 314 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 356 ARG cc_start: 0.8378 (pmm-80) cc_final: 0.8028 (ptp-170) REVERT: B 19 ARG cc_start: 0.7288 (ttm110) cc_final: 0.6990 (ttm110) REVERT: B 32 GLN cc_start: 0.8718 (tp-100) cc_final: 0.8411 (tp40) REVERT: B 46 ARG cc_start: 0.8402 (ptp-110) cc_final: 0.7709 (mtt90) REVERT: B 160 SER cc_start: 0.8877 (m) cc_final: 0.8544 (p) REVERT: B 170 ASP cc_start: 0.8067 (t0) cc_final: 0.7863 (t0) REVERT: B 260 GLU cc_start: 0.8622 (pt0) cc_final: 0.8045 (pt0) REVERT: B 266 HIS cc_start: 0.8455 (t70) cc_final: 0.8225 (t70) REVERT: G 17 GLU cc_start: 0.8347 (tp30) cc_final: 0.8127 (tp30) REVERT: G 42 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7835 (tm-30) REVERT: N 89 GLU cc_start: 0.9127 (mp0) cc_final: 0.8910 (mp0) REVERT: N 105 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7727 (mtm-85) outliers start: 21 outliers final: 10 residues processed: 148 average time/residue: 0.6551 time to fit residues: 101.8669 Evaluate side-chains 138 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 78 optimal weight: 0.0570 chunk 87 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 94 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 GLN G 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107224 restraints weight = 9770.570| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.63 r_work: 0.3143 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8089 Z= 0.094 Angle : 0.482 7.285 10969 Z= 0.249 Chirality : 0.040 0.138 1252 Planarity : 0.004 0.056 1402 Dihedral : 4.142 47.945 1118 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 18.36 % Favored : 79.38 % 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: 0.52 (0.27), residues: 1002 helix: 2.17 (0.28), residues: 381 sheet: 0.00 (0.33), residues: 216 loop : -1.26 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 19 TYR 0.010 0.001 TYR N 80 PHE 0.025 0.001 PHE R 119 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 ( 8086) covalent geometry : angle 0.48182 / 0.25 (10963) SS BOND : bond 0.00189 / 0.09 ( 3) SS BOND : angle 1.05836 / 0.47 ( 6) hydrogen bonds : bond 0.02923 / 1.96 ( 394) hydrogen bonds : angle 3.62812 / 2.57 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7041 (t80) cc_final: 0.6729 (t80) REVERT: R 116 MET cc_start: 0.6892 (tpp) cc_final: 0.6327 (tpt) REVERT: R 228 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6784 (mtp85) REVERT: R 278 LEU cc_start: 0.7749 (mt) cc_final: 0.7436 (mt) REVERT: R 282 ILE cc_start: 0.8407 (tt) cc_final: 0.8140 (pt) REVERT: A 20 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6845 (tpp80) REVERT: A 24 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7064 (ttmm) REVERT: A 27 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7368 (mm-30) REVERT: A 314 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 356 ARG cc_start: 0.8476 (pmm-80) cc_final: 0.8185 (ptp-170) REVERT: B 19 ARG cc_start: 0.7207 (ttm110) cc_final: 0.6927 (ttm110) REVERT: B 32 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8368 (tp40) REVERT: B 46 ARG cc_start: 0.8379 (ptp-110) cc_final: 0.7651 (mtt90) REVERT: B 160 SER cc_start: 0.8816 (m) cc_final: 0.8555 (p) REVERT: B 214 ARG cc_start: 0.7741 (mpt180) cc_final: 0.7398 (mpt180) REVERT: B 260 GLU cc_start: 0.8608 (pt0) cc_final: 0.8030 (pt0) REVERT: B 266 HIS cc_start: 0.8421 (t70) cc_final: 0.8195 (t70) REVERT: G 42 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7815 (tm-30) REVERT: N 86 LEU cc_start: 0.9102 (mp) cc_final: 0.8863 (mp) REVERT: N 89 GLU cc_start: 0.9117 (mp0) cc_final: 0.8894 (mp0) REVERT: N 105 ARG cc_start: 