Starting phenix.real_space_refine on Wed Mar 4 00:13:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8l_31803/03_2026/7v8l_31803_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8l_31803/03_2026/7v8l_31803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v8l_31803/03_2026/7v8l_31803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8l_31803/03_2026/7v8l_31803.map" model { file = "/net/cci-nas-00/data/ceres_data/7v8l_31803/03_2026/7v8l_31803_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8l_31803/03_2026/7v8l_31803_neut_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4 atoms to isotropic. 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 51 5.16 5 C 6066 2.51 5 N 1648 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9505 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3010 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 394} Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 3, 'TRP:plan': 1, 'GLN:plan1': 4, 'ASN:plan1': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 104 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 2, 'TRANS': 11} Chain: "C" Number of atoms: 2845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2845 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 21, 'TRANS': 374} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 8, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 104 Chain: "D" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1742 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1742 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'PCJ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.24 Number of scatterers: 9505 At special positions: 0 Unit cell: (106.08, 82.16, 154.96, 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 51 16.00 O 1740 8.00 N 1648 7.00 C 6066 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: 0.70 Conformation dependent library (CDL) restraints added in 463.9 milliseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB PCJ C 401 " Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 7 sheets defined 51.9% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'E' and resid 5 through 7 No H-bonds generated for 'chain 'E' and resid 5 through 7' Processing helix chain 'E' and resid 8 through 16 Processing helix chain 'E' and resid 24 through 59 Processing helix chain 'E' and resid 77 through 87 removed outlier: 3.823A pdb=" N LYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 removed outlier: 3.836A pdb=" N ARG E 125 " --> pdb=" O GLN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.595A pdb=" N LEU E 179 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET E 180 " --> pdb=" O HIS E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 180' Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 233 through 245 removed outlier: 3.537A pdb=" N LEU E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 298 removed outlier: 6.061A pdb=" N TYR E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N MET E 261 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 307 Processing helix chain 'E' and resid 313 through 341 removed outlier: 3.527A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 376 through 404 removed outlier: 4.487A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix Processing helix chain 'E' and resid 406 through 412 Processing helix chain 'C' and resid 4 through 14 removed outlier: 4.313A pdb=" N PHE C 8 " --> pdb=" O PRO C 4 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 28 Processing helix chain 'C' and resid 28 through 59 Processing helix chain 'C' and resid 60 through 63 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 125 through 127 No H-bonds generated for 'chain 'C' and resid 125 through 127' Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 194 through 198 Processing helix chain 'C' and resid 205 through 212 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 249 through 271 removed outlier: 3.621A pdb=" N GLY C 254 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 271 " --> pdb=" O MET C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 303 removed outlier: 3.997A pdb=" N VAL C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 337 removed outlier: 3.505A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 Processing helix chain 'C' and resid 361 through 390 removed outlier: 4.276A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Proline residue: C 383 - end of helix Processing helix chain 'C' and resid 391 through 397 removed outlier: 3.786A pdb=" N ALA C 395 " --> pdb=" O GLN C 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 56 removed outlier: 3.634A pdb=" N LEU D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 103 through 115 Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 118 through 134 removed outlier: 3.675A pdb=" N ILE D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 147 through 160 Processing helix chain 'D' and resid 177 through 194 removed outlier: 