Starting phenix.real_space_refine on Sun Jul 27 14:56:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8l_31803/07_2025/7v8l_31803_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8l_31803/07_2025/7v8l_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_31803/07_2025/7v8l_31803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8l_31803/07_2025/7v8l_31803.map" model { file = "/net/cci-nas-00/data/ceres_data/7v8l_31803/07_2025/7v8l_31803_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8l_31803/07_2025/7v8l_31803_neut_trim.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 6} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} 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: 5.84, per 1000 atoms: 0.61 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: 2.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.13 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: 2.99 Time building geometry restraints manager: 3.05 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.050 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (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 TRP 0.048 0.002 TRP E 321 HIS 0.005 0.001 HIS D 96 PHE 0.028 0.001 PHE E 367 TYR 0.021 0.002 TYR E 366 ARG 0.102 0.001 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.14067 ( 526) hydrogen bonds : angle 6.31143 ( 1539) covalent geometry : bond 0.00499 ( 9659) covalent geometry : angle 0.79221 (13109) *********************** 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 : 0.974 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: 0.6304 (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: 0.2239 time to fit residues: 75.3849 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 : 0.962 ------------------------------------------------------------------------------- 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 104 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.0170 chunk 50 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 84 HIS ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN C 218 ASN D 53 HIS D 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.232248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186940 restraints weight = 13674.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.189677 restraints weight = 7640.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.191252 restraints weight = 4767.863| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9659 Z= 0.167 Angle : 0.697 9.138 13109 Z= 0.344 Chirality : 0.046 0.226 1561 Planarity : 0.005 0.052 1685 Dihedral : 10.289 157.944 1427 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.77 % Allowed : 12.10 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1267 helix: 0.77 (0.21), residues: 609 sheet: -0.25 (0.39), residues: 177 loop : -0.56 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 321 HIS 0.006 0.001 HIS E 84 PHE 0.012 0.001 PHE E 319 TYR 0.015 0.001 TYR E 260 ARG 0.006 0.001 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 526) hydrogen bonds : angle 4.95279 ( 1539) covalent geometry : bond 0.00371 ( 9659) covalent geometry : angle 0.69654 (13109) *********************** 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 231 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 86 GLN cc_start: 0.7174 (tt0) cc_final: 0.6872 (mt0) REVERT: E 205 MET cc_start: 0.6477 (mtm) cc_final: 0.6090 (mtm) REVERT: E 228 MET cc_start: 0.7536 (mmp) cc_final: 0.7153 (mmt) REVERT: E 289 SER cc_start: 0.8633 (m) cc_final: 0.8399 (t) REVERT: C 48 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7782 (mtt) REVERT: C 293 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8253 (mtpp) REVERT: D 153 ARG cc_start: 0.5121 (ttp-170) cc_final: 0.3669 (tpt-90) REVERT: F 38 MET cc_start: 0.4106 (mtp) cc_final: 0.3669 (mtt) REVERT: F 52 LEU cc_start: 0.7314 (tt) cc_final: 0.6355 (mt) REVERT: F 53 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6438 (t-90) REVERT: F 146 LEU cc_start: 0.5722 (mt) cc_final: 0.5432 (mt) outliers start: 27 outliers final: 15 residues processed: 219 average time/residue: 0.1819 time to fit residues: 57.5416 Evaluate side-chains 197 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 166 VAL 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 60 THR 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 15 optimal weight: 0.0970 chunk 64 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 84 HIS E 119 ASN E 359 GLN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 218 ASN D 53 HIS D 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.218587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170213 restraints weight = 13698.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.175632 restraints weight = 6838.