Starting phenix.real_space_refine on Sat Aug 23 00:29:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hbd_34619/08_2025/8hbd_34619_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hbd_34619/08_2025/8hbd_34619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hbd_34619/08_2025/8hbd_34619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hbd_34619/08_2025/8hbd_34619.map" model { file = "/net/cci-nas-00/data/ceres_data/8hbd_34619/08_2025/8hbd_34619_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hbd_34619/08_2025/8hbd_34619_neut.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5635 2.51 5 N 1481 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8803 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1717 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2540 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1726 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 123 Classifications: {'peptide': 14} Modifications used: {'COO': 1} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2293 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 12, 'TRANS': 288} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Time building chain proxies: 1.72, per 1000 atoms: 0.20 Number of scatterers: 8803 At special positions: 0 Unit cell: (107.12, 112.32, 130, 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 63 16.00 O 1624 8.00 N 1481 7.00 C 5635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 318.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.4% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.520A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.587A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 13 removed outlier: 4.107A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 26 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.365A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.881A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.660A pdb=" N LYS H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.970A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 Processing helix chain 'L' and resid 10 through 18 removed outlier: 4.143A pdb=" N PHE L 14 " --> pdb=" O GLU L 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA L 15 " --> pdb=" O ALA L 11 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU L 17 " --> pdb=" O TYR L 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 129 removed outlier: 3.982A pdb=" N ILE R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN R 104 " --> pdb=" O PHE R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 149 Processing helix chain 'R' and resid 154 through 165 Processing helix chain 'R' and resid 176 through 205 removed outlier: 3.610A pdb=" N LEU R 192 " --> pdb=" O THR R 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS R 193 " --> pdb=" O VAL R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 233 removed outlier: 3.576A pdb=" N VAL R 223 " --> pdb=" O ALA R 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP R 226 " --> pdb=" O ILE R 222 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER R 229 " --> pdb=" O ILE R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 237 Processing helix chain 'R' and resid 263 through 272 Processing helix chain 'R' and resid 272 through 280 removed outlier: 3.594A pdb=" N PHE R 280 " --> pdb=" O TRP R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 301 removed outlier: 4.362A pdb=" N ALA R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE R 291 " --> pdb=" O ALA R 287 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR R 297 " --> pdb=" O TYR R 293 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS R 298 " --> pdb=" O THR R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 349 removed outlier: 4.000A pdb=" N LYS R 316 " --> pdb=" O ASN R 312 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN R 317 " --> pdb=" O ASP R 313 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU R 320 " --> pdb=" O LYS R 316 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL R 321 " --> pdb=" O GLN R 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU R 328 " --> pdb=" O THR R 324 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) Proline residue: R 338 - end of helix removed outlier: 3.933A pdb=" N ARG R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE R 344 " --> pdb=" O HIS R 340 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 345 " --> pdb=" O LEU R 341 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LYS R 346 " --> pdb=" O SER R 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU R 347 " --> pdb=" O ARG R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 380 removed outlier: 3.892A pdb=" N PHE R 363 " --> pdb=" O GLU R 359 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER R 379 " --> pdb=" O ALA R 375 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 389 removed outlier: 3.723A pdb=" N ILE R 384 " --> pdb=" O CYS R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 399 removed outlier: 4.075A pdb=" N CYS R 396 " --> pdb=" O ARG R 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.921A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.589A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.154A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 7.014A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.751A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.909A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.819A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.551A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.904A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.538A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.659A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 