Starting phenix.real_space_refine on Tue Apr 29 14:55:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jvr_22511/04_2025/7jvr_22511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvr_22511/04_2025/7jvr_22511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jvr_22511/04_2025/7jvr_22511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvr_22511/04_2025/7jvr_22511.map" model { file = "/net/cci-nas-00/data/ceres_data/7jvr_22511/04_2025/7jvr_22511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvr_22511/04_2025/7jvr_22511.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 64 5.16 5 C 5648 2.51 5 N 1496 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2164 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'08Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8872 At special positions: 0 Unit cell: (103.455, 123.31, 118.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 64 16.00 O 1663 8.00 N 1496 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.0 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.6% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'R' and resid 34 through 62 removed outlier: 3.718A pdb=" N LEU R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 removed outlier: 3.521A pdb=" N TYR R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 98 Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.914A pdb=" N TYR R 142 " --> pdb=" O MET R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 173 Proline residue: R 169 - end of helix removed outlier: 3.705A pdb=" N PHE R 172 " --> pdb=" O CYS R 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY R 173 " --> pdb=" O PRO R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.747A pdb=" N VAL R 190 " --> pdb=" O ASN R 186 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 225 Processing helix chain 'R' and resid 366 through 386 Processing helix chain 'R' and resid 386 through 400 removed outlier: 3.985A pdb=" N PHE R 390 " --> pdb=" O TRP R 386 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS R 393 " --> pdb=" O PHE R 389 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 427 removed outlier: 4.268A pdb=" N TYR R 408 " --> pdb=" O PRO R 404 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 removed outlier: 3.577A pdb=" N ARG R 434 " --> pdb=" O ASN R 430 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 436 " --> pdb=" O GLU R 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.623A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.677A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.569A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.785A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.938A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.840A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.866A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.749A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.294A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.345A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.715A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.507A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.003A 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: 3.630A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.590A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.693A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.615A 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: 6.677A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.663A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.663A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.608A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.769A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1441 1.32 - 1.45: 2608 1.45 - 1.59: 4912 1.59 - 1.73: 0 1.73 - 1.87: 94 Bond restraints: 9055 Sorted by residual: bond pdb=" C15 08Y R 500 " pdb=" N3 08Y R 500 " ideal model delta sigma weight residual 1.359 1.493 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C25 08Y R 500 " pdb=" C26 08Y R 500 " ideal model delta sigma weight residual 1.420 1.318 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C26 