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.179028 restraints weight = 4340.926| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9659 Z= 0.118 Angle : 0.603 8.893 13109 Z= 0.298 Chirality : 0.043 0.238 1561 Planarity : 0.004 0.051 1685 Dihedral : 9.984 161.143 1417 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 16.51 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1267 helix: 1.08 (0.21), residues: 606 sheet: -0.26 (0.39), residues: 173 loop : -0.47 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 321 HIS 0.007 0.001 HIS D 96 PHE 0.012 0.001 PHE E 319 TYR 0.016 0.001 TYR C 214 ARG 0.003 0.000 ARG D 151 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 526) hydrogen bonds : angle 4.68250 ( 1539) covalent geometry : bond 0.00252 ( 9659) covalent geometry : angle 0.60319 (13109) *********************** 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 222 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7415 (pp20) cc_final: 0.7211 (pp20) REVERT: E 84 HIS cc_start: 0.6940 (m-70) cc_final: 0.6667 (m-70) REVERT: E 205 MET cc_start: 0.6419 (mtm) cc_final: 0.6164 (mtm) REVERT: A 23 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7862 (tt) REVERT: C 48 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8039 (mtt) REVERT: C 266 MET cc_start: 0.8251 (tpp) cc_final: 0.7930 (tpp) REVERT: D 37 MET cc_start: 0.4881 (tmm) cc_final: 0.4341 (tmm) REVERT: D 153 ARG cc_start: 0.5197 (ttp-170) cc_final: 0.3934 (tpt-90) REVERT: F 37 MET cc_start: 0.5518 (tmm) cc_final: 0.5316 (tmm) REVERT: F 38 MET cc_start: 0.4273 (mtp) cc_final: 0.3914 (mtt) REVERT: F 52 LEU cc_start: 0.7474 (tt) cc_final: 0.6569 (mt) REVERT: F 53 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6412 (t-90) REVERT: F 146 LEU cc_start: 0.5701 (mt) cc_final: 0.5395 (mt) outliers start: 30 outliers final: 20 residues processed: 203 average time/residue: 0.1844 time to fit residues: 55.0146 Evaluate side-chains 206 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 60 LEU 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 276 MET 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 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 107 ASN 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 96 optimal weight: 0.0030 chunk 74 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 0.0170 chunk 80 optimal weight: 30.0000 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 119 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 218 ASN D 53 HIS D 97 HIS D 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.218767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.170525 restraints weight = 13620.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.175906 restraints weight = 6851.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.179443 restraints weight = 4360.046| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3288 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 : 0.584 8.611 13109 Z= 0.288 Chirality : 0.043 0.206 1561 Planarity : 0.004 0.052 1685 Dihedral : 9.862 161.703 1417 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.38 % Allowed : 17.95 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1267 helix: 1.27 (0.21), residues: 602 sheet: -0.18 (0.39), residues: 173 loop : -0.46 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.010 0.001 HIS E 84 PHE 0.011 0.001 PHE E 319 TYR 0.022 0.001 TYR C 214 ARG 0.003 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 526) hydrogen bonds : angle 4.50787 ( 1539) covalent geometry : bond 0.00237 ( 9659) covalent geometry : angle 0.58433 (13109) *********************** 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 226 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7655 (pp20) cc_final: 0.7307 (pp20) REVERT: E 83 ASP cc_start: 0.7280 (p0) cc_final: 0.7079 (p0) REVERT: E 84 HIS cc_start: 0.6956 (m-70) cc_final: 0.6685 (m-70) REVERT: E 205 MET cc_start: 0.6258 (mtm) cc_final: 0.6021 (mtm) REVERT: E 368 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8377 (pt) REVERT: C 48 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8090 (mtt) REVERT: C 262 MET cc_start: 0.7509 (ttm) cc_final: 0.7194 (ttm) REVERT: C 266 MET cc_start: 0.8350 (tpp) cc_final: 0.7970 (tpp) REVERT: C 303 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.5718 (mp10) REVERT: C 344 MET cc_start: 0.3405 (mmt) cc_final: 0.2989 (tpp) REVERT: D 37 MET cc_start: 0.4908 (tmm) cc_final: 0.4412 (tmm) REVERT: D 73 MET cc_start: 0.7449 (ppp) cc_final: 0.6330 (ppp) REVERT: D 97 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.6435 (m90) REVERT: D 153 ARG cc_start: 0.5210 (ttp-170) cc_final: 0.3750 (tpt-90) REVERT: D 171 GLU cc_start: 0.6182 (tt0) cc_final: 0.5420 (mp0) REVERT: F 53 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6834 (t-90) REVERT: F 