155 through 160 Processing sheet with id=AB5, first strand: chain 'R' and resid 240 through 246 removed outlier: 3.683A pdb=" N ASP R 241 " --> pdb=" O LEU R 256 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU R 256 " --> pdb=" O ASP R 241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET R 245 " --> pdb=" O LEU R 252 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU R 252 " --> pdb=" O MET R 245 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1143 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: 0.96 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1528 1.32 - 1.45: 2385 1.45 - 1.57: 4983 1.57 - 1.69: 0 1.69 - 1.82: 88 Bond restraints: 8984 Sorted by residual: bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.455 1.503 -0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.23e-02 6.61e+03 8.69e+00 bond pdb=" C PRO R 178 " pdb=" O PRO R 178 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.30e-02 5.92e+03 7.43e+00 bond pdb=" N ARG A 313 " pdb=" CA ARG A 313 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.77e+00 bond pdb=" N PRO R 178 " pdb=" CA PRO R 178 " ideal model delta sigma weight residual 1.469 1.439 0.030 1.28e-02 6.10e+03 5.35e+00 ... (remaining 8979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11849 1.92 - 3.83: 273 3.83 - 5.75: 58 5.75 - 7.67: 16 7.67 - 9.58: 7 Bond angle restraints: 12203 Sorted by residual: angle pdb=" N GLN A 52 " pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 112.04 102.46 9.58 1.44e+00 4.82e-01 4.43e+01 angle pdb=" N TRP R 206 " pdb=" CA TRP R 206 " pdb=" C TRP R 206 " ideal model delta sigma weight residual 113.20 104.38 8.82 1.36e+00 5.41e-01 4.21e+01 angle pdb=" N ARG R 343 " pdb=" CA ARG R 343 " pdb=" C ARG R 343 " ideal model delta sigma weight residual 114.75 108.35 6.40 1.26e+00 6.30e-01 2.58e+01 angle pdb=" N ILE R 209 " pdb=" CA ILE R 209 " pdb=" C ILE R 209 " ideal model delta sigma weight residual 109.34 118.89 -9.55 2.08e+00 2.31e-01 2.11e+01 angle pdb=" N THR B 184 " pdb=" CA THR B 184 " pdb=" C THR B 184 " ideal model delta sigma weight residual 113.61 106.75 6.86 1.50e+00 4.44e-01 2.09e+01 ... (remaining 12198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4556 17.51 - 35.01: 545 35.01 - 52.52: 156 52.52 - 70.03: 24 70.03 - 87.53: 7 Dihedral angle restraints: 5288 sinusoidal: 1929 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 139.64 -46.64 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" C ARG R 208 " pdb=" N ARG R 208 " pdb=" CA ARG R 208 " pdb=" CB ARG R 208 " ideal model delta harmonic sigma weight residual -122.60 -132.34 9.74 0 2.50e+00 1.60e-01 1.52e+01 dihedral pdb=" CA LEU B 14 " pdb=" C LEU B 14 " pdb=" N LYS B 15 " pdb=" CA LYS B 15 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 5285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1251 0.062 - 0.125: 146 0.125 - 0.187: 16 0.187 - 0.249: 4 0.249 - 0.311: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ARG R 208 " pdb=" N ARG R 208 " pdb=" C ARG R 208 " pdb=" CB ARG R 208 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB VAL R 177 " pdb=" CA VAL R 177 " pdb=" CG1 VAL R 177 " pdb=" CG2 VAL R 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA GLN A 52 " pdb=" N GLN A 52 " pdb=" C GLN A 52 " pdb=" CB GLN A 52 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1416 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 313 " -0.038 2.00e-02 2.50e+03 7.40e-02 5.47e+01 pdb=" C ASN B 313 " 0.128 2.00e-02 2.50e+03 pdb=" O ASN B 313 " -0.048 2.00e-02 2.50e+03 pdb=" N ARG B 314 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 307 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.80e+01 pdb=" C PHE A 307 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 307 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU A 308 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 180 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C PHE B 180 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 181 " 0.023 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 68 2.51 - 3.11: 6276 3.11 - 3.70: 13791 3.70 - 4.30: 19315 4.30 - 4.90: 31914 Nonbonded interactions: 71364 Sorted by model distance: nonbonded pdb=" CE1 TYR A 296 " pdb=" OE1 GLU A 297 " model vdw 1.912 3.340 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.034 3.040 nonbonded pdb=" OE1 GLU A 289 " pdb=" OH TYR A 302 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.218 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.232 3.040 ... (remaining 71359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.003 0.048 8986 Z= 0.188 Angle : 0.709 9.582 12207 Z= 0.408 Chirality : 0.044 0.311 1419 Planarity : 0.004 0.074 1536 Dihedral : 16.471 87.532 3110 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 1.85 % Allowed : 29.55 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1134 helix: 0.26 (0.27), residues: 397 sheet: 1.16 (0.32), residues: 281 loop : -0.42 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 13 TYR 0.011 0.001 TYR H 175 PHE 0.011 0.001 PHE A 336 TRP 0.013 0.001 TRP H 111 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8984) covalent geometry : angle 0.70870 (12203) SS BOND : bond 0.01315 ( 2) SS BOND : angle 1.50321 ( 4) hydrogen bonds : bond 0.23612 ( 410) hydrogen bonds : angle 7.76222 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 245 GLU cc_start: 0.6956 (tp30) cc_final: 0.6466 (tp30) REVERT: A 274 PHE cc_start: 0.8423 (t80) cc_final: 0.8209 (t80) REVERT: A 289 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 308 GLU cc_start: 0.7807 (mp0) cc_final: 0.7243 (mp0) REVERT: B 19 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.6866 (mtm-85) REVERT: B 114 CYS cc_start: 0.7945 (t) cc_final: 