4.233A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 removed outlier: 3.617A pdb=" N ARG D 211 " --> pdb=" O GLN D 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 56 removed outlier: 3.932A pdb=" N LEU F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 103 through 115 Proline residue: F 111 - end of helix removed outlier: 3.598A pdb=" N GLY F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 134 removed outlier: 3.955A pdb=" N ILE F 122 " --> pdb=" O LYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 138 Processing helix chain 'F' and resid 147 through 160 Processing helix chain 'F' and resid 177 through 194 removed outlier: 4.186A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 210 Processing sheet with id=AA1, first strand: chain 'E' and resid 250 through 253 removed outlier: 7.434A pdb=" N ILE E 150 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE E 192 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 204 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 129 through 130 removed outlier: 4.029A pdb=" N THR C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL C 144 " --> pdb=" O GLY C 188 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N PHE C 190 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 146 " --> pdb=" O PHE C 190 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 147 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU C 200 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N MET C 201 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 113 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL C 203 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU C 115 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 130 removed outlier: 4.029A pdb=" N THR C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N GLY C 176 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N SER C 170 " --> pdb=" O GLY C 176 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N ILE C 178 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N SER C 168 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N ALA C 169 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 14.759A pdb=" N THR C 98 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 21.151A pdb=" N GLN C 171 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 26.416A pdb=" N ILE C 96 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 33.208A pdb=" N THR C 173 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 38.245A pdb=" N ALA C 94 " --> pdb=" O THR C 173 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 7 through 12 removed outlier: 4.369A pdb=" N LEU D 11 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER D 63 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE D 68 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.823A pdb=" N ILE D 40 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA D 39 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET D 218 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA D 225 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ARG D 219 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 6 through 12 removed outlier: 4.701A pdb=" N LEU F 11 " --> pdb=" O SER F 63 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER F 63 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 89 through 92 removed outlier: 3.699A pdb=" N ASP F 170 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA F 39 " --> pdb=" O LEU F 216 " (cutoff:3.500A) 540 hydrogen bonds defined for protein. 1539 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: 1.56 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1589 1.30 - 1.43: 2242 1.43 - 1.55: 5732 1.55 - 1.68: 0 1.68 - 1.81: 96 Bond restraints: 9659 Sorted by residual: bond pdb=" CA ILE E 365 " pdb=" CB ILE E 365 " ideal model delta sigma weight residual 1.540 1.455 0.085 1.36e-02 5.41e+03 3.91e+01 bond pdb=" CA ASN C 265 " pdb=" C ASN C 265 " ideal model delta sigma weight residual 1.523 1.449 0.075 1.30e-02 5.92e+03 3.29e+01 bond pdb=" CA MET C 267 " pdb=" C MET C 267 " ideal model delta sigma weight residual 1.523 1.443 0.080 1.41e-02 5.03e+03 3.22e+01 bond pdb=" N ASN C 265 " pdb=" CA ASN C 265 " ideal model delta sigma weight residual 1.459 1.391 0.068 1.21e-02 6.83e+03 3.17e+01 bond pdb=" C ASN C 265 " pdb=" O ASN C 265 " ideal model delta sigma weight residual 1.237 1.173 0.064 1.17e-02 7.31e+03 3.00e+01 ... (remaining 9654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 12977 3.09 - 6.18: 109 6.18 - 9.28: 16 9.28 - 12.37: 5 12.37 - 15.46: 2 Bond angle restraints: 13109 Sorted by residual: angle pdb=" N MET C 267 " pdb=" CA MET C 267 " pdb=" C MET C 267 " ideal model delta sigma weight residual 113.20 97.74 15.46 1.21e+00 6.83e-01 1.63e+02 angle pdb=" N PHE E 367 " pdb=" CA PHE E 367 " pdb=" C PHE E 367 " ideal model delta sigma weight residual 112.72 120.52 -7.80 1.14e+00 7.69e-01 4.68e+01 angle pdb=" N LYS C 264 " pdb=" CA LYS C 264 " pdb=" C LYS C 264 " ideal model