Starting phenix.real_space_refine on Wed Sep 17 12:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ejk_31162/09_2025/7ejk_31162_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ejk_31162/09_2025/7ejk_31162.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ejk_31162/09_2025/7ejk_31162.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ejk_31162/09_2025/7ejk_31162.map" model { file = "/net/cci-nas-00/data/ceres_data/7ejk_31162/09_2025/7ejk_31162_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ejk_31162/09_2025/7ejk_31162_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.189 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 59 5.16 5 C 5484 2.51 5 N 1460 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1699 Classifications: {'peptide': 215} Link IDs: {'CIS': 7, 'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2567 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 5, 'TRANS': 324} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 48} Chain: "H" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2089 Classifications: {'peptide': 257} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 246} Chain breaks: 2 Chain: "R" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'J5C': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 2.24, per 1000 atoms: 0.26 Number of scatterers: 8586 At special positions: 0 Unit cell: (90.1, 119.85, 124.95, 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 59 16.00 O 1583 8.00 N 1460 7.00 C 5484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 426.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 35.5% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.520A pdb=" N PHE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'G' and resid 10 through 23 removed outlier: 3.776A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.582A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.809A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 212 removed outlier: 3.700A pdb=" N VAL H 212 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 76 removed outlier: 3.529A pdb=" N SER R 76 " --> pdb=" O ALA R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 108 removed outlier: 4.201A pdb=" N ILE R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Proline residue: R 103 - end of helix Processing helix chain 'R' and resid 117 through 151 removed outlier: 4.180A pdb=" N CYS R 121 " --> pdb=" O GLY R 117 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU R 122 " --> pdb=" O LYS R 118 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 136 " --> pdb=" O CYS R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 158 Processing helix chain 'R' and resid 161 through 181 Processing helix chain 'R' and resid 208 through 241 removed outlier: 4.057A pdb=" N SER R 214 " --> pdb=" O TRP R 210 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA R 222 " --> pdb=" O GLY R 218 " (cutoff:3.500A) Proline residue: R 223 - end of helix Processing helix chain 'R' and resid 382 through 414 removed outlier: 3.697A pdb=" N ARG R 386 " --> pdb=" O ASN R 382 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL R 390 " --> pdb=" O ARG R 386 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N PHE R 398 " --> pdb=" O VAL R 394 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL R 399 " --> pdb=" O ILE R 395 " (cutoff:3.500A) Proline residue: R 404 - end of helix removed outlier: 3.658A pdb=" N ALA R 413 " --> pdb=" O TYR R 409 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL R 414 " --> pdb=" O THR R 410 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 444 removed outlier: 3.740A pdb=" N TYR R 431 " --> pdb=" O PHE R 427 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS R 432 " --> pdb=" O TRP R 428 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN R 433 " --> pdb=" O PHE R 429 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER R 434 " --> pdb=" O GLY R 430 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER R 435 " --> pdb=" O TYR R 431 " (cutoff:3.500A) Proline residue: R 438 - end of helix removed outlier: 3.511A pdb=" N THR R 442 " --> pdb=" O PRO R 438 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE R 444 " --> pdb=" O ILE R 440 " (cutoff:3.500A) Processing helix chain 'R' and resid 445 through 457 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.994A pdb=" N VAL A 186 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.817A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.853A 