146 LEU cc_start: 0.5890 (mt) cc_final: 0.5550 (mt) outliers start: 33 outliers final: 18 residues processed: 209 average time/residue: 0.2726 time to fit residues: 84.1986 Evaluate side-chains 209 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 LEU 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 276 MET Chi-restraints excluded: chain E residue 277 VAL 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 181 GLN Chi-restraints excluded: chain C residue 218 ASN Chi-restraints excluded: chain C residue 269 LEU 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 97 HIS 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 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 0.0970 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 49 ASN E 119 ASN ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 218 ASN D 53 HIS D 97 HIS D 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.217412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.168372 restraints weight = 13573.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.173712 restraints weight = 6838.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.177152 restraints weight = 4368.058| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3620 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= 0.116 Angle : 0.599 9.550 13109 Z= 0.292 Chirality : 0.043 0.199 1561 Planarity : 0.004 0.054 1685 Dihedral : 9.764 162.073 1417 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.69 % Allowed : 19.08 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1267 helix: 1.39 (0.21), residues: 599 sheet: -0.01 (0.40), residues: 169 loop : -0.51 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 246 HIS 0.014 0.001 HIS D 97 PHE 0.010 0.001 PHE E 319 TYR 0.028 0.001 TYR C 214 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 526) hydrogen bonds : angle 4.40423 ( 1539) covalent geometry : bond 0.00252 ( 9659) covalent geometry : angle 0.59927 (13109) *********************** 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 229 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 HIS cc_start: 0.6954 (m-70) cc_final: 0.6751 (m90) REVERT: C 48 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: C 262 MET cc_start: 0.7520 (ttm) cc_final: 0.7268 (ttm) REVERT: C 299 ILE cc_start: 0.8456 (mm) cc_final: 0.7733 (mm) REVERT: C 303 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.5620 (mp10) REVERT: C 344 MET cc_start: 0.3545 (mmt) cc_final: 0.3116 (tpp) REVERT: D 37 MET cc_start: 0.5141 (tmm) cc_final: 0.4374 (tmm) REVERT: D 73 MET cc_start: 0.7544 (ppp) cc_final: 0.6665 (ppp) REVERT: D 97 HIS cc_start: 0.6715 (OUTLIER) cc_final: 0.6255 (m90) REVERT: D 153 ARG cc_start: 0.5278 (ttp-170) cc_final: 0.3664 (tpt170) REVERT: D 171 GLU cc_start: 0.6183 (tt0) cc_final: 0.5349 (mp0) REVERT: F 53 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6925 (t-90) REVERT: F 146 LEU cc_start: 0.5934 (mt) cc_final: 0.5579 (mt) outliers start: 36 outliers final: 21 residues processed: 214 average time/residue: 0.1857 time to fit residues: 58.3168 Evaluate side-chains 209 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 276 MET Chi-restraints excluded: chain E residue 277 VAL 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 62 LEU 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 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 107 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 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 122 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 218 ASN D 53 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.225827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.178909 restraints weight = 13688.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.181295 restraints weight = 7877.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.183396 restraints weight = 5072.843| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9659 Z= 0.114 Angle : 0.608 13.207 13109 Z= 0.291 Chirality : 0.043 0.235 1561 Planarity : 0.004 0.052 1685 Dihedral : 9.715 160.644 1415 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.69 % Allowed : 19.69 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1267 helix: 1.47 (0.21), residues: 600 sheet: -0.17 (0.39), residues: 173 loop : -0.45 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 246 HIS 0.021 0.002 HIS D 97 PHE 0.011 0.001 PHE E 319 TYR 0.042 0.001 TYR C 214 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 526) hydrogen bonds : angle 4.35408 ( 1539) covalent geometry : bond 0.00257 ( 9659) covalent geometry : angle 0.60765 (13109) *********************** 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 226 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 84 HIS cc_start: 0.7047 (m-70) cc_final: 0.6784 (m170) REVERT: C 48 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8145 (mtt) REVERT: C 92 ARG cc_start: 0.7062 (ttt90) cc_final: 0.6601 (ttt90) REVERT: C 299 ILE cc_start: 0.8534 (mm) cc_final: 0.7837 (mm) REVERT: C 303 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.5834 (mp10) REVERT: C 344 MET cc_start: 0.3447 (mmt) cc_final: 0.3008 (tpp) REVERT: D 37 MET cc_start: 0.5380 (tmm) cc_final: 0.4277 (tmm) REVERT: D 73 MET cc_start: 0.7458 (ppp) cc_final: 0.6732 (ppp) REVERT: D 106 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6197 (mm-30) REVERT: D 153 ARG cc_start: 0.5347 (ttp-170) cc_final: 0.3824 (tpt-90) REVERT: F 37 MET cc_start: 0.5488 (tmm) cc_final: 0.5278 (tmm) REVERT: F 53 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.7040 (t-90) REVERT: F 146 LEU cc_start: 0.5983 (mt) cc_final: 0.5605 (mt) outliers start: 36 outliers final: 25 residues processed: 209 average time/residue: 0.2683 time to fit residues: 82.9061 Evaluate side-chains 211 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 262 TYR Chi-restraints excluded: chain E residue 276 MET 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 E residue 393 LEU 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 218 ASN 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 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain F residue 11 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN D 53 HIS D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.225628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.181810 restraints weight = 13875.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.183733 restraints weight = 7662.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.185546 restraints weight = 5076.818| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9659 Z= 0.121 Angle : 0.630 14.809 13109 Z= 0.302 Chirality : 0.043 0.207 1561 Planarity : 0.004 0.052 1685 Dihedral : 9.773 161.465 1415 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.79 % Allowed : 20.10 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.24), residues: 1267 helix: 1.53 (0.21), residues: 599 sheet: -0.15 (0.39), residues: 176 loop : -0.43 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.007 0.001 HIS D 96 PHE 0.010 0.001 PHE E 319 TYR 0.049 0.002 TYR C 214 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 526) hydrogen bonds : angle 4.31339 ( 1539) covalent geometry : bond 0.00271 ( 9659) covalent geometry : angle 0.62980 (13109) *********************** 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 237 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.6498 (tpp) cc_final: 0.6252 (tpp) REVERT: E 60 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8073 (tt) REVERT: E 80 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7325 (pp20) REVERT: E 84 HIS cc_start: 0.7118 (m-70) cc_final: 0.6869 (m-70) REVERT: C 48 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8223 (mtt) REVERT: C 92 ARG cc_start: 0.7081 (ttt90) cc_final: 0.6610 (ttt90) REVERT: C 299 ILE cc_start: 0.8610 (mm) cc_final: 0.7944 (mm) REVERT: C 303 GLN cc_start: 0.7678 (OUTLIER) cc_final: 0.5909 (mp10) REVERT: C 344 MET cc_start: 0.3698 (mmt) cc_final: 0.3269 (tpp) REVERT: D 37 MET cc_start: 0.5585 (tmm) cc_final: 0.4212 (mpp) REVERT: D 73 MET cc_start: 0.7464 (ppp) cc_final: 0.6884 (ppp) REVERT: D 106 GLU cc_start: 0.6843 (mm-30) cc_final: 0.6257 (mm-30) REVERT: D 112 LEU cc_start: 0.7800 (mm) cc_final: 0.7571 (mm) REVERT: D 153 ARG cc_start: 0.5483 (ttp-170) cc_final: 0.3826 (tpt-90) REVERT: F 53 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7276 (t-90) REVERT: F 146 LEU cc_start: 0.6038 (mt) cc_final: 0.5688 (mt) REVERT: F 214 ARG cc_start: 0.4313 (ttt180) cc_final: 0.3940 (ttt180) outliers start: 37 outliers final: 23 residues processed: 220 average time/residue: 0.1770 time to fit residues: 57.0642 Evaluate side-chains 214 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 60 LEU 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 255 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 276 MET 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 E residue 393 LEU 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 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 MET Chi-restraints excluded: chain F residue 11 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 0.0370 chunk 67 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 218 ASN D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.224658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.177306 restraints weight = 13856.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.180622 restraints weight = 7871.