delta sigma weight residual 111.28 104.93 6.35 1.09e+00 8.42e-01 3.40e+01 angle pdb=" N ASN C 265 " pdb=" CA ASN C 265 " pdb=" C ASN C 265 " ideal model delta sigma weight residual 111.28 105.33 5.95 1.09e+00 8.42e-01 2.98e+01 angle pdb=" C GLU C 263 " pdb=" CA GLU C 263 " pdb=" CB GLU C 263 " ideal model delta sigma weight residual 110.90 103.10 7.80 1.58e+00 4.01e-01 2.44e+01 ... (remaining 13104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.01: 5513 26.01 - 52.02: 288 52.02 - 78.03: 45 78.03 - 104.04: 2 104.04 - 130.05: 3 Dihedral angle restraints: 5851 sinusoidal: 2217 harmonic: 3634 Sorted by residual: dihedral pdb=" C PCJ C 401 " pdb=" N PCJ C 401 " pdb=" CA PCJ C 401 " pdb=" C66 PCJ C 401 " ideal model delta sinusoidal sigma weight residual 226.93 96.88 130.05 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C TYR E 366 " pdb=" N TYR E 366 " pdb=" CA TYR E 366 " pdb=" CB TYR E 366 " ideal model delta harmonic sigma weight residual -122.60 -112.46 -10.14 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" CB PCJ C 401 " pdb=" N PCJ C 401 " pdb=" CA PCJ C 401 " pdb=" C66 PCJ C 401 " ideal model delta sinusoidal sigma weight residual 103.11 -19.47 122.58 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 5848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1449 0.088 - 0.175: 104 0.175 - 0.263: 4 0.263 - 0.351: 2 0.351 - 0.438: 2 Chirality restraints: 1561 Sorted by residual: chirality pdb=" CA PHE E 367 " pdb=" N PHE E 367 " pdb=" C PHE E 367 " pdb=" CB PHE E 367 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" CA ASP E 364 " pdb=" N ASP E 364 " pdb=" C ASP E 364 " pdb=" CB ASP E 364 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA MET C 266 " pdb=" N MET C 266 " pdb=" C MET C 266 " pdb=" CB MET C 266 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1558 not shown) Planarity restraints: 1685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 25 " 0.139 9.50e-02 1.11e+02 8.16e-02 3.73e+01 pdb=" NE ARG A 25 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 25 " 0.101 2.00e-02 2.50e+03 pdb=" NH1 ARG A 25 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG A 25 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 262 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C MET C 262 " -0.091 2.00e-02 2.50e+03 pdb=" O MET C 262 " 0.033 2.00e-02 2.50e+03 pdb=" N GLU C 263 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 321 " 0.023 2.00e-02 2.50e+03 1.77e-02 7.84e+00 pdb=" CG TRP E 321 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP E 321 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 321 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 321 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 321 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 321 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 321 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 321 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 321 " 0.002 2.00e-02 2.50e+03 ... (remaining 1682 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 691 2.74 - 3.28: 9685 3.28 - 3.82: 15033 3.82 - 4.36: 17065 4.36 - 4.90: 29629 Nonbonded interactions: 72103 Sorted by model distance: nonbonded pdb=" N MET C 267 " pdb=" N GLY C 268 " model vdw 2.198 2.560 nonbonded pdb=" O ASP C 123 " pdb=" OG1 THR C 126 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASP C 233 " pdb=" N SER C 234 " model vdw 2.233 3.120 nonbonded pdb=" OE1 GLU F 217 " pdb=" OG1 THR F 224 " model vdw 2.265 3.040 nonbonded pdb=" O SER F 43 " pdb=" OG SER F 46 " model vdw 2.282 3.040 ... (remaining 72098 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 'D' selection = chain 'F' } 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.780 Find NCS groups from input model: 0.070 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 9659 Z= 0.310 Angle : 0.792 15.459 13109 Z= 0.442 Chirality : 0.048 0.438 1561 Planarity : 0.006 0.082 1685 Dihedral : 15.566 130.054 3511 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.24 % Favored : 96.61 % Rotamer: Outliers : 1.03 % Allowed : 0.62 % Favored : 98.36 % Cbeta Deviations : 0.09 % 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 (0.23), residues: 1267 helix: 0.77 (0.22), residues: 596 sheet: -0.20 (0.39), residues: 166 loop : -0.81 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.001 ARG A 25 TYR 0.021 0.002 TYR E 366 PHE 0.028 0.001 PHE E 367 TRP 0.048 0.002 TRP E 321 HIS 0.005 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 9659) covalent geometry : angle 0.79221 (13109) hydrogen bonds : bond 0.14067 ( 526) hydrogen bonds : angle 6.31143 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: E 228 MET cc_start: 0.6321 (mmp) cc_final: 0.6071 (mmt) REVERT: E 364 ASP cc_start: 0.5531 (OUTLIER) cc_final: 0.5186 (p0) REVERT: C 264 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8445 (ttmt) REVERT: D 81 LYS cc_start: 0.6582 (mttp) cc_final: 0.6067 (mtpt) REVERT: D 153 ARG cc_start: 0.4461 (ttp-170) cc_final: 0.3550 (tpt170) REVERT: D 212 MET cc_start: -0.1773 (mmp) cc_final: -0.2320 (tpt) REVERT: F 37 MET cc_start: 0.6303 (tmm) cc_final: 0.6066 (mtp) REVERT: F 52 LEU cc_start: 0.6337 (tt) cc_final: 0.5924 (mt) REVERT: F 212 MET cc_start: 0.2951 (mmp) cc_final: 0.0864 (mmm) outliers start: 10 outliers final: 4 residues processed: 247 average time/residue: 0.0920 time to fit residues: 31.4700 Evaluate side-chains 182 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 176 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 218 ASN D 53 HIS D 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.231636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.186077 restraints weight = 13690.