08Y R 500 " pdb=" C28 08Y R 500 " ideal model delta sigma weight residual 1.407 1.325 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C6 08Y R 500 " pdb=" C7 08Y R 500 " ideal model delta sigma weight residual 1.533 1.472 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C LEU R 387 " pdb=" N PRO R 388 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.38e-02 5.25e+03 5.84e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11889 2.07 - 4.13: 336 4.13 - 6.20: 34 6.20 - 8.26: 18 8.26 - 10.33: 6 Bond angle restraints: 12283 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 123.47 130.29 -6.82 1.53e+00 4.27e-01 1.99e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" C ASP A 237 " pdb=" N GLU A 238 " pdb=" CA GLU A 238 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.05 128.04 -4.99 1.57e+00 4.06e-01 1.01e+01 ... (remaining 12278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 5179 14.08 - 28.17: 205 28.17 - 42.25: 52 42.25 - 56.34: 13 56.34 - 70.42: 5 Dihedral angle restraints: 5454 sinusoidal: 2172 harmonic: 3282 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 93.00 161.30 -68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1148 0.061 - 0.121: 211 0.121 - 0.182: 36 0.182 - 0.242: 10 0.242 - 0.303: 2 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB ILE E 70 " pdb=" CA ILE E 70 " pdb=" CG1 ILE E 70 " pdb=" CG2 ILE E 70 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1404 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 08Y R 500 " -0.018 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C16 08Y R 500 " 0.030 2.00e-02 2.50e+03 pdb=" C5 08Y R 500 " 0.037 2.00e-02 2.50e+03 pdb=" N3 08Y R 500 " -0.045 2.00e-02 2.50e+03 pdb=" O5 08Y R 500 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 08Y R 500 " 0.027 2.00e-02 2.50e+03 3.02e-02 1.14e+01 pdb=" C17 08Y R 500 " -0.018 2.00e-02 2.50e+03 pdb=" C21 08Y R 500 " 0.031 2.00e-02 2.50e+03 pdb=" C22 08Y R 500 " -0.050 2.00e-02 2.50e+03 pdb=" C24 08Y R 500 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 403 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO R 404 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 404 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1137 2.77 - 3.30: 8461 3.30 - 3.83: 14656 3.83 - 4.37: 17086 4.37 - 4.90: 30161 Nonbonded interactions: 71501 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 263 " pdb=" O GLU A 318 " model vdw 2.332 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.347 3.040 nonbonded pdb=" OG1 THR R 69 " pdb=" OH TYR R 142 " model vdw 2.356 3.040 nonbonded pdb=" O CYS B 218 " pdb=" NE2 GLN C 18 " model vdw 2.364 3.120 ... (remaining 71496 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: 0.630 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 9060 Z= 0.236 Angle : 0.854 10.326 12293 Z= 0.472 Chirality : 0.052 0.303 1407 Planarity : 0.006 0.060 1543 Dihedral : 8.952 70.421 3319 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1110 helix: 1.15 (0.22), residues: 384 sheet: -0.83 (0.32), residues: 251 loop : -1.86 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP E 111 HIS 0.009 0.002 HIS B 62 PHE 0.024 0.003 PHE B 151 TYR 0.026 0.002 TYR R 408 ARG 0.015 0.001 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.25429 ( 439) hydrogen bonds : angle 7.97003 ( 1290) SS BOND : bond 0.00418 ( 5) SS BOND : angle 1.19412 ( 10) covalent geometry : bond 0.00464 ( 9055) covalent geometry : angle 0.85349 (12283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5462 (mtp) cc_final: 0.5188 (mtp) REVERT: R 158 ILE cc_start: 0.8055 (mt) cc_final: 0.7781 (tt) REVERT: A 189 PHE cc_start: 0.7927 (p90) cc_final: 0.7617 (p90) REVERT: A 201 VAL cc_start: 0.7929 (m) cc_final: 0.7701 (p) REVERT: A 209 LYS cc_start: 0.7902 (ttpm) cc_final: 0.7700 (ttpm) REVERT: A 225 VAL cc_start: 0.8115 (t) cc_final: 0.7883 (m) REVERT: A 259 PHE cc_start: 0.8279 (m-80) cc_final: 0.7907 (m-80) REVERT: A 273 LEU cc_start: 0.8322 (tp) cc_final: 0.8111 (tt) REVERT: A 345 LYS cc_start: 0.7957 (mttm) cc_final: 0.7752 (mptp) REVERT: B 47 THR cc_start: 0.8039 (t) cc_final: 0.6898 (p) REVERT: B 50 THR cc_start: 