0.7727 (t) REVERT: B 183 HIS cc_start: 0.8509 (m-70) cc_final: 0.8144 (m-70) REVERT: B 262 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7689 (tpp) REVERT: B 313 ASN cc_start: 0.8352 (t0) cc_final: 0.8074 (t0) REVERT: R 175 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8261 (tttp) REVERT: R 374 MET cc_start: 0.7887 (mmm) cc_final: 0.7450 (mmm) outliers start: 17 outliers final: 8 residues processed: 252 average time/residue: 0.3679 time to fit residues: 100.5785 Evaluate side-chains 241 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 231 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 296 TYR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 176 LEU Chi-restraints excluded: chain R residue 207 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN H 179 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.124127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112866 restraints weight = 14282.076| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.21 r_work: 0.3483 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8986 Z= 0.212 Angle : 0.632 10.336 12207 Z= 0.333 Chirality : 0.044 0.188 1419 Planarity : 0.004 0.036 1536 Dihedral : 5.858 54.176 1257 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 6.22 % Allowed : 23.56 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1134 helix: 0.47 (0.26), residues: 403 sheet: 0.91 (0.31), residues: 286 loop : -0.16 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.022 0.002 TYR A 296 PHE 0.029 0.002 PHE A 336 TRP 0.022 0.002 TRP H 111 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8984) covalent geometry : angle 0.63198 (12203) SS BOND : bond 0.01461 ( 2) SS BOND : angle 0.96154 ( 4) hydrogen bonds : bond 0.04301 ( 410) hydrogen bonds : angle 4.94050 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 317 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7463 (tp30) cc_final: 0.6969 (tp30) REVERT: A 257 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (pttt) REVERT: A 274 PHE cc_start: 0.8574 (t80) cc_final: 0.8256 (t80) REVERT: A 289 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7599 (tm-30) REVERT: B 32 GLN cc_start: 0.8497 (mt0) cc_final: 0.8227 (mm-40) REVERT: B 43 ILE cc_start: 0.8744 (mm) cc_final: 0.8485 (mm) REVERT: B 71 VAL cc_start: 0.8545 (t) cc_final: 0.8133 (p) REVERT: B 75 GLN cc_start: 0.6861 (OUTLIER) cc_final: 0.6571 (pm20) REVERT: B 96 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7986 (mtp-110) REVERT: B 110 ASN cc_start: 0.8139 (m110) cc_final: 0.7790 (m110) REVERT: B 212 ASP cc_start: 0.7761 (m-30) cc_final: 0.7057 (m-30) REVERT: B 214 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8130 (mmm-85) REVERT: B 217 MET cc_start: 0.8321 (pmm) cc_final: 0.8043 (pmm) REVERT: B 219 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7793 (ttm-80) REVERT: B 228 ASP cc_start: 0.7788 (m-30) cc_final: 0.7142 (m-30) REVERT: B 239 ASN cc_start: 0.8394 (m-40) cc_final: 0.8157 (m110) REVERT: B 243 THR cc_start: 0.8611 (m) cc_final: 0.8259 (p) REVERT: B 258 ASP cc_start: 0.8066 (t0) cc_final: 0.7855 (t70) REVERT: B 295 ASN cc_start: 0.8396 (m-40) cc_final: 0.8167 (m110) REVERT: H 30 SER cc_start: 0.8776 (p) cc_final: 0.8443 (t) REVERT: H 32 PHE cc_start: 0.8492 (m-80) cc_final: 0.8229 (m-80) REVERT: H 60 TYR cc_start: 0.8856 (m-80) cc_final: 0.8590 (m-80) REVERT: H 156 SER cc_start: 0.8346 (m) cc_final: 0.8110 (t) REVERT: H 212 PHE cc_start: 0.8188 (m-80) cc_final: 0.7976 (m-80) REVERT: H 227 TYR cc_start: 0.7519 (m-80) cc_final: 0.7201 (m-10) REVERT: H 235 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.6642 (t80) REVERT: L 14 PHE cc_start: 0.8690 (t80) cc_final: 0.8349 (t80) REVERT: R 102 TYR cc_start: 0.7846 (m-80) cc_final: 0.7359 (m-80) REVERT: R 109 CYS cc_start: 0.8219 (t) cc_final: 0.7998 (t) REVERT: R 221 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: R 225 ILE cc_start: 0.8616 (tp) cc_final: 0.8319 (mp) REVERT: R 243 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7900 (pp) REVERT: R 245 MET cc_start: 0.7095 (mpm) cc_final: 0.6878 (mpm) REVERT: R 254 ILE cc_start: 0.8229 (mt) cc_final: 0.7863 (mm) REVERT: R 374 MET cc_start: 0.8281 (mmm) cc_final: 0.7827 (mmm) REVERT: R 389 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8089 (p) outliers start: 57 outliers final: 19 residues processed: 339 average time/residue: 0.2909 time to fit residues: 108.4539 Evaluate side-chains 327 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 221 GLU Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 243 ILE Chi-restraints excluded: chain R residue 389 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 17 GLN B 125 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.119847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109002 restraints weight = 14434.341| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.18 r_work: 0.3427 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8986 Z= 0.203 Angle : 0.632 9.607 12207 Z= 0.323 Chirality : 0.044 0.201 1419 Planarity : 0.004 0.065 1536 Dihedral : 5.138 49.982 1243 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 7.09 % Allowed : 24.65 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1134 helix: 0.39 (0.27), residues: 405 sheet: 0.78 (0.32), residues: 275 loop : -0.28 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.034 0.002 TYR H 190 PHE 0.017 0.002 PHE A 189 TRP 0.019 0.002 TRP H 111 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8984) covalent geometry : angle 0.63182 (12203) SS BOND : bond 0.01489 ( 2) SS BOND : angle 0.75446 ( 4) hydrogen bonds : bond 0.03993 ( 410) hydrogen bonds : angle 4.74199 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 306 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 