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: 4.061A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.494A 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: 5.807A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.542A 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 153 removed outlier: 6.609A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.658A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.543A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.846A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.900A 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 6 removed outlier: 3.644A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.757A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 134 through 135 removed outlier: 3.512A pdb=" N THR H 231 " --> pdb=" O TYR H 215 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU H 162 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR H 178 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 147 through 148 removed outlier: 3.556A pdb=" N SER H 194 " --> pdb=" O THR H 201 " (cutoff:3.500A) 369 hydrogen bonds defined for protein. 1050 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1381 1.31 - 1.44: 2461 1.44 - 1.56: 4846 1.56 - 1.69: 0 1.69 - 1.82: 81 Bond restraints: 8769 Sorted by residual: bond pdb=" C9 J5C R 501 " pdb=" N13 J5C R 501 " ideal model delta sigma weight residual 1.277 1.473 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" CA ARG R 146 " pdb=" C ARG R 146 " ideal model delta sigma weight residual 1.524 1.455 0.069 1.24e-02 6.50e+03 3.09e+01 bond pdb=" CA PHE R 406 " pdb=" C PHE R 406 " ideal model delta sigma weight residual 1.524 1.453 0.070 1.29e-02 6.01e+03 2.98e+01 bond pdb=" C9 J5C R 501 " pdb=" N10 J5C R 501 " ideal model delta sigma weight residual 1.373 1.472 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" C ARG R 146 " pdb=" O ARG R 146 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.15e-02 7.56e+03 2.39e+01 ... (remaining 8764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 11677 2.62 - 5.25: 160 5.25 - 7.87: 38 7.87 - 10.49: 3 10.49 - 13.12: 3 Bond angle restraints: 11881 Sorted by residual: angle pdb=" N ILE R 154 " pdb=" CA ILE R 154 " pdb=" C ILE R 154 " ideal model delta sigma weight residual 110.53 117.54 -7.01 9.40e-01 1.13e+00 5.56e+01 angle pdb=" N ALA R 153 " pdb=" CA ALA R 153 " pdb=" C ALA R 153 " ideal model delta sigma weight residual 111.28 117.87 -6.59 1.09e+00 8.42e-01 3.66e+01 angle pdb=" C ASP A 328 " pdb=" CA ASP A 328 " pdb=" CB ASP A 328 " ideal model delta sigma weight residual 109.76 120.37 -10.61 1.99e+00 2.53e-01 2.84e+01 angle pdb=" N PHE R 405 " pdb=" CA PHE R 405 " pdb=" C PHE R 405 " ideal model delta sigma weight residual 111.07 116.64 -5.57 1.07e+00 8.73e-01 2.71e+01 angle pdb=" N ARG R 146 " pdb=" CA ARG R 146 " pdb=" C ARG R 146 " ideal model delta sigma weight residual 110.97 105.32 5.65 1.09e+00 8.42e-01 2.68e+01 ... (remaining 11876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4724 17.61 - 35.22: 390 35.22 - 52.83: 57 52.83 - 70.44: 10 70.44 - 88.05: 6 Dihedral angle restraints: 5187 sinusoidal: 2022 harmonic: 3165 Sorted by residual: dihedral pdb=" CA THR B 29 " pdb=" C THR B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta harmonic sigma weight residual 0.00 26.27 -26.27 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" C LEU A 348 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " pdb=" CB LEU A 348 " ideal model delta harmonic sigma weight residual -122.60 -112.09 -10.51 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" C HIS R 446 " pdb=" N HIS R 446 " pdb=" CA HIS R 446 " pdb=" CB HIS R 446 " ideal model delta harmonic sigma weight residual -122.60 -132.59 9.99 0 2.50e+00 1.60e-01 1.60e+01 ... (remaining 5184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1267 0.103 - 0.205: 71 0.205 - 0.308: 5 0.308 - 0.411: 1 0.411 - 0.514: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" CA HIS R 446 " pdb=" N HIS R 446 " pdb=" C HIS R 446 " pdb=" CB HIS R 446 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA SER H 85 " pdb=" N SER H 85 " pdb=" C SER H 85 " pdb=" CB SER H 85 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ALA R 153 " pdb=" N ALA R 153 " pdb=" C ALA R 153 " pdb=" CB ALA R 153 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1342 not shown) Planarity restraints: 1497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.31e+00 pdb=" C ARG A 349 " 0.031 2.00e-02 2.50e+03 pdb=" O