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.183078 restraints weight = 4764.906| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9659 Z= 0.116 Angle : 0.639 12.956 13109 Z= 0.305 Chirality : 0.043 0.240 1561 Planarity : 0.004 0.052 1685 Dihedral : 9.737 162.307 1415 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.38 % Allowed : 20.92 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.24), residues: 1267 helix: 1.66 (0.21), residues: 600 sheet: 0.01 (0.39), residues: 174 loop : -0.32 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 246 HIS 0.007 0.001 HIS D 96 PHE 0.009 0.001 PHE E 319 TYR 0.044 0.001 TYR C 214 ARG 0.002 0.000 ARG F 214 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 526) hydrogen bonds : angle 4.26717 ( 1539) covalent geometry : bond 0.00261 ( 9659) covalent geometry : angle 0.63875 (13109) *********************** 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: 33 poor density : 192 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 22 MET cc_start: 0.6216 (tpp) cc_final: 0.5860 (tpp) REVERT: E 60 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7984 (tt) REVERT: E 80 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: E 84 HIS cc_start: 0.7127 (m-70) cc_final: 0.6871 (m-70) REVERT: C 92 ARG cc_start: 0.7052 (ttt90) cc_final: 0.6571 (ttt90) REVERT: C 299 ILE cc_start: 0.8604 (mm) cc_final: 0.8208 (mm) REVERT: C 303 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6098 (mp10) REVERT: C 344 MET cc_start: 0.3561 (mmt) cc_final: 0.3132 (tpp) REVERT: D 37 MET cc_start: 0.5414 (tmm) cc_final: 0.4313 (tmm) REVERT: D 73 MET cc_start: 0.7481 (ppp) cc_final: 0.6892 (ppp) REVERT: D 106 GLU cc_start: 0.6656 (mm-30) cc_final: 0.5974 (mm-30) REVERT: D 112 LEU cc_start: 0.7842 (mm) cc_final: 0.7629 (mm) REVERT: D 153 ARG cc_start: 0.5386 (ttp-170) cc_final: 0.3759 (tpt-90) REVERT: F 53 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7243 (t-90) REVERT: F 146 LEU cc_start: 0.6034 (mt) cc_final: 0.5680 (mt) REVERT: F 214 ARG cc_start: 0.3900 (ttt180) cc_final: 0.3606 (ttt180) outliers start: 33 outliers final: 23 residues processed: 210 average time/residue: 0.1804 time to fit residues: 55.6324 Evaluate side-chains 209 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 60 LEU 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 205 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 276 MET 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 E residue 393 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 230 MET 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 62 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 0.0470 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 90 optimal weight: 0.0570 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.224741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.177291 restraints weight = 13838.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.180920 restraints weight = 7844.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.183012 restraints weight = 4679.837| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9659 Z= 0.112 Angle : 0.630 11.509 13109 Z= 0.304 Chirality : 0.043 0.227 1561 Planarity : 0.004 0.053 1685 Dihedral : 9.628 162.167 1415 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.08 % Allowed : 20.51 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1267 helix: 1.74 (0.21), residues: 602 sheet: 0.03 (0.40), residues: 175 loop : -0.34 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 246 HIS 0.005 0.001 HIS D 96 PHE 0.006 0.001 PHE D 199 TYR 0.036 0.001 TYR C 214 ARG 0.002 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 526) hydrogen bonds : angle 4.21715 ( 1539) covalent geometry : bond 0.00253 ( 9659) covalent geometry : angle 0.62968 (13109) *********************** 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 218 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 188 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: E 84 HIS cc_start: 0.7288 (m-70) cc_final: 0.6814 (m-70) REVERT: C 48 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: C 92 ARG cc_start: 0.7089 (ttt90) cc_final: 0.6605 (ttt90) REVERT: C 266 MET cc_start: 0.8084 (tpp) cc_final: 0.7702 (ttt) REVERT: C 299 ILE cc_start: 0.8752 (mm) cc_final: 0.8213 (mm) REVERT: C 303 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.6072 (mp10) REVERT: C 344 MET cc_start: 0.3656 (mmt) cc_final: 0.3247 (tpp) REVERT: D 37 MET cc_start: 0.5297 (tmm) cc_final: 0.4236 (tmm) REVERT: D 73 MET cc_start: 0.7527 (ppp) cc_final: 0.7019 (ppp) REVERT: D 106 GLU cc_start: 0.6676 (mm-30) cc_final: 0.5967 (mm-30) REVERT: D 112 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7681 (mm) REVERT: D 153 ARG cc_start: 0.5405 (ttp-170) cc_final: 0.3708 (tpt-90) REVERT: F 37 MET cc_start: 0.5914 (tmm) cc_final: 0.5691 (tmm) REVERT: F 53 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7184 (t-90) REVERT: F 146 LEU cc_start: 0.6141 (mt) cc_final: 0.5824 (mt) REVERT: F 214 ARG cc_start: 0.3922 (ttt180) cc_final: 0.3710 (ttt180) outliers start: 30 outliers final: 22 residues processed: 204 average time/residue: 0.1790 time to fit residues: 52.9501 Evaluate side-chains 204 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 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 262 TYR Chi-restraints excluded: chain E residue 276 MET 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 E residue 393 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU 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 D residue 230 MET 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 101 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 53 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.223234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.179735 restraints weight = 13407.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.184878 restraints weight = 6633.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.188198 restraints weight = 4161.836| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9659 Z= 0.118 Angle : 0.634 10.370 13109 Z= 0.306 Chirality : 0.043 0.229 1561 Planarity : 0.004 0.052 1685 Dihedral : 9.578 161.794 1415 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.28 % Allowed : 21.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1267 helix: 1.71 (0.21), residues: 602 sheet: 0.12 (0.40), residues: 174 loop : -0.35 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 321 HIS 0.005 0.001 HIS E 84 PHE 0.007 0.001 PHE E 100 TYR 0.029 0.001 TYR C 214 ARG 0.002 0.000 ARG E 125 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 526) hydrogen bonds : angle 4.16649 ( 1539) covalent geometry : bond 0.00265 ( 9659) covalent geometry : angle 0.63441 (13109) ********************** 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 216 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7215 (pp20) REVERT: E 180 MET cc_start: 0.2776 (mmt) cc_final: 0.1825 (ptp) REVERT: C 48 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.7938 (mtp) REVERT: C 92 ARG cc_start: 0.7068 (ttt90) cc_final: 0.6605 (ttt90) REVERT: C 266 MET cc_start: 0.8020 (tpp) cc_final: 0.7657 (ttt) REVERT: C 303 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6676 (mt0) REVERT: C 341 ASN cc_start: 0.7369 (p0) cc_final: 0.7136 (p0) REVERT: C 344 MET cc_start: 0.4149 (mmt) cc_final: 0.3798 (tpp) REVERT: D 37 MET cc_start: 0.5660 (tmm) cc_final: 0.5424 (tmm) REVERT: D 73 MET cc_start: 0.7576 (ppp) cc_final: 0.7253 (ppp) REVERT: D 106 GLU cc_start: 0.6515 (mm-30) cc_final: 0.5826 (mm-30) REVERT: D 112 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7655 (mm) REVERT: D 153 ARG cc_start: 0.5428 (ttp-170) cc_final: 0.3696 (tpt-90) REVERT: F 146 LEU cc_start: 0.6082 (mt) cc_final: 0.5831 (mt) outliers start: 32 outliers final: 23 residues processed: 202 average time/residue: 0.1923 time to fit residues: 56.1254 Evaluate side-chains 202 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 262 TYR Chi-restraints excluded: chain E residue 276 MET 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 E residue 393 LEU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 303 GLN Chi-restraints excluded: chain C residue 356 LEU 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 D residue 230 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.0020 chunk 106 optimal weight: 40.0000 chunk 77 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.221500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.174077 restraints weight = 13838.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.178159 restraints weight = 7740.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.184646 restraints weight = 4987.762| |-----------------------------------------------------------------------------| r_work (final): 0.4254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9659 Z= 0.117 Angle : 0.648 10.163 13109 Z= 0.309 Chirality : 0.043 0.219 1561 Planarity : 0.004 0.052 1685 Dihedral : 9.726 161.866 1415 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.08 % Allowed : 22.05 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1267 helix: 1.78 (0.21), residues: 601 sheet: 0.14 (0.39), residues: 174 loop : -0.34 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 321 HIS 0.009 0.001 HIS D 97 PHE 0.008 0.001 PHE D 91 TYR 0.028 0.001 TYR C 214 ARG 0.002 0.000 ARG F 214 Details of bonding type rmsd hydrogen bonds : bond 0.03325 ( 526) hydrogen bonds : angle 4.15781 ( 1539) covalent geometry : bond 0.00263 ( 9659) covalent geometry : angle 0.64775 (13109) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3708.00 seconds wall clock time: 67 minutes 54.55 seconds (4074.55 seconds total)