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.188389 restraints weight = 7743.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.190391 restraints weight = 4944.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.191515 restraints weight = 4397.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.191278 restraints weight = 3676.110| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9659 Z= 0.177 Angle : 0.708 9.922 13109 Z= 0.349 Chirality : 0.047 0.229 1561 Planarity : 0.005 0.054 1685 Dihedral : 10.302 156.817 1427 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.67 % Allowed : 11.59 % Favored : 85.74 % 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: 0.09 (0.23), residues: 1267 helix: 0.76 (0.21), residues: 609 sheet: -0.24 (0.39), residues: 178 loop : -0.59 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 53 TYR 0.016 0.001 TYR E 260 PHE 0.013 0.002 PHE E 319 TRP 0.028 0.002 TRP E 321 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 9659) covalent geometry : angle 0.70791 (13109) hydrogen bonds : bond 0.04122 ( 526) hydrogen bonds : angle 4.95172 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 84 HIS cc_start: 0.7044 (m170) cc_final: 0.6740 (m-70) REVERT: E 86 GLN cc_start: 0.7132 (tt0) cc_final: 0.6859 (mt0) REVERT: E 205 MET cc_start: 0.6441 (mtm) cc_final: 0.6046 (mtm) REVERT: E 228 MET cc_start: 0.7512 (mmp) cc_final: 0.7141 (mmt) REVERT: E 289 SER cc_start: 0.8649 (m) cc_final: 0.8412 (t) REVERT: C 48 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7935 (mtt) REVERT: C 293 LYS cc_start: 0.8491 (ttmm) cc_final: 0.8220 (mtpp) REVERT: D 153 ARG cc_start: 0.5159 (ttp-170) cc_final: 0.3696 (tpt-90) REVERT: D 170 ASP cc_start: 0.6739 (m-30) cc_final: 0.6532 (m-30) REVERT: F 38 MET cc_start: 0.4336 (mtp) cc_final: 0.3886 (mtt) REVERT: F 52 LEU cc_start: 0.7314 (tt) cc_final: 0.6369 (mt) REVERT: F 53 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6347 (t-90) REVERT: F 146 LEU cc_start: 0.5675 (mt) cc_final: 0.5385 (mt) outliers start: 26 outliers final: 14 residues processed: 217 average time/residue: 0.0795 time to fit residues: 25.2532 Evaluate side-chains 193 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 108 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN E 359 GLN C 153 GLN C 218 ASN D 53 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.215461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.170745 restraints weight = 13609.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.171819 restraints weight = 7385.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.173928 restraints weight = 5140.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.175077 restraints weight = 3784.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175080 restraints weight = 3478.262| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9659 Z= 0.134 Angle : 0.616 8.823 13109 Z= 0.304 Chirality : 0.044 0.232 1561 Planarity : 0.005 0.051 1685 Dihedral : 9.975 161.031 1417 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.49 % Allowed : 15.90 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1267 helix: 0.99 (0.21), residues: 606 sheet: -0.29 (0.39), residues: 173 loop : -0.48 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.017 0.001 TYR C 214 PHE 0.013 0.001 PHE E 319 TRP 0.016 0.001 TRP E 321 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9659) covalent geometry : angle 0.61609 (13109) hydrogen bonds : bond 0.03762 ( 526) hydrogen bonds : angle 4.71531 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7578 (pp20) cc_final: 0.7362 (pp20) REVERT: E 86 GLN cc_start: 0.7198 (tt0) cc_final: 0.6967 (mt0) REVERT: A 23 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7926 (tt) REVERT: C 48 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: C 266 MET cc_start: 0.8328 (tpp) cc_final: 0.7993 (tpp) REVERT: C 293 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8353 (mtpp) REVERT: D 37 MET cc_start: 0.4994 (tmm) cc_final: 0.4558 (tmm) REVERT: D 153 ARG cc_start: 0.5304 (ttp-170) cc_final: 0.3982 (tpt-90) REVERT: F 37 MET cc_start: 0.5463 (tmm) cc_final: 0.5243 (tmm) REVERT: F 38 MET cc_start: 0.4177 (mtp) cc_final: 0.3781 (mtt) REVERT: F 53 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.6872 (t-90) outliers start: 34 outliers final: 21 residues processed: 206 average time/residue: 0.0759 time to fit residues: 23.0303 Evaluate side-chains 208 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN C 153 GLN C 218 ASN D 53 HIS D 97 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.211913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.163833 restraints weight = 13677.