0.8368 (mtp180) cc_final: 0.7721 (mtm-85) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 0.6157 time to fit residues: 94.5460 Evaluate side-chains 142 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 MET Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 228 ARG Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 68 HIS R 307 ASN B 17 GLN B 266 HIS G 5 ASN N 77 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100249 restraints weight = 9849.224| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.59 r_work: 0.3068 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8089 Z= 0.267 Angle : 0.629 9.903 10969 Z= 0.324 Chirality : 0.045 0.161 1252 Planarity : 0.005 0.056 1402 Dihedral : 4.654 45.220 1118 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.81 % Allowed : 19.19 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.39 (0.27), residues: 1002 helix: 2.01 (0.28), residues: 383 sheet: -0.08 (0.33), residues: 219 loop : -1.30 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 19 TYR 0.019 0.002 TYR B 105 PHE 0.038 0.002 PHE R 119 TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 ( 8086) covalent geometry : angle 0.62754 / 0.32 (10963) SS BOND : bond 0.00326 / 0.16 ( 3) SS BOND : angle 2.20590 / 0.96 ( 6) hydrogen bonds : bond 0.04314 / 2.89 ( 394) hydrogen bonds : angle 4.12187 / 2.93 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: R 48 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.6097 (ttp-170) REVERT: R 76 PHE cc_start: 0.7131 (t80) cc_final: 0.6797 (t80) REVERT: R 116 MET cc_start: 0.7072 (tpp) cc_final: 0.6454 (tpt) REVERT: R 282 ILE cc_start: 0.8398 (tt) cc_final: 0.8129 (pt) REVERT: A 20 ARG cc_start: 0.7240 (mtp85) cc_final: 0.6983 (tpp80) REVERT: A 24 LYS cc_start: 0.7736 (ttpp) cc_final: 0.7234 (ttmm) REVERT: B 32 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8426 (tp-100) REVERT: B 96 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8080 (ttp-110) REVERT: B 111 TYR cc_start: 0.9054 (m-80) cc_final: 0.8800 (m-80) REVERT: B 214 ARG cc_start: 0.7835 (mpt180) cc_final: 0.7506 (mpt180) REVERT: B 260 GLU cc_start: 0.8629 (pt0) cc_final: 0.8014 (pt0) REVERT: B 271 CYS cc_start: 0.8933 (p) cc_final: 0.8375 (p) REVERT: G 42 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7844 (tm-30) REVERT: N 73 ASP cc_start: 0.7162 (t70) cc_final: 0.6663 (t70) REVERT: N 89 GLU cc_start: 0.9118 (mp0) cc_final: 0.8904 (mp0) REVERT: N 105 ARG cc_start: 0.8330 (mtp180) cc_final: 0.7707 (mtm-85) outliers start: 32 outliers final: 14 residues processed: 144 average time/residue: 0.5729 time to fit residues: 86.9704 Evaluate side-chains 142 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 ARG Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 5 ASN Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 0.0670 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 307 ASN B 340 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104383 restraints weight = 9821.349| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.61 r_work: 0.3125 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8089 Z= 0.110 Angle : 0.530 8.741 10969 Z= 0.270 Chirality : 0.041 0.141 1252 Planarity : 0.004 0.055 1402 Dihedral : 4.278 36.735 1118 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.10 % Allowed : 19.55 % Favored : 77.35 % 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: 0.56 (0.27), residues: 1002 helix: 2.16 (0.28), residues: 382 sheet: 0.01 (0.33), residues: 222 loop : -1.23 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 19 TYR 0.012 0.001 TYR N 80 PHE 0.039 0.001 PHE R 119 