0.7875 (m) cc_final: 0.7638 (t) REVERT: B 110 ASN cc_start: 0.7360 (m-40) cc_final: 0.7072 (m110) REVERT: B 125 ASN cc_start: 0.8274 (t0) cc_final: 0.8008 (t0) REVERT: B 186 ASP cc_start: 0.7662 (m-30) cc_final: 0.7254 (m-30) REVERT: B 290 ASP cc_start: 0.7651 (p0) cc_final: 0.7447 (p0) REVERT: B 298 ASP cc_start: 0.7505 (t0) cc_final: 0.7227 (t70) REVERT: E 52 SER cc_start: 0.8142 (m) cc_final: 0.7938 (p) REVERT: E 116 THR cc_start: 0.8494 (m) cc_final: 0.8277 (p) REVERT: E 220 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6620 (mt-10) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.8175 time to fit residues: 255.8509 Evaluate side-chains 244 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 0.0670 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 ASN R 106 HIS R 398 HIS A 188 HIS A 244 HIS A 322 HIS B 237 ASN B 239 ASN B 259 GLN B 340 ASN C 44 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.159713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137126 restraints weight = 11881.176| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.13 r_work: 0.3650 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9060 Z= 0.178 Angle : 0.634 8.588 12293 Z= 0.330 Chirality : 0.044 0.200 1407 Planarity : 0.004 0.058 1543 Dihedral : 5.489 52.953 1300 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.60 % Allowed : 11.20 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1110 helix: 2.19 (0.24), residues: 391 sheet: -0.74 (0.31), residues: 264 loop : -1.45 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.004 0.001 HIS E 35 PHE 0.019 0.002 PHE R 110 TYR 0.016 0.002 TYR B 289 ARG 0.007 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.05402 ( 439) hydrogen bonds : angle 5.25245 ( 1290) SS BOND : bond 0.00706 ( 5) SS BOND : angle 1.85847 ( 10) covalent geometry : bond 0.00398 ( 9055) covalent geometry : angle 0.63181 (12283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5701 (mtp) cc_final: 0.5411 (mtp) REVERT: R 158 ILE cc_start: 0.7944 (mt) cc_final: 0.7649 (tt) REVERT: R 411 PHE cc_start: 0.7500 (m-10) cc_final: 0.7262 (m-10) REVERT: A 209 LYS cc_start: 0.7948 (ttpm) cc_final: 0.7742 (ttpm) REVERT: A 272 ASP cc_start: 0.7945 (t0) cc_final: 0.7513 (t0) REVERT: A 318 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 323 PHE cc_start: 0.8051 (m-10) cc_final: 0.7626 (m-10) REVERT: B 96 ARG cc_start: 0.7598 (mtt-85) cc_final: 0.7354 (mtt180) REVERT: B 137 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6558 (ttp-110) REVERT: B 251 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8379 (mtt90) REVERT: B 291 ASP cc_start: 0.8096 (p0) cc_final: 0.7879 (p0) REVERT: B 314 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7424 (ptt180) REVERT: E 52 SER cc_start: 0.8366 (m) cc_final: 0.8137 (p) REVERT: E 116 THR cc_start: 0.8618 (m) cc_final: 0.8385 (p) REVERT: E 192 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7790 (ptp) outliers start: 35 outliers final: 10 residues processed: 279 average time/residue: 0.8820 time to fit residues: 267.6736 Evaluate side-chains 242 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 229 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 0.0470 chunk 28 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 422 ASN B 88 ASN B 295 ASN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.159060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.136303 restraints weight = 11943.626| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.13 r_work: 0.3645 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9060 Z= 0.141 Angle : 0.595 8.203 12293 Z= 0.306 Chirality : 0.043 0.172 1407 Planarity : 0.004 0.052 1543 Dihedral : 5.342 48.630 1300 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.32 % Allowed : 15.62 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1110 helix: 2.38 (0.25), residues: 388 sheet: -0.68 (0.30), residues: 273 loop : -1.18 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE R 110 TYR 0.023 0.002 TYR R 142 ARG 0.009 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 439) hydrogen bonds : angle 4.95312 ( 1290) SS BOND : bond 0.00753 ( 5) SS