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.167512 restraints weight = 8534.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.171444 restraints weight = 4693.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.171787 restraints weight = 3635.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.172085 restraints weight = 3411.374| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9659 Z= 0.143 Angle : 0.628 9.258 13109 Z= 0.307 Chirality : 0.044 0.233 1561 Planarity : 0.005 0.052 1685 Dihedral : 9.907 161.621 1417 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.49 % Allowed : 18.56 % 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: 0.42 (0.24), residues: 1267 helix: 1.15 (0.21), residues: 602 sheet: -0.26 (0.39), residues: 176 loop : -0.51 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.024 0.002 TYR C 214 PHE 0.013 0.001 PHE E 319 TRP 0.017 0.001 TRP C 246 HIS 0.004 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9659) covalent geometry : angle 0.62832 (13109) hydrogen bonds : bond 0.03646 ( 526) hydrogen bonds : angle 4.59176 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7554 (pp20) cc_final: 0.6936 (pp20) REVERT: E 84 HIS cc_start: 0.7055 (m170) cc_final: 0.6566 (m170) REVERT: C 48 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: C 293 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8185 (mmmm) REVERT: C 303 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: D 37 MET cc_start: 0.4911 (tmm) cc_final: 0.4466 (tmm) REVERT: D 97 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6702 (m90) REVERT: D 153 ARG cc_start: 0.5540 (ttp-170) cc_final: 0.3947 (tpt-90) REVERT: F 37 MET cc_start: 0.5353 (tmm) cc_final: 0.5139 (tmm) REVERT: F 38 MET cc_start: 0.3850 (mtp) cc_final: 0.3610 (mtt) REVERT: F 53 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7109 (t-90) REVERT: F 150 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7804 (mm-30) outliers start: 34 outliers final: 18 residues processed: 224 average time/residue: 0.0736 time to fit residues: 24.2084 Evaluate side-chains 219 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN E 99 ASN C 76 ASN C 153 GLN D 53 HIS ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.224717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.180351 restraints weight = 13880.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.182404 restraints weight = 7185.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.184335 restraints weight = 4597.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.184689 restraints weight = 4131.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.184900 restraints weight = 3651.614| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9659 Z= 0.110 Angle : 0.602 10.307 13109 Z= 0.290 Chirality : 0.043 0.205 1561 Planarity : 0.004 0.051 1685 Dihedral : 9.806 160.968 1415 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.90 % Allowed : 20.51 % Favored : 75.59 % 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: 0.65 (0.24), residues: 1267 helix: 1.38 (0.21), residues: 600 sheet: -0.17 (0.40), residues: 176 loop : -0.44 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 53 TYR 0.034 0.002 TYR C 214 PHE 0.011 0.001 PHE E 319 TRP 0.014 0.001 TRP C 246 HIS 0.016 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9659) covalent geometry : angle 0.60175 (13109) hydrogen bonds : bond 0.03460 ( 526) hydrogen bonds : angle 4.42439 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 HIS cc_start: 0.7103 (m170) cc_final: 0.6716 (m170) REVERT: C 48 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8153 (mtt) REVERT: C 92 ARG cc_start: 0.7068 (ttt90) cc_final: 0.6544 (ttt90) REVERT: C 293 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8326 (mmmm) REVERT: C 299 ILE cc_start: 0.8613 (mm) cc_final: 0.7918 (mm) REVERT: C 303 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.5870 (mp10) REVERT: C 344 MET cc_start: 0.3853 (mmt) cc_final: 0.3410 (tpp) REVERT: D 37 MET cc_start: 0.5384 (tmm) cc_final: 0.4416 (tmm) REVERT: D 73 MET cc_start: 0.7574 (ppp) cc_final: 0.6661 (ppp) REVERT: D 153 ARG cc_start: 0.5523 (ttp-170) cc_final: 0.3892 (tpt-90) REVERT: F 37 MET cc_start: 0.5592 (tmm) cc_final: 0.5383 (tmm) REVERT: F 38 MET cc_start: 0.4222 (mtp) cc_final: 0.3930 (mtt) REVERT: F 53 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.7063 (t-90) REVERT: F 214 ARG cc_start: 0.4464 (ttt180) cc_final: 0.4039 (ttt-90) outliers start: 38 outliers final: 20 residues processed: 222 average time/residue: 0.0762 time to fit residues: 25.3427 Evaluate side-chains 208 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 181 GLN Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.214525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.167878 restraints weight = 13899.