GLU cc_start: 0.7640 (tp30) cc_final: 0.7245 (tp30) REVERT: A 289 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7625 (tm-30) REVERT: A 294 ASN cc_start: 0.8021 (t0) cc_final: 0.7757 (t0) REVERT: A 304 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: B 66 ASP cc_start: 0.7913 (p0) cc_final: 0.7697 (p0) REVERT: B 71 VAL cc_start: 0.8529 (t) cc_final: 0.8281 (p) REVERT: B 72 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8158 (p) REVERT: B 75 GLN cc_start: 0.6851 (OUTLIER) cc_final: 0.6511 (pm20) REVERT: B 110 ASN cc_start: 0.8187 (m110) cc_final: 0.7823 (m110) REVERT: B 146 LEU cc_start: 0.8658 (tt) cc_final: 0.8446 (tt) REVERT: B 212 ASP cc_start: 0.7966 (m-30) cc_final: 0.7638 (m-30) REVERT: B 219 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7877 (mtt-85) REVERT: B 239 ASN cc_start: 0.8419 (m-40) cc_final: 0.8190 (m110) REVERT: B 243 THR cc_start: 0.8636 (m) cc_final: 0.8282 (p) REVERT: B 329 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 331 SER cc_start: 0.8316 (p) cc_final: 0.8082 (p) REVERT: H 30 SER cc_start: 0.8703 (p) cc_final: 0.8428 (m) REVERT: H 32 PHE cc_start: 0.8673 (m-80) cc_final: 0.8274 (m-80) REVERT: H 60 TYR cc_start: 0.8858 (m-80) cc_final: 0.8585 (m-80) REVERT: H 87 ARG cc_start: 0.8450 (ptp90) cc_final: 0.8160 (ptp-170) REVERT: H 156 SER cc_start: 0.8462 (m) cc_final: 0.8166 (t) REVERT: H 213 THR cc_start: 0.8232 (m) cc_final: 0.7999 (t) REVERT: H 232 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.7871 (m-70) REVERT: H 235 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7110 (t80) REVERT: L 14 PHE cc_start: 0.8713 (t80) cc_final: 0.8444 (t80) REVERT: R 102 TYR cc_start: 0.7968 (m-80) cc_final: 0.7383 (m-80) REVERT: R 138 ILE cc_start: 0.8432 (pt) cc_final: 0.8190 (pp) REVERT: R 346 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8487 (tttp) REVERT: R 374 MET cc_start: 0.8258 (mmm) cc_final: 0.7843 (mmm) REVERT: R 380 CYS cc_start: 0.8390 (m) cc_final: 0.8170 (m) outliers start: 65 outliers final: 30 residues processed: 335 average time/residue: 0.3273 time to fit residues: 120.0125 Evaluate side-chains 332 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 346 LYS Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 331 ASN B 17 GLN B 125 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.118877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.107913 restraints weight = 14678.071| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.20 r_work: 0.3420 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8986 Z= 0.174 Angle : 0.610 9.837 12207 Z= 0.311 Chirality : 0.043 0.154 1419 Planarity : 0.004 0.056 1536 Dihedral : 4.987 53.450 1240 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.98 % Allowed : 27.15 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.25), residues: 1134 helix: 0.44 (0.27), residues: 406 sheet: 0.78 (0.31), residues: 275 loop : -0.34 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 13 TYR 0.013 0.001 TYR B 105 PHE 0.016 0.002 PHE B 234 TRP 0.015 0.002 TRP H 111 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8984) covalent geometry : angle 0.60957 (12203) SS BOND : bond 0.01681 ( 2) SS BOND : angle 0.58994 ( 4) hydrogen bonds : bond 0.03619 ( 410) hydrogen bonds : angle 4.66685 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 291 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8646 (m-10) cc_final: 0.8170 (m-80) REVERT: A 272 ASP cc_start: 0.7804 (t0) cc_final: 0.7429 (t70) REVERT: A 289 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7635 (tm-30) REVERT: A 294 ASN cc_start: 0.8065 (t0) cc_final: 0.7796 (t0) REVERT: A 337 ASP cc_start: 0.7880 (m-30) cc_final: 0.7636 (m-30) REVERT: B 19 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7876 (mtm-85) REVERT: B 66 ASP cc_start: 0.7822 (p0) cc_final: 0.7586 (p0) REVERT: B 75 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: B 212 ASP cc_start: 0.7955 (m-30) cc_final: 0.6961 (m-30) REVERT: B 217 MET cc_start: 0.8322 (pmm) cc_final: 0.8004 (pmm) REVERT: B 219 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7709 (mtt-85) REVERT: B 243 THR cc_start: 0.8660 (m) cc_final: 0.8303 (p) REVERT: B 329 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8398 (p) REVERT: B 331 SER cc_start: 0.8352 (p) cc_final: 0.8151 (p) REVERT: H 30 SER cc_start: 0.8739 (p) cc_final: 0.8473 (m) REVERT: H 32 PHE cc_start: 0.8678 (m-80) cc_final: 0.8381 (m-80) REVERT: H 103 TYR cc_start: 0.8469 (t80) cc_final: 0.8146 (t80) REVERT: H 156 SER cc_start: 0.8523 (m) cc_final: 0.8210 (t) REVERT: H 213 THR cc_start: 0.8284 (m) cc_final: 0.8043 (t) REVERT: H 220 GLU cc_start: 0.8250 (tt0) cc_final: 0.8037 (mt-10) REVERT: H 230 MET cc_start: 0.8066 (tpp) cc_final: 0.7789 (ttp) REVERT: H 235 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7312 (t80) REVERT: L 14 PHE cc_start: 0.8635 (t80) cc_final: 0.8337 (t80) REVERT: R 102 TYR cc_start: 0.7951 (m-80) cc_final: 0.7344 (m-80) REVERT: R 138 ILE cc_start: 0.8438 (pt) cc_final: 0.8197 (pp) REVERT: R 254 ILE cc_start: 0.8267 (mt) cc_final: 0.8007 (mp) REVERT: R 374 MET cc_start: 0.8287 (mmm) cc_final: 0.7841 (mmm) REVERT: R 380 CYS cc_start: 0.8313 (m) cc_final: 0.8087 (m) outliers start: 64 outliers final: 34 residues processed: 323 average time/residue: 0.3274 time to fit residues: 116.0144 Evaluate side-chains 316 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 191 ARG Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 245 MET Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 60 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 331 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.107930 restraints weight = 14702.558| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.19 