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 ( 8086) covalent geometry : angle 0.52952 / 0.27 (10963) SS BOND : bond 0.00176 / 0.09 ( 3) SS BOND : angle 1.29457 / 0.56 ( 6) hydrogen bonds : bond 0.03317 / 2.21 ( 394) hydrogen bonds : angle 3.82262 / 2.71 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7056 (t80) cc_final: 0.6722 (t80) REVERT: R 116 MET cc_start: 0.6988 (tpp) cc_final: 0.6539 (tpt) REVERT: R 278 LEU cc_start: 0.7651 (mt) cc_final: 0.7328 (mt) REVERT: R 282 ILE cc_start: 0.8378 (tt) cc_final: 0.8104 (pt) REVERT: A 20 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6839 (tpp80) REVERT: A 24 LYS cc_start: 0.7673 (ttpp) cc_final: 0.7155 (ttmm) REVERT: A 314 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 356 ARG cc_start: 0.8409 (pmm-80) cc_final: 0.8128 (ptp-170) REVERT: B 32 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8374 (tp-100) REVERT: B 46 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7574 (mtt90) REVERT: B 96 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8093 (ttp-110) REVERT: B 214 ARG cc_start: 0.7806 (mpt180) cc_final: 0.7435 (mpt180) REVERT: B 234 PHE cc_start: 0.9288 (OUTLIER) cc_final: 0.7737 (m-80) REVERT: B 260 GLU cc_start: 0.8524 (pt0) cc_final: 0.7956 (pt0) REVERT: B 266 HIS cc_start: 0.8341 (t70) cc_final: 0.8108 (t70) REVERT: B 271 CYS cc_start: 0.8822 (p) cc_final: 0.8260 (p) REVERT: N 88 PRO cc_start: 0.9426 (Cg_exo) cc_final: 0.9136 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9117 (mp0) cc_final: 0.8791 (mp0) REVERT: N 105 ARG cc_start: 0.8297 (mtp180) cc_final: 0.7676 (mtm-85) outliers start: 26 outliers final: 16 residues processed: 147 average time/residue: 0.5946 time to fit residues: 91.8742 Evaluate side-chains 143 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 65 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 307 ASN A 29 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.156170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105490 restraints weight = 9770.756| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.61 r_work: 0.3146 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8089 Z= 0.107 Angle : 0.526 9.325 10969 Z= 0.268 Chirality : 0.041 0.140 1252 Planarity : 0.004 0.051 1402 Dihedral : 4.094 28.363 1118 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.74 % Allowed : 19.55 % Favored : 77.71 % 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: 0.66 (0.27), residues: 1002 helix: 2.23 (0.28), residues: 382 sheet: 0.11 (0.33), residues: 218 loop : -1.16 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 38 TYR 0.010 0.001 TYR N 80 PHE 0.019 0.001 PHE R 119 TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8086) covalent geometry : angle 0.52510 / 0.27 (10963) SS BOND : bond 0.00168 / 0.08 ( 3) SS BOND : angle 1.26174 / 0.55 ( 6) hydrogen bonds : bond 0.03142 / 2.10 ( 394) hydrogen bonds : angle 3.71704 / 2.64 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7075 (t80) cc_final: 0.6777 (t80) REVERT: R 116 MET cc_start: 0.6971 (tpp) cc_final: 0.6340 (tpt) REVERT: R 278 LEU cc_start: 0.7641 (mt) cc_final: 0.7298 (mt) REVERT: R 282 ILE cc_start: 0.8398 (tt) cc_final: 0.8122 (pt) REVERT: A 20 ARG cc_start: 0.7057 (mtp85) cc_final: 0.6815 (tpp80) REVERT: A 24 LYS cc_start: 0.7653 (ttpp) cc_final: 0.7131 (ttmm) REVERT: A 314 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 356 ARG cc_start: 0.8330 (pmm-80) cc_final: 0.8108 (ptp-170) REVERT: B 19 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6855 (ttm110) REVERT: B 32 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8373 (tp-100) REVERT: B 46 ARG cc_start: 0.8349 (ptp-110) cc_final: 0.7554 (mtt90) REVERT: B 96 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8133 (ttp-110) REVERT: B 214 ARG cc_start: 0.7855 (mpt180) cc_final: 0.7497 (mpt180) REVERT: B 266 HIS cc_start: 0.8360 (t70) cc_final: 0.8127 (t70) REVERT: B 271 CYS cc_start: 0.8795 (p) cc_final: 0.8196 (p) REVERT: N 86 LEU cc_start: 0.9086 (mp) cc_final: 0.8828 (mp) REVERT: N 88 PRO cc_start: 0.9426 (Cg_exo) cc_final: 0.9168 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9095 (mp0) cc_final: 0.8645 (mp0) REVERT: N 105 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7703 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 140 average time/residue: 0.5567 time to fit residues: 82.2929 Evaluate side-chains 144 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 1.9990 chunk 97 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 0.0010 chunk 10 optimal weight: 0.0970 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 68 HIS R 307 ASN B 17 GLN B 266 HIS N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.155842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105383 restraints weight = 9764.720| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.60 r_work: 0.3105 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8089 Z= 0.119 Angle : 0.529 9.020 10969 Z= 0.269 Chirality : 0.041 0.149 1252 Planarity : 0.004 0.051 1402 Dihedral : 4.077 23.286 1118 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.74 % Allowed : 19.67 % Favored : 77.59 % 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: 0.72 (0.27), residues: 1002 helix: 2.25 (0.28), residues: 383 sheet: 0.15 (0.33), residues: 217 loop : -1.11 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 19 TYR 0.016 0.001 TYR R 161 PHE 0.023 0.001 PHE R 119 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8086) covalent geometry : angle 0.52771 / 0.27 (10963) SS BOND : bond 0.00172 / 0.08 ( 3) SS BOND : angle 1.34612 / 0.58 ( 6) hydrogen bonds : bond 0.03193 / 2.14 ( 394) hydrogen bonds : angle 3.72706 / 2.65 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7104 (t80) cc_final: 0.6795 (t80) REVERT: R 116 MET cc_start: 0.7078 (tpp) cc_final: 0.6502 (tpt) REVERT: R 130 MET cc_start: 0.7582 (ttm) cc_final: 0.7366 (mtm) REVERT: R 278 LEU cc_start: 0.7690 (mt) cc_final: 0.7355 (mt) REVERT: R 282 ILE cc_start: 0.8531 (tt) cc_final: 0.8276 (pt) REVERT: A 20 ARG cc_start: 0.7108 (mtp85) cc_final: 0.6877 (tpp80) REVERT: A 24 LYS cc_start: 0.7716 (ttpp) cc_final: 0.7194 (ttmm) REVERT: A 314 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 19 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6851 (ttm110) REVERT: B 32 GLN cc_start: 0.8706 (tp-100) cc_final: 0.8380 (tp-100) REVERT: B 46 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7613 (mtt90) REVERT: B 96 ARG cc_start: 0.8530 (mmm-85) cc_final: 0.8118 (ttp-110) REVERT: B 214 ARG cc_start: 0.7910 (mpt180) cc_final: 0.7546 (mpt180) REVERT: B 234 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.7868 (m-80) REVERT: B 266 HIS cc_start: 0.8296 (t-170) cc_final: 0.8093 (t70) REVERT: N 86 LEU cc_start: 0.9087 (mp) cc_final: 0.8853 (mp) REVERT: N 88 PRO cc_start: 0.9463 (Cg_exo) cc_final: 0.9222 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9100 (mp0) cc_final: 0.8561 (mp0) REVERT: N 105 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7710 (mtm-85) outliers start: 23 outliers final: 18 residues processed: 144 average time/residue: 0.5676 time to fit residues: 86.1582 Evaluate side-chains 149 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 305 