BOND : angle 1.07056 ( 10) covalent geometry : bond 0.00314 ( 9055) covalent geometry : angle 0.59426 (12283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 240 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7808 (mt) cc_final: 0.7585 (mp) REVERT: R 57 MET cc_start: 0.5531 (mtp) cc_final: 0.5261 (mtp) REVERT: R 81 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7386 (mm) REVERT: R 155 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6452 (mpp) REVERT: R 158 ILE cc_start: 0.7960 (mt) cc_final: 0.7697 (tt) REVERT: R 411 PHE cc_start: 0.7458 (m-10) cc_final: 0.7194 (m-10) REVERT: R 418 ASN cc_start: 0.6877 (t0) cc_final: 0.6531 (t0) REVERT: A 272 ASP cc_start: 0.7870 (t0) cc_final: 0.7500 (t0) REVERT: A 318 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7448 (mt-10) REVERT: A 323 PHE cc_start: 0.7942 (m-10) cc_final: 0.7543 (m-10) REVERT: B 96 ARG cc_start: 0.7664 (mtt-85) cc_final: 0.7419 (mtt180) REVERT: B 197 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7620 (ttm-80) REVERT: B 217 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7280 (pmt) REVERT: B 314 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7393 (ptt180) REVERT: B 331 SER cc_start: 0.8271 (p) cc_final: 0.7782 (p) REVERT: E 27 PHE cc_start: 0.8274 (p90) cc_final: 0.8053 (p90) REVERT: E 46 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7624 (mt-10) REVERT: E 52 SER cc_start: 0.8396 (m) cc_final: 0.8148 (p) REVERT: E 71 SER cc_start: 0.8188 (p) cc_final: 0.7979 (p) REVERT: E 91 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7724 (p) REVERT: E 155 VAL cc_start: 0.8075 (p) cc_final: 0.7555 (m) REVERT: E 192 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7814 (ptp) outliers start: 42 outliers final: 14 residues processed: 259 average time/residue: 0.8998 time to fit residues: 254.9125 Evaluate side-chains 244 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 224 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 62 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.155588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133285 restraints weight = 11884.017| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.07 r_work: 0.3608 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9060 Z= 0.179 Angle : 0.612 9.354 12293 Z= 0.314 Chirality : 0.043 0.181 1407 Planarity : 0.004 0.047 1543 Dihedral : 5.201 44.928 1300 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.21 % Allowed : 16.65 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1110 helix: 2.19 (0.25), residues: 397 sheet: -0.54 (0.30), residues: 273 loop : -1.08 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS E 232 PHE 0.022 0.002 PHE R 110 TYR 0.021 0.002 TYR R 142 ARG 0.016 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 439) hydrogen bonds : angle 4.87448 ( 1290) SS BOND : bond 0.00865 ( 5) SS BOND : angle 1.21465 ( 10) covalent geometry : bond 0.00413 ( 9055) covalent geometry : angle 0.61120 (12283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7812 (mt) cc_final: 0.7543 (mp) REVERT: R 57 MET cc_start: 0.5392 (mtp) cc_final: 0.5130 (mtp) REVERT: R 81 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7279 (mm) REVERT: R 155 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6467 (mpp) REVERT: R 158 ILE cc_start: 0.7927 (mt) cc_final: 0.7624 (tt) REVERT: R 372 THR cc_start: 0.7255 (m) cc_final: 0.7012 (m) REVERT: R 411 PHE cc_start: 0.7480 (m-10) cc_final: 0.7258 (m-10) REVERT: A 272 ASP cc_start: 0.7872 (t0) cc_final: 0.7511 (t0) REVERT: A 277 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8085 (ttmt) REVERT: A 316 THR cc_start: 0.8193 (p) cc_final: 0.7950 (p) REVERT: A 318 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7462 (mt-10) REVERT: A 323 PHE cc_start: 0.8019 (m-10) cc_final: 0.7615 (m-10) REVERT: B 17 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7623 (tm130) REVERT: B 19 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7222 (ttp80) REVERT: B 96 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.7458 (mtt180) REVERT: B 170 ASP cc_start: 0.8183 (t70) cc_final: 0.7862 (t0) REVERT: B 217 