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.169672 restraints weight = 8042.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.173038 restraints weight = 5339.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173062 restraints weight = 4387.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.173177 restraints weight = 4000.741| |-----------------------------------------------------------------------------| r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9659 Z= 0.190 Angle : 0.696 9.700 13109 Z= 0.341 Chirality : 0.046 0.242 1561 Planarity : 0.005 0.052 1685 Dihedral : 9.938 159.982 1415 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.82 % Allowed : 20.82 % Favored : 74.36 % 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: 0.41 (0.24), residues: 1267 helix: 1.14 (0.21), residues: 600 sheet: -0.43 (0.39), residues: 174 loop : -0.42 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 17 TYR 0.032 0.002 TYR C 214 PHE 0.014 0.002 PHE E 100 TRP 0.022 0.002 TRP C 246 HIS 0.005 0.001 HIS E 188 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9659) covalent geometry : angle 0.69576 (13109) hydrogen bonds : bond 0.03953 ( 526) hydrogen bonds : angle 4.68029 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 84 HIS cc_start: 0.7300 (m170) cc_final: 0.7025 (m170) REVERT: E 180 MET cc_start: 0.2972 (mmt) cc_final: 0.1811 (ptp) REVERT: C 48 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: C 92 ARG cc_start: 0.7211 (ttt90) cc_final: 0.6565 (ttt90) REVERT: C 289 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7760 (ttm) REVERT: C 293 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8303 (mmmm) REVERT: C 303 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.6774 (mt0) REVERT: D 37 MET cc_start: 0.5342 (tmm) cc_final: 0.4040 (mmt) REVERT: D 73 MET cc_start: 0.7682 (ppp) cc_final: 0.7042 (ppp) REVERT: D 97 HIS cc_start: 0.7638 (m170) cc_final: 0.7430 (m-70) REVERT: D 112 LEU cc_start: 0.8206 (mm) cc_final: 0.7873 (mm) REVERT: D 153 ARG cc_start: 0.5667 (ttp-170) cc_final: 0.3988 (tpt-90) REVERT: F 37 MET cc_start: 0.5565 (tmm) cc_final: 0.5280 (tmm) REVERT: F 38 MET cc_start: 0.4113 (mtp) cc_final: 0.3725 (mtt) outliers start: 47 outliers final: 24 residues processed: 236 average time/residue: 0.0804 time to fit residues: 27.8553 Evaluate side-chains 224 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 352 ILE Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 49 optimal weight: 0.1980 chunk 112 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 96 optimal weight: 0.0070 chunk 103 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 94 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.217419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.176020 restraints weight = 13289.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179939 restraints weight = 6538.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.180937 restraints weight = 4402.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.181369 restraints weight = 3606.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.181673 restraints weight = 3337.658| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9659 Z= 0.114 Angle : 0.633 12.991 13109 Z= 0.304 Chirality : 0.043 0.230 1561 Planarity : 0.004 0.050 1685 Dihedral : 9.882 164.198 1415 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.08 % Allowed : 24.62 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1267 helix: 1.43 (0.21), residues: 596 sheet: -0.26 (0.40), residues: 173 loop : -0.39 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 53 TYR 0.041 0.002 TYR C 214 PHE 0.008 0.001 PHE E 100 TRP 0.015 0.001 TRP E 321 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9659) covalent geometry : angle 0.63308 (13109) hydrogen bonds : bond 0.03486 ( 526) hydrogen bonds : angle 4.41364 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6952 (pp20) REVERT: E 84 HIS cc_start: 0.7280 (m170) cc_final: 0.6936 (m170) REVERT: E 180 MET cc_start: 0.2730 (mmt) cc_final: 0.1660 (ptp) REVERT: C 48 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: C 92 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6556 (ttt90) REVERT: C 293 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8256 (mmmm) REVERT: C 303 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6283 (mp10) REVERT: C 344 MET cc_start: 0.4039 (mmt) cc_final: 0.3679 (tpp) REVERT: D 37 MET cc_start: 0.5679 (tmm) cc_final: 0.4546 (tmm) REVERT: D 73 MET cc_start: 0.7669 (ppp) cc_final: 0.7162 (ppp) REVERT: D 112 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7867 (mm) REVERT: D 153 ARG cc_start: 0.5623 (ttp-170) cc_final: 0.3956 (tpt-90) REVERT: F 214 ARG cc_start: 0.4875 (ttt180) cc_final: 0.4643 (ttt-90) outliers start: 30 outliers final: 16 residues processed: 211 average time/residue: 0.0785 time to fit residues: 24.6751 Evaluate side-chains 210 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.0060 chunk 24 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 ASN D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.217896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.173970 restraints weight = 13324.