r_work: 0.3410 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8986 Z= 0.152 Angle : 0.594 10.183 12207 Z= 0.304 Chirality : 0.042 0.158 1419 Planarity : 0.004 0.053 1536 Dihedral : 4.966 56.053 1240 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 6.00 % Allowed : 29.88 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.26), residues: 1134 helix: 0.60 (0.27), residues: 400 sheet: 0.69 (0.31), residues: 279 loop : -0.33 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.017 0.002 TYR L 13 PHE 0.017 0.002 PHE H 27 TRP 0.012 0.001 TRP H 111 HIS 0.005 0.001 HIS R 314 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8984) covalent geometry : angle 0.59380 (12203) SS BOND : bond 0.01727 ( 2) SS BOND : angle 0.76064 ( 4) hydrogen bonds : bond 0.03491 ( 410) hydrogen bonds : angle 4.60155 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8608 (m-10) cc_final: 0.8153 (m-80) REVERT: A 272 ASP cc_start: 0.7844 (t0) cc_final: 0.7296 (t0) REVERT: A 289 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7661 (tm-30) REVERT: A 294 ASN cc_start: 0.8101 (t0) cc_final: 0.7832 (t0) REVERT: A 337 ASP cc_start: 0.7808 (m-30) cc_final: 0.7571 (m-30) REVERT: B 19 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7807 (mtm-85) REVERT: B 66 ASP cc_start: 0.7766 (p0) cc_final: 0.7495 (p0) REVERT: B 71 VAL cc_start: 0.8497 (t) cc_final: 0.8150 (p) REVERT: B 75 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6482 (pm20) REVERT: B 171 ILE cc_start: 0.8674 (mm) cc_final: 0.8452 (mt) REVERT: B 217 MET cc_start: 0.8383 (pmm) cc_final: 0.8050 (pmm) REVERT: B 243 THR cc_start: 0.8624 (m) cc_final: 0.8243 (p) REVERT: B 329 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 331 SER cc_start: 0.8328 (p) cc_final: 0.7853 (p) REVERT: G 20 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8426 (ptpp) REVERT: H 30 SER cc_start: 0.8686 (p) cc_final: 0.8432 (m) REVERT: H 32 PHE cc_start: 0.8633 (m-80) cc_final: 0.8117 (m-80) REVERT: H 103 TYR cc_start: 0.8498 (t80) cc_final: 0.8222 (t80) REVERT: H 144 THR cc_start: 0.7312 (t) cc_final: 0.7102 (p) REVERT: H 156 SER cc_start: 0.8470 (m) cc_final: 0.8133 (t) REVERT: H 213 THR cc_start: 0.8158 (m) cc_final: 0.7931 (t) REVERT: H 220 GLU cc_start: 0.8222 (tt0) cc_final: 0.8004 (mt-10) REVERT: H 230 MET cc_start: 0.8106 (tpp) cc_final: 0.7782 (ttp) REVERT: H 235 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7448 (t80) REVERT: L 14 PHE cc_start: 0.8568 (t80) cc_final: 0.8309 (t80) REVERT: R 102 TYR cc_start: 0.7941 (m-80) cc_final: 0.7423 (m-80) REVERT: R 138 ILE cc_start: 0.8426 (pt) cc_final: 0.8186 (pp) REVERT: R 254 ILE cc_start: 0.8167 (mt) cc_final: 0.7883 (mm) REVERT: R 350 TYR cc_start: 0.7794 (t80) cc_final: 0.7452 (t80) REVERT: R 364 LEU cc_start: 0.8688 (mm) cc_final: 0.8469 (tp) REVERT: R 374 MET cc_start: 0.8232 (mmm) cc_final: 0.7802 (mmm) REVERT: R 380 CYS cc_start: 0.8262 (m) cc_final: 0.8028 (m) outliers start: 55 outliers final: 35 residues processed: 328 average time/residue: 0.2985 time to fit residues: 107.3749 Evaluate side-chains 323 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 34 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107168 restraints weight = 14441.231| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.24 r_work: 0.3381 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8986 Z= 0.193 Angle : 0.624 10.359 12207 Z= 0.319 Chirality : 0.044 0.172 1419 Planarity : 0.004 0.054 1536 Dihedral : 5.080 55.439 1240 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.56 % Allowed : 30.43 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.25), residues: 1134 helix: 0.56 (0.27), residues: 402 sheet: 0.75 (0.31), residues: 265 loop : -0.39 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.013 0.002 TYR H 227 PHE 0.018 0.002 PHE A 336 TRP 0.013 0.002 TRP B 211 HIS 0.005 0.001 HIS R 314 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8984) covalent geometry : angle 0.62353 (12203) SS BOND : bond 0.01385 ( 2) SS BOND : angle 0.86046 ( 4) hydrogen bonds : bond 0.03545 ( 410) hydrogen bonds : angle 4.58268 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 296 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8564 (m-10) cc_final: 0.8080 (m-80) REVERT: A 272 ASP cc_start: 0.7922 (t0) cc_final: 0.7109 (t0) REVERT: A 276 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7201 (mt-10) REVERT: A 289 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 294 ASN cc_start: 0.8165 (t0) cc_final: 0.7897 (t0) REVERT: A 337 ASP cc_start: 0.7822 (m-30) cc_final: 0.7587 (m-30) REVERT: B 15 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7941 (ttmm) REVERT: B 19 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.7820 (mtm-85) REVERT: B 66 ASP cc_start: 0.7761 (p0) cc_final: 0.7498 (p0) REVERT: B 75 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6572 (pm20) REVERT: B 134 ARG cc_start: 0.8327 (ptt90) cc_final: 0.8108 (ptp90) REVERT: B 212 ASP cc_start: 0.7965 (m-30) cc_final: 0.7635 (m-30) REVERT: B 217 MET cc_start: 0.8345 (pmm) cc_final: 0.8008 (pmm) REVERT: B 243 THR cc_start: 0.8670 (m) cc_final: 0.8241 (p) REVERT: B 246 ASP cc_start: 0.7947 (t0) cc_final: 0.7424 (t0) REVERT: B 329 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8321 (p) REVERT: G 20 LYS cc_start: 0.8740 (ptmt) cc_final: 0.8508 (ptpp) REVERT: H 30 SER cc_start: 0.8692 (p) cc_final: 0.8472 (m) REVERT: H 32 PHE cc_start: 0.8648 (m-80) cc_final: 0.8319 (m-80) REVERT: H 95 TYR cc_start: 0.8348 (m-10) cc_final: 0.8129 (m-10) REVERT: H 140 MET cc_start: 0.8487 (mmm) cc_final: 0.8194 (mmm) REVERT: H 144 THR cc_start: 0.7487 (t) cc_final: 0.7241 (p) REVERT: H 161 SER cc_start: 0.8194 (t) cc_final: 0.7991 (p) REVERT: H 220 GLU cc_start: 0.8252 (tt0) cc_final: 0.8039 (mt-10) REVERT: H 230 MET cc_start: 0.8091 (tpp) cc_final: 0.7804 (ttp) REVERT: H 235 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7543 (t80) REVERT: L 14 PHE cc_start: 0.8574 (t80) cc_final: 0.8366 (t80) REVERT: R 102 TYR cc_start: 0.7962 (m-80) cc_final: 0.7480 (m-80) REVERT: R 110 LEU cc_start: 0.8579 (tp) cc_final: 0.8330 (tm) REVERT: R 138 ILE cc_start: 0.8426 (pt) cc_final: 0.8181 (pp) REVERT: R 254 ILE cc_start: 0.8272 (mt) cc_final: 0.7958 (mp) REVERT: R 301 LEU cc_start: 0.7766 (mm) cc_final: 0.7517 (mp) REVERT: R 347 LEU cc_start: 0.8643 (mm) cc_final: 0.8412 (mm) REVERT: R 350 TYR cc_start: 0.7853 (t80) cc_final: 0.7535 (t80) REVERT: R 374 MET cc_start: 0.8305 (mmm) cc_final: 0.7880 (mmm) REVERT: R 380 CYS cc_start: 0.8300 (m) cc_final: 0.8059 (m) outliers start: 51 outliers final: 37 residues processed: 324 average time/residue: 0.3326 time to fit residues: 117.9930 Evaluate side-chains 331 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 290 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 155 ILE Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 0.1980 chunk 100 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 304 GLN A 331 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108243 restraints weight = 14569.322| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.21 r_work: 0.3390 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8986 Z= 0.173 Angle : 0.624 11.625 12207 Z= 0.317 Chirality : 0.043 0.171 1419 Planarity : 0.004 0.054 1536 Dihedral : 5.079 58.648 1240 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.67 % Allowed : 31.52 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1134 helix: 0.61 (0.27), residues: 403 sheet: 0.63 (0.31), residues: 265 loop : -0.34 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.015 0.002 TYR L 13 PHE 0.016 0.002 PHE A 336 TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 8984) covalent geometry : angle 0.62364 (12203) SS BOND : bond 0.01577 ( 2) SS BOND : angle 0.89563 ( 4) hydrogen bonds : bond 0.03465 ( 410) hydrogen bonds : angle 4.53916 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8633 (m) cc_final: 0.8422 (p) REVERT: A 267 PHE cc_start: 0.8577 (m-10) cc_final: 0.8092 (m-80) REVERT: A 272 ASP cc_start: 0.7937 (t0) cc_final: 0.6951 (t0) REVERT: A 276 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 289 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 294 ASN cc_start: 0.8264 (t0) cc_final: 0.7989 (t0) REVERT: A 296 TYR cc_start: 0.8404 (t80) cc_final: 0.8025 (t80) REVERT: A 336 PHE cc_start: 0.8813 (t80) cc_final: 0.8593 (t80) REVERT: A 337 ASP cc_start: 0.7848 (m-30) cc_final: 0.7617 (m-30) REVERT: B 15 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7964 (ttmm) REVERT: B 19 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.7813 (mtm-85) REVERT: B 66 ASP cc_start: 0.7739 (p0) cc_final: 0.7463 (p0) REVERT: B 75 GLN cc_start: 0.6933 (OUTLIER) cc_final: 0.6555 (pm20) REVERT: B 134 ARG cc_start: 0.8265 (ptt90) cc_final: 0.8051 (ptp90) REVERT: B 243 THR cc_start: 0.8652 (m) cc_final: 0.8256 (p) REVERT: B 298 ASP cc_start: 0.8397 (t0) cc_final: 0.8122 (t0) REVERT: B 329 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8310 (p) REVERT: G 20 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8496 (ptpp) REVERT: H 30 SER cc_start: 0.8586 (p) cc_final: 0.8385 (m) REVERT: H 32 PHE cc_start: 0.8644 (m-80) cc_final: 0.8368 (m-80) REVERT: H 72 ARG cc_start: 0.8835 (ptm160) cc_final: 0.8516 (ptp-170) REVERT: H 140 MET cc_start: 0.8456 (mmm) cc_final: 0.8119 (mmm) REVERT: H 144 THR cc_start: 0.7495 (t) cc_final: 0.7239 (p) REVERT: H 161 SER cc_start: 0.8189 (t) cc_final: 0.7979 (p) REVERT: H 220 GLU cc_start: 0.8247 (tt0) cc_final: 0.8027 (mt-10) REVERT: H 230 MET cc_start: 0.8070 (tpp) cc_final: 0.7788 (ttp) REVERT: H 235 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7526 (t80) REVERT: L 13 TYR cc_start: 0.8074 (t80) cc_final: 0.7774 (t80) REVERT: R 102 TYR cc_start: 0.7951 (m-80) cc_final: 0.7515 (m-80) REVERT: R 110 LEU cc_start: 0.8557 (tp) cc_final: 0.8311 (tm) REVERT: R 138 ILE cc_start: 0.8430 (pt) cc_final: 0.8164 (pp) REVERT: R 292 PHE cc_start: 0.7820 (m-10) cc_final: 0.7606 (m-10) REVERT: R 301 LEU cc_start: 0.7798 (mm) cc_final: 0.7507 (mp) REVERT: R 320 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8036 (mp0) REVERT: R 347 LEU cc_start: 0.8623 (mm) cc_final: 0.8399 (mm) REVERT: R 350 TYR cc_start: 0.7894 (t80) cc_final: 0.7562 (t80) REVERT: R 374 MET cc_start: 0.8290 (mmm) cc_final: 0.7864 (mmm) REVERT: R 380 CYS cc_start: 0.8340 (m) cc_final: 0.8087 (m) outliers start: 52 outliers final: 38 residues processed: 327 average time/residue: 0.3422 time to fit residues: 122.5759 Evaluate side-chains 333 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 291 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 104 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 99 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.119264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108118 restraints weight = 14442.404| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.24 r_work: 0.3398 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8986 Z= 0.148 Angle : 0.633 10.462 12207 Z= 0.318 Chirality : 0.043 0.166 1419 Planarity : 0.004 0.052 1536 Dihedral : 4.544 24.762 1236 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 5.34 % Allowed : 31.84 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (0.25), residues: 1134 helix: 0.58 (0.27), residues: 402 sheet: 0.55 (0.31), residues: 265 loop : -0.33 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 13 TYR 0.015 0.001 TYR L 13 PHE 0.021 0.002 PHE L 14 TRP 0.011 0.001 TRP B 169 HIS 0.005 0.001 