SER Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 68 HIS R 307 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102994 restraints weight = 9809.214| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.57 r_work: 0.3099 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8089 Z= 0.188 Angle : 0.594 11.903 10969 Z= 0.302 Chirality : 0.043 0.162 1252 Planarity : 0.004 0.050 1402 Dihedral : 4.285 24.018 1118 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.03 % Allowed : 20.02 % Favored : 77.95 % 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: 0.64 (0.27), residues: 1002 helix: 2.12 (0.28), residues: 385 sheet: 0.15 (0.33), residues: 217 loop : -1.12 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.016 0.002 TYR R 161 PHE 0.026 0.002 PHE R 119 TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 8086) covalent geometry : angle 0.59266 / 0.30 (10963) SS BOND : bond 0.00239 / 0.11 ( 3) SS BOND : angle 1.81575 / 0.79 ( 6) hydrogen bonds : bond 0.03704 / 2.48 ( 394) hydrogen bonds : angle 3.90541 / 2.78 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: R 76 PHE cc_start: 0.7206 (t80) cc_final: 0.6871 (t80) REVERT: R 116 MET cc_start: 0.7027 (tpp) cc_final: 0.6589 (tpt) REVERT: R 282 ILE cc_start: 0.8404 (tt) cc_final: 0.8133 (pt) REVERT: A 20 ARG cc_start: 0.7091 (mtp85) cc_final: 0.6846 (tpp80) REVERT: A 24 LYS cc_start: 0.7708 (ttpp) cc_final: 0.7191 (ttmm) REVERT: A 356 ARG cc_start: 0.8265 (pmm-80) cc_final: 0.7997 (ptp-170) REVERT: B 32 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8387 (tp-100) REVERT: B 46 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7555 (mtt90) REVERT: B 96 ARG cc_start: 0.8571 (mmm-85) cc_final: 0.8132 (ttp-110) REVERT: B 214 ARG cc_start: 0.7942 (mpt180) cc_final: 0.7579 (mpt180) REVERT: B 234 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: B 271 CYS cc_start: 0.8910 (p) cc_final: 0.8326 (p) REVERT: N 86 LEU cc_start: 0.9085 (mp) cc_final: 0.8847 (mp) REVERT: N 88 PRO cc_start: 0.9470 (Cg_exo) cc_final: 0.9212 (Cg_endo) REVERT: N 89 GLU cc_start: 0.9096 (mp0) cc_final: 0.8571 (mp0) REVERT: N 105 ARG cc_start: 0.8330 (mtp180) cc_final: 0.7731 (mtm-85) outliers start: 17 outliers final: 14 residues processed: 136 average time/residue: 0.5937 time to fit residues: 84.8760 Evaluate side-chains 140 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 169 SER Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 307 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 68 HIS R 191 HIS N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106137 restraints weight = 9777.996| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.61 r_work: 0.3126 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8089 Z= 0.100 Angle : 0.527 9.228 10969 Z= 0.268 Chirality : 0.041 0.152 1252 Planarity : 0.004 0.051 1402 Dihedral : 4.045 26.085 1118 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.15 % Allowed : 20.14 % Favored : 77.71 % 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: 0.83 (0.27), residues: 1002 helix: 2.39 (0.28), residues: 377 sheet: 0.17 (0.33), residues: 217 loop : -1.02 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 19 TYR 0.015 0.001 TYR R 161 PHE 0.016 0.001 PHE A 212 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 8086) covalent geometry : angle 0.52700 / 0.27 (10963) SS BOND : bond 0.00172 / 0.08 ( 3) SS BOND : angle 1.07101 / 0.47 ( 6) hydrogen bonds : bond 0.03064 / 2.05 ( 394) hydrogen bonds : angle 3.68008 / 2.61 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3191.07 seconds wall clock time: 54 minutes 55.05 seconds (3295.05 seconds total)