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7495 (pmt) REVERT: B 277 SER cc_start: 0.8333 (t) cc_final: 0.7864 (m) REVERT: B 312 ASP cc_start: 0.7459 (m-30) cc_final: 0.7256 (m-30) REVERT: B 314 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7513 (ptt180) REVERT: E 46 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7622 (mt-10) REVERT: E 91 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7702 (p) REVERT: E 192 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7904 (ptp) outliers start: 41 outliers final: 15 residues processed: 266 average time/residue: 1.0539 time to fit residues: 303.5883 Evaluate side-chains 258 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 1.9990 chunk 100 optimal weight: 0.0070 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 239 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.156852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.133842 restraints weight = 11513.308| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.09 r_work: 0.3645 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9060 Z= 0.138 Angle : 0.575 8.072 12293 Z= 0.296 Chirality : 0.042 0.177 1407 Planarity : 0.004 0.044 1543 Dihedral : 4.982 40.644 1300 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.52 % Allowed : 17.06 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1110 helix: 2.26 (0.25), residues: 397 sheet: -0.45 (0.31), residues: 270 loop : -0.99 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.024 0.002 PHE R 110 TYR 0.023 0.002 TYR E 50 ARG 0.009 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 439) hydrogen bonds : angle 4.72311 ( 1290) SS BOND : bond 0.00694 ( 5) SS BOND : angle 0.97378 ( 10) covalent geometry : bond 0.00315 ( 9055) covalent geometry : angle 0.57481 (12283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 243 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7845 (mt) cc_final: 0.7607 (mp) REVERT: R 57 MET cc_start: 0.5348 (mtp) cc_final: 0.5114 (mtp) REVERT: R 81 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7325 (mm) REVERT: R 117 MET cc_start: 0.6420 (mmt) cc_final: 0.6194 (mmm) REVERT: R 155 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6525 (mpp) REVERT: R 158 ILE cc_start: 0.7993 (mt) cc_final: 0.7686 (tt) REVERT: R 372 THR cc_start: 0.7311 (m) cc_final: 0.7066 (m) REVERT: R 411 PHE cc_start: 0.7480 (m-10) cc_final: 0.7264 (m-10) REVERT: A 316 THR cc_start: 0.8207 (p) cc_final: 0.7947 (p) REVERT: A 318 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7480 (mt-10) REVERT: A 323 PHE cc_start: 0.7938 (m-10) cc_final: 0.7600 (m-10) REVERT: B 17 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7483 (tm130) REVERT: B 19 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7276 (ttp80) REVERT: B 48 ARG cc_start: 0.8532 (mmt90) cc_final: 0.8179 (mpt-90) REVERT: B 96 ARG cc_start: 0.7690 (mtt-85) cc_final: 0.7435 (mtt180) REVERT: B 170 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7834 (t0) REVERT: B 217 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7224 (pmt) REVERT: B 258 ASP cc_start: 0.7550 (t0) cc_final: 0.6814 (t0) REVERT: B 314 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7470 (ptt180) REVERT: E 46 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7572 (mt-10) REVERT: E 91 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7647 (p) REVERT: E 192 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7863 (ptp) outliers start: 44 outliers final: 24 residues processed: 258 average time/residue: 0.9545 time to fit residues: 266.6413 Evaluate side-chains 269 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.156173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133405 restraints weight = 11529.346| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.08 r_work: 0.3640 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9060 Z= 0.143 Angle : 0.580 8.201 12293 Z= 0.298 Chirality : 0.042 0.187 1407 Planarity : 0.004 0.039 1543 Dihedral : 4.923 39.271 1300 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.32 % Allowed : 17.16 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1110 helix: 2.32 (0.25), residues: 397 sheet: -0.50 (0.30), residues: 274 loop : -0.90 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 188 PHE 0.023 0.002 PHE R 110 TYR 0.022 0.002 TYR R 142 ARG 0.009 0.001 ARG B 251 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 439) hydrogen bonds : angle 4.67408 ( 1290) SS BOND : bond 0.00711 ( 5) SS BOND : angle 0.93032 ( 10) covalent geometry : bond 0.00330 ( 9055) covalent geometry : angle 0.57971 (12283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 247 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7840 (mt) cc_final: 0.7596 (mp) REVERT: R 57 MET cc_start: 0.5368 (mtp) cc_final: 0.5136 (mtp) REVERT: R 81 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7306 (mm) REVERT: R 117 MET cc_start: 0.6483 (mmt) cc_final: 0.6218 (mmm) REVERT: R 155 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6509 (mpp) REVERT: R 158 ILE cc_start: 0.7978 (mt) cc_final: 0.7669 (tt) REVERT: R 372 THR cc_start: 0.7324 (m) cc_final: 0.7060 (m) REVERT: R 411 PHE cc_start: 0.7489 (m-10) cc_final: 0.7272 (m-10) REVERT: A 308 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6417 (mp0) REVERT: A 316 THR cc_start: 0.8232 (p) cc_final: 0.8002 (p) REVERT: A 318 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7460 (mt-10) REVERT: A 323 PHE cc_start: 0.7951 (m-10) cc_final: 0.7612 (m-10) REVERT: B 17 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7438 (tm130) REVERT: B 32 GLN cc_start: 0.8091 (mt0) cc_final: 0.7829 (mt0) REVERT: B 48 ARG cc_start: 0.8522 (mmt90) cc_final: 0.8206 (mpt-90) REVERT: B 170 ASP cc_start: 0.8122 (t70) cc_final: 0.7827 (t0) REVERT: B 217 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7252 (pmt) REVERT: B 258 ASP cc_start: 0.7476 (t0) cc_final: 0.6760 (t0) REVERT: B 314 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7485 (ptt180) REVERT: E 52 SER cc_start: 0.8447 (m) cc_final: 0.8162 (p) REVERT: E 91 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7677 (p) REVERT: E 117 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7868 (tt) REVERT: E 192 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7873 (ptp) outliers start: 42 outliers final: 27 residues processed: 259 average time/residue: 1.1619 time to fit residues: 325.0078 Evaluate side-chains 276 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7831 > 50: distance: 9 - 12: 4.169 distance: 12 - 13: 8.968 distance: 13 - 14: 5.126 distance: 13 - 16: 8.191 distance: 14 - 15: 7.646 distance: 14 - 19: 14.704 distance: 16 - 17: 4.397 distance: 16 - 18: 11.141 distance: 19 - 20: 10.702 distance: 20 - 21: 6.687 distance: 20 - 23: 12.087 distance: 21 - 22: 12.818 distance: 21 - 25: 14.728 distance: 23 - 24: 20.335 distance: 25 - 26: 12.119 distance: 26 - 27: 10.466 distance: 26 - 29: 6.189 distance: 27 - 28: 18.768 distance: 27 - 31: 31.063 distance: 29 - 30: 8.445 distance: 31 - 32: 53.937 distance: 31 - 125: 24.740 distance: 32 - 33: 54.717 distance: 32 - 35: 29.298 distance: 33 - 34: 50.957 distance: 33 - 38: 43.835 distance: 35 - 36: 10.326 distance: 35 - 37: 8.469 distance: 38 - 39: 41.757 distance: 38 - 44: 26.095 distance: 39 - 40: 54.137 distance: 39 - 42: 25.132 distance: 40 - 41: 22.462 distance: 40 - 45: 26.309 distance: 42 - 43: 12.142 distance: 43 - 44: 15.119 distance: 45 - 46: 7.943 distance: 46 - 47: 32.600 distance: 46 - 49: 10.172 distance: 47 - 48: 36.077 distance: 47 - 52: 45.607 distance: 49 - 50: 15.285 distance: 49 - 51: 23.579 distance: 52 - 53: 56.783 distance: 53 - 54: 38.496 distance: 53 - 56: 50.388 distance: 54 - 55: 25.813 distance: 54 - 59: 24.280 distance: 56 - 57: 15.834 distance: 56 - 58: 10.283 distance: 59 - 60: 22.757 distance: 59 - 65: 32.782 distance: 60 - 61: 26.078 distance: 60 - 63: 18.843 distance: 61 - 62: 40.160 distance: 61 - 66: 40.037 distance: 63 - 64: 36.300 distance: 64 - 65: 17.040 distance: 66 - 67: 12.973 distance: 67 - 68: 4.237 distance: 68 - 69: 9.791 distance: 68 - 70: 12.166 distance: 70 - 71: 10.358 distance: 71 - 72: 11.153 distance: 71 - 74: 11.860 distance: 72 - 73: 20.253 distance: 72 - 79: 7.563 distance: 74 - 75: 15.634 distance: 75 - 76: 9.779 distance: 76 - 77: 18.356 distance: 76 - 78: 18.060