HIS R 314 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 8984) covalent geometry : angle 0.63334 (12203) SS BOND : bond 0.01285 ( 2) SS BOND : angle 0.78672 ( 4) hydrogen bonds : bond 0.03406 ( 410) hydrogen bonds : angle 4.52815 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 289 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8349 (mt) cc_final: 0.8111 (mm) REVERT: A 267 PHE cc_start: 0.8593 (m-10) cc_final: 0.8121 (m-80) REVERT: A 272 ASP cc_start: 0.7930 (t0) cc_final: 0.6944 (t0) REVERT: A 276 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 289 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7695 (tm-30) REVERT: A 294 ASN cc_start: 0.8258 (t0) cc_final: 0.7987 (t0) REVERT: A 296 TYR cc_start: 0.8382 (t80) cc_final: 0.7995 (t80) REVERT: A 313 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7430 (mmp-170) REVERT: A 318 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 334 PHE cc_start: 0.8698 (t80) cc_final: 0.8465 (t80) REVERT: A 337 ASP cc_start: 0.7792 (m-30) cc_final: 0.7551 (m-30) REVERT: B 15 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7947 (ttmm) REVERT: B 19 ARG cc_start: 0.8324 (mtp-110) cc_final: 0.7788 (mtm-85) REVERT: B 66 ASP cc_start: 0.7737 (p0) cc_final: 0.7451 (p0) REVERT: B 71 VAL cc_start: 0.8508 (t) cc_final: 0.8234 (p) REVERT: B 75 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: B 134 ARG cc_start: 0.8267 (ptt90) cc_final: 0.8055 (ptp90) REVERT: B 171 ILE cc_start: 0.8501 (mm) cc_final: 0.8061 (OUTLIER) REVERT: B 212 ASP cc_start: 0.7904 (m-30) cc_final: 0.7548 (m-30) REVERT: B 243 THR cc_start: 0.8650 (m) cc_final: 0.8267 (p) REVERT: B 246 ASP cc_start: 0.7933 (t0) cc_final: 0.7658 (t70) REVERT: B 329 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8315 (p) REVERT: G 20 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8488 (ptpp) REVERT: H 32 PHE cc_start: 0.8588 (m-80) cc_final: 0.8120 (m-80) REVERT: H 72 ARG cc_start: 0.8814 (ptm160) cc_final: 0.8495 (ptp-170) REVERT: H 140 MET cc_start: 0.8486 (mmm) cc_final: 0.8153 (mmm) REVERT: H 144 THR cc_start: 0.7467 (t) cc_final: 0.7223 (p) REVERT: H 161 SER cc_start: 0.8204 (t) cc_final: 0.7993 (p) REVERT: H 220 GLU cc_start: 0.8221 (tt0) cc_final: 0.8004 (mt-10) REVERT: H 230 MET cc_start: 0.8076 (tpp) cc_final: 0.7738 (ttm) REVERT: H 235 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7594 (t80) REVERT: R 102 TYR cc_start: 0.7940 (m-80) cc_final: 0.7488 (m-80) REVERT: R 110 LEU cc_start: 0.8548 (tp) cc_final: 0.8301 (tm) REVERT: R 138 ILE cc_start: 0.8425 (pt) cc_final: 0.8168 (pp) REVERT: R 301 LEU cc_start: 0.7847 (mm) cc_final: 0.7572 (mp) REVERT: R 347 LEU cc_start: 0.8547 (mm) cc_final: 0.8328 (mm) REVERT: R 350 TYR cc_start: 0.7840 (t80) cc_final: 0.7495 (t80) REVERT: R 364 LEU cc_start: 0.8704 (mm) cc_final: 0.8462 (tp) REVERT: R 374 MET cc_start: 0.8254 (mmm) cc_final: 0.7841 (mmm) REVERT: R 380 CYS cc_start: 0.8305 (m) cc_final: 0.8079 (m) outliers start: 49 outliers final: 36 residues processed: 316 average time/residue: 0.3756 time to fit residues: 129.8748 Evaluate side-chains 319 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN A 304 GLN A 331 ASN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.108369 restraints weight = 14457.660| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.21 r_work: 0.3397 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8986 Z= 0.158 Angle : 0.640 10.722 12207 Z= 0.322 Chirality : 0.043 0.182 1419 Planarity : 0.004 0.053 1536 Dihedral : 4.612 25.023 1236 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.34 % Allowed : 32.39 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.25), residues: 1134 helix: 0.63 (0.27), residues: 401 sheet: 0.49 (0.32), residues: 255 loop : -0.40 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.009 0.001 TYR B 105 PHE 0.055 0.002 PHE L 14 TRP 0.011 0.001 TRP B 169 HIS 0.007 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8984) covalent geometry : angle 0.63955 (12203) SS BOND : bond 0.01604 ( 2) SS BOND : angle 1.07675 ( 4) hydrogen bonds : bond 0.03422 ( 410) hydrogen bonds : angle 4.45923 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8357 (mt) cc_final: 0.8114 (mm) REVERT: A 267 PHE cc_start: 0.8528 (m-10) cc_final: 0.8027 (m-80) REVERT: A 272 ASP cc_start: 0.7926 (t0) cc_final: 0.6941 (t0) REVERT: A 276 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7178 (mm-30) REVERT: A 289 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 294 ASN cc_start: 0.8281 (t0) cc_final: 0.8022 (t0) REVERT: A 313 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7508 (mmp-170) REVERT: A 318 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 15 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7915 (ttmm) REVERT: B 19 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.7753 (mtm-85) REVERT: B 66 ASP cc_start: 0.7726 (p0) cc_final: 0.7439 (p0) REVERT: B 75 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6469 (pm20) REVERT: B 134 ARG cc_start: 0.8262 (ptt90) cc_final: 0.8056 (ptp90) REVERT: B 212 ASP cc_start: 0.7867 (m-30) cc_final: 0.7572 (m-30) REVERT: B 243 THR cc_start: 0.8642 (m) cc_final: 0.8238 (p) REVERT: B 246 ASP cc_start: 0.7938 (t0) cc_final: 0.7685 (t70) REVERT: G 20 LYS cc_start: 0.8726 (ptmt) cc_final: 0.8497 (ptpp) REVERT: H 32 PHE cc_start: 0.8564 (m-80) cc_final: 0.8124 (m-80) REVERT: H 72 ARG cc_start: 0.8815 (ptm160) cc_final: 0.8508 (ptp-170) REVERT: H 140 MET cc_start: 0.8490 (mmm) cc_final: 0.8160 (mmm) REVERT: H 144 THR cc_start: 0.7507 (t) cc_final: 0.7263 (p) REVERT: H 161 SER cc_start: 0.8217 (t) cc_final: 0.7983 (p) REVERT: H 212 PHE cc_start: 0.8363 (m-80) cc_final: 0.8124 (m-80) REVERT: H 220 GLU cc_start: 0.8212 (tt0) cc_final: 0.7988 (mt-10) REVERT: H 230 MET cc_start: 0.8103 (tpp) cc_final: 0.7841 (ttp) REVERT: H 235 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7596 (t80) REVERT: R 102 TYR cc_start: 0.7946 (m-80) cc_final: 0.7493 (m-80) REVERT: R 138 ILE cc_start: 0.8419 (pt) cc_final: 0.8156 (pp) REVERT: R 320 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8064 (mp0) REVERT: R 350 TYR cc_start: 0.7889 (t80) cc_final: 0.7544 (t80) REVERT: R 374 MET cc_start: 0.8265 (mmm) cc_final: 0.7840 (mmm) REVERT: R 380 CYS cc_start: 0.8301 (m) cc_final: 0.8076 (m) outliers start: 49 outliers final: 34 residues processed: 303 average time/residue: 0.3456 time to fit residues: 114.4316 Evaluate side-chains 314 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 276 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 187 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 296 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 72 optimal weight: 0.0070 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.0010 chunk 108 optimal weight: 0.0050 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.120159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.109424 restraints weight = 14514.607| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.19 r_work: 0.3439 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8986 Z= 0.120 Angle : 0.624 11.035 12207 Z= 0.312 Chirality : 0.042 0.167 1419 Planarity : 0.004 0.053 1536 Dihedral : 4.440 23.588 1236 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.38 % Allowed : 34.46 % Favored : 62.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.26), residues: 1134 helix: 0.69 (0.27), residues: 398 sheet: 0.37 (0.30), residues: 286 loop : -0.28 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.020 0.001 TYR L 13 PHE 0.054 0.002 PHE L 14 TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8984) covalent geometry : angle 0.62415 (12203) SS BOND : bond 0.01031 ( 2) SS BOND : angle 0.81375 ( 4) hydrogen bonds : bond 0.03220 ( 410) hydrogen bonds : angle 4.41325 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 LEU cc_start: 0.8280 (mt) cc_final: 0.8065 (mm) REVERT: A 267 PHE cc_start: 0.8421 (m-10) cc_final: 0.8052 (m-80) REVERT: A 272 ASP cc_start: 0.7871 (t0) cc_final: 0.6889 (t0) REVERT: A 274 PHE cc_start: 0.8585 (t80) cc_final: 0.8329 (t80) REVERT: A 276 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7113 (mm-30) REVERT: A 289 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7736 (tm-30) REVERT: A 294 ASN cc_start: 0.8268 (t0) cc_final: 0.7929 (t0) REVERT: A 313 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7378 (mmp-170) REVERT: A 318 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7200 (mm-30) REVERT: B 15 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8067 (ttmm) REVERT: B 71 VAL cc_start: 0.8475 (t) cc_final: 0.8168 (p) REVERT: B 75 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6435 (pm20) REVERT: B 110 ASN cc_start: 0.8339 (m110) cc_final: 0.7932 (m110) REVERT: B 134 ARG cc_start: 0.8242 (ptt90) cc_final: 0.8023 (ptp90) REVERT: B 217 MET cc_start: 0.8265 (pmt) cc_final: 0.7591 (pp-130) REVERT: B 239 ASN cc_start: 0.8468 (m-40) cc_final: 0.8145 (m110) REVERT: B 243 THR cc_start: 0.8607 (m) cc_final: 0.8210 (p) REVERT: B 246 ASP cc_start: 0.7836 (t0) cc_final: 0.7613 (t70) REVERT: B 313 ASN cc_start: 0.8607 (t0) cc_final: 0.8407 (t0) REVERT: H 32 PHE cc_start: 0.8485 (m-80) cc_final: 0.8203 (m-80) REVERT: H 140 MET cc_start: 0.8467 (mmm) cc_final: 0.8182 (mmm) REVERT: H 144 THR cc_start: 0.7378 (t) cc_final: 0.7134 (p) REVERT: H 161 SER cc_start: 0.8154 (t) cc_final: 0.7921 (p) REVERT: H 212 PHE cc_start: 0.8300 (m-80) cc_final: 0.8067 (m-80) REVERT: H 220 GLU cc_start: 0.8178 (tt0) cc_final: 0.7969 (mt-10) REVERT: H 230 MET cc_start: 0.8008 (tpp) cc_final: 0.7762 (ttp) REVERT: H 235 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.7640 (t80) REVERT: R 102 TYR cc_start: 0.7828 (m-80) cc_final: 0.7364 (m-80) REVERT: R 110 LEU cc_start: 0.8523 (tp) cc_final: 0.8289 (tm) REVERT: R 138 ILE cc_start: 0.8406 (pt) cc_final: 0.8150 (pp) REVERT: R 374 MET cc_start: 0.8194 (mmm) cc_final: 0.7779 (mmm) REVERT: R 380 CYS cc_start: 0.8254 (m) cc_final: 0.8032 (m) outliers start: 31 outliers final: 22 residues processed: 294 average time/residue: 0.3391 time to fit residues: 108.8887 Evaluate side-chains 304 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 166 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 232 HIS Chi-restraints excluded: chain H residue 235 TYR Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 142 SER Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 125 ASN B 132 ASN B 220 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.107344 restraints weight = 14265.953| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.21 r_work: 0.3384 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8986 Z= 0.205 Angle : 0.688 11.144 12207 Z= 0.345 Chirality : 0.045 0.190 1419 Planarity : 0.004 0.052 1536 Dihedral : 4.723 25.939 1236 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.71 % Allowed : 35.01 % Favored : 61.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.26), residues: 1134 helix: 0.64 (0.27), residues: 394 sheet: 0.42 (0.32), residues: 256 loop : -0.30 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 219 TYR 0.011 0.002 TYR H 102 PHE 0.030 0.002 PHE H 27 TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8984) covalent geometry : angle 0.68804 (12203) SS BOND : bond 0.01485 ( 2) SS BOND : angle 1.15627 ( 4) hydrogen bonds : bond 0.03533 ( 410) hydrogen bonds : angle 4.51595 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3110.42 seconds wall clock time: 53 minutes 43.68 seconds (3223.68 seconds total)