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.179118 restraints weight = 6641.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182401 restraints weight = 4167.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.184564 restraints weight = 3118.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.185476 restraints weight = 2598.377| |-----------------------------------------------------------------------------| r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9659 Z= 0.115 Angle : 0.642 13.936 13109 Z= 0.303 Chirality : 0.043 0.225 1561 Planarity : 0.004 0.051 1685 Dihedral : 9.816 163.290 1415 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.59 % Allowed : 24.31 % Favored : 72.10 % 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: 0.86 (0.24), residues: 1267 helix: 1.51 (0.21), residues: 602 sheet: -0.15 (0.40), residues: 171 loop : -0.24 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 214 TYR 0.047 0.002 TYR C 214 PHE 0.009 0.001 PHE E 100 TRP 0.015 0.001 TRP E 321 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9659) covalent geometry : angle 0.64216 (13109) hydrogen bonds : bond 0.03387 ( 526) hydrogen bonds : angle 4.31635 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: E 125 ARG cc_start: 0.7556 (ttp-170) cc_final: 0.7268 (ptt180) REVERT: E 180 MET cc_start: 0.2737 (mmt) cc_final: 0.1747 (ptp) REVERT: E 195 LEU cc_start: 0.7223 (mp) cc_final: 0.6956 (mp) REVERT: E 322 TYR cc_start: 0.8447 (t80) cc_final: 0.8170 (t80) REVERT: C 48 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8416 (mtt) REVERT: C 92 ARG cc_start: 0.7116 (ttt90) cc_final: 0.6544 (ttt90) REVERT: C 293 LYS cc_start: 0.8764 (ttmm) cc_final: 0.8323 (mmmm) REVERT: C 303 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.6249 (mp10) REVERT: C 341 ASN cc_start: 0.7303 (p0) cc_final: 0.7052 (p0) REVERT: C 344 MET cc_start: 0.4256 (mmt) cc_final: 0.3923 (tpp) REVERT: D 73 MET cc_start: 0.7667 (ppp) cc_final: 0.7219 (ppp) REVERT: D 112 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7918 (mm) REVERT: D 153 ARG cc_start: 0.5619 (ttp-170) cc_final: 0.3878 (tpt-90) REVERT: D 171 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6305 (tm-30) REVERT: F 53 HIS cc_start: 0.7579 (OUTLIER) cc_final: 0.7207 (t70) REVERT: F 214 ARG cc_start: 0.4974 (ttt180) cc_final: 0.4641 (ttt-90) outliers start: 35 outliers final: 26 residues processed: 207 average time/residue: 0.0787 time to fit residues: 23.9422 Evaluate side-chains 220 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 163 ASN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 68 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 0.0670 chunk 23 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 84 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.218761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.174177 restraints weight = 13886.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177248 restraints weight = 7453.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.179212 restraints weight = 4890.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180127 restraints weight = 4165.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179877 restraints weight = 3913.982| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9659 Z= 0.126 Angle : 0.667 14.281 13109 Z= 0.312 Chirality : 0.044 0.280 1561 Planarity : 0.005 0.050 1685 Dihedral : 9.892 163.347 1415 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.49 % Allowed : 24.31 % Favored : 72.21 % 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: 0.89 (0.24), residues: 1267 helix: 1.55 (0.21), residues: 602 sheet: -0.13 (0.40), residues: 171 loop : -0.24 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 165 TYR 0.045 0.002 TYR C 214 PHE 0.010 0.001 PHE E 100 TRP 0.015 0.001 TRP C 246 HIS 0.017 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9659) covalent geometry : angle 0.66729 (13109) hydrogen bonds : bond 0.03408 ( 526) hydrogen bonds : angle 4.31726 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 125 ARG cc_start: 0.7631 (ttp-170) cc_final: 0.7330 (ptt180) REVERT: E 180 MET cc_start: 0.2896 (mmt) cc_final: 0.1863 (ptp) REVERT: E 195 LEU cc_start: 0.7306 (mp) cc_final: 0.7056 (mp) REVERT: E 322 TYR cc_start: 0.8433 (t80) cc_final: 0.8206 (t80) REVERT: C 92 ARG cc_start: 0.7125 (ttt90) cc_final: 0.6632 (ttt90) REVERT: C 212 MET cc_start: 0.7088 (mtt) cc_final: 0.6503 (mtt) REVERT: C 293 LYS cc_start: 0.8794 (ttmm) cc_final: 0.8352 (mmmm) REVERT: C 303 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6872 (mt0) REVERT: C 341 ASN cc_start: 0.7347 (p0) cc_final: 0.7077 (p0) REVERT: C 344 MET cc_start: 0.3962 (mmt) cc_final: 0.3589 (tpp) REVERT: D 37 MET cc_start: 0.4672 (tmm) cc_final: 0.3587 (mmt) REVERT: D 73 MET cc_start: 0.7754 (ppp) cc_final: 0.7261 (ppp) REVERT: D 112 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7991 (mm) REVERT: D 153 ARG cc_start: 0.5732 (ttp-170) cc_final: 0.3932 (tpt-90) REVERT: D 171 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6379 (tm-30) REVERT: F 53 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.7365 (t70) REVERT: F 175 ASN cc_start: 0.6862 (t0) cc_final: 0.6473 (t0) outliers start: 34 outliers final: 20 residues processed: 208 average time/residue: 0.0814 time to fit residues: 24.8284 Evaluate side-chains 212 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 111 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 109 optimal weight: 0.0670 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.218870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.176083 restraints weight = 13266.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.181191 restraints weight = 6613.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.184466 restraints weight = 4162.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.186460 restraints weight = 3103.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.187486 restraints weight = 2603.478| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9659 Z= 0.114 Angle : 0.659 13.009 13109 Z= 0.309 Chirality : 0.044 0.282 1561 Planarity : 0.004 0.049 1685 Dihedral : 9.817 163.877 1415 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.56 % Allowed : 25.23 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.25), residues: 1267 helix: 1.64 (0.21), residues: 603 sheet: -0.14 (0.39), residues: 172 loop : -0.22 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 151 TYR 0.035 0.001 TYR C 214 PHE 0.009 0.001 PHE E 319 TRP 0.016 0.001 TRP E 321 HIS 0.006 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9659) covalent geometry : angle 0.65920 (13109) hydrogen bonds : bond 0.03310 ( 526) hydrogen bonds : angle 4.22817 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 125 ARG cc_start: 0.7520 (ttp-170) cc_final: 0.7268 (ptt180) REVERT: E 180 MET cc_start: 0.2828 (mmt) cc_final: 0.2404 (ppp) REVERT: E 195 LEU cc_start: 0.7268 (mp) cc_final: 0.7015 (mp) REVERT: E 322 TYR cc_start: 0.8411 (t80) cc_final: 0.8172 (t80) REVERT: C 92 ARG cc_start: 0.7032 (ttt90) cc_final: 0.6547 (ttt90) REVERT: C 293 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8049 (mmmm) REVERT: C 303 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: C 341 ASN cc_start: 0.7350 (p0) cc_final: 0.7106 (p0) REVERT: C 344 MET cc_start: 0.4120 (mmt) cc_final: 0.3901 (tpp) REVERT: D 37 MET cc_start: 0.5078 (tmm) cc_final: 0.4000 (mmt) REVERT: D 73 MET cc_start: 0.7736 (ppp) cc_final: 0.7351 (ppp) REVERT: D 112 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7930 (mm) REVERT: D 153 ARG cc_start: 0.5702 (ttp-170) cc_final: 0.3865 (tpt-90) REVERT: D 171 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: F 53 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7300 (t70) REVERT: F 150 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7776 (mm-30) outliers start: 25 outliers final: 18 residues processed: 207 average time/residue: 0.0803 time to fit residues: 24.5806 Evaluate side-chains 205 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 GLU Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 190 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 105 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 98 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.221486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.176405 restraints weight = 13774.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.180315 restraints weight = 7499.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.185434 restraints weight = 5057.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.186276 restraints weight = 3358.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.186260 restraints weight = 2897.349| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9659 Z= 0.111 Angle : 0.652 13.076 13109 Z= 0.306 Chirality : 0.044 0.267 1561 Planarity : 0.005 0.050 1685 Dihedral : 9.733 163.642 1415 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.36 % Allowed : 25.74 % Favored : 71.90 % 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: 1.08 (0.25), residues: 1267 helix: 1.72 (0.21), residues: 603 sheet: -0.05 (0.40), residues: 172 loop : -0.17 (0.31), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 151 TYR 0.012 0.001 TYR E 258 PHE 0.008 0.001 PHE E 319 TRP 0.015 0.001 TRP E 321 HIS 0.005 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9659) covalent geometry : angle 0.65221 (13109) hydrogen bonds : bond 0.03267 ( 526) hydrogen bonds : angle 4.18379 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.38 seconds wall clock time: 29 minutes 27.86 seconds (1767.86 seconds total)