ARG A 349 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 350 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 402 " 0.013 2.00e-02 2.50e+03 1.06e-02 2.78e+00 pdb=" CG TRP R 402 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP R 402 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 402 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 402 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 402 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 402 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 402 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 402 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 402 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 422 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LEU R 422 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU R 422 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 423 " 0.010 2.00e-02 2.50e+03 ... (remaining 1494 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.18: 5 2.18 - 2.86: 3289 2.86 - 3.54: 12125 3.54 - 4.22: 18721 4.22 - 4.90: 33360 Nonbonded interactions: 67500 Sorted by model distance: nonbonded pdb=" O THR R 408 " pdb=" O LEU R 411 " model vdw 1.495 2.432 nonbonded pdb=" O LEU A 353 " pdb=" CD1 LEU A 353 " model vdw 1.855 3.460 nonbonded pdb=" O PHE R 405 " pdb=" OG1 THR R 408 " model vdw 2.024 3.040 nonbonded pdb=" O ILE B 33 " pdb=" OG1 THR B 34 " model vdw 2.163 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.166 3.040 ... (remaining 67495 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=0.00 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: 1.260 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.600 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.006 0.196 8772 Z= 0.350 Angle : 0.773 13.116 11887 Z= 0.477 Chirality : 0.050 0.514 1345 Planarity : 0.003 0.036 1497 Dihedral : 13.043 88.054 3136 Min Nonbonded Distance : 1.495 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.43 % Allowed : 0.64 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: -0.01 (0.27), residues: 1072 helix: 1.86 (0.30), residues: 338 sheet: -0.02 (0.33), residues: 261 loop : -1.41 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 450 TYR 0.007 0.001 TYR H 178 PHE 0.024 0.001 PHE R 427 TRP 0.028 0.001 TRP R 402 HIS 0.004 0.001 HIS R 446 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8769) covalent geometry : angle 0.77321 (11881) SS BOND : bond 0.00381 ( 3) SS BOND : angle 1.14768 ( 6) hydrogen bonds : bond 0.20215 ( 369) hydrogen bonds : angle 7.79438 ( 1050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 0.351 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.8684 (t0) cc_final: 0.8393 (t0) REVERT: A 53 MET cc_start: 0.7795 (ptp) cc_final: 0.7091 (ptm) REVERT: B 78 LYS cc_start: 0.9029 (mttm) cc_final: 0.8786 (mmtm) REVERT: B 215 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7578 (mp0) REVERT: B 217 MET cc_start: 0.7694 (ppp) cc_final: 0.7398 (ppp) REVERT: H 76 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8626 (tppp) REVERT: H 208 GLU cc_start: 0.7826 (pt0) cc_final: 0.6203 (pt0) REVERT: R 94 ASP cc_start: 0.7561 (m-30) cc_final: 0.7304 (m-30) REVERT: R 175 ILE cc_start: 0.9111 (tp) cc_final: 0.8835 (mm) REVERT: R 423 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7950 (t80) REVERT: R 445 ASN cc_start: 0.8824 (t0) cc_final: 0.8619 (t0) outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.1135 time to fit residues: 32.4634 Evaluate side-chains 166 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN A 305 GLN A 331 ASN A 347 ASN B 239 ASN B 268 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.091663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075951 restraints weight = 24395.830| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.19 r_work: 0.3114 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8772 Z= 0.158 Angle : 0.704 15.401 11887 Z= 0.369 Chirality : 0.045 0.173 1345 Planarity : 0.004 0.044 1497 Dihedral : 4.969 52.067 1197 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 1.92 % Allowed : 12.29 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.14 (0.26), residues: 1072 helix: 1.84 (0.29), residues: 341 sheet: 0.29 (0.32), residues: 260 loop : -1.38 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 206 TYR 0.017 0.002 TYR B 264 PHE 0.026 0.002 PHE R 387 TRP 0.020 0.001 TRP R 402 HIS 0.009 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8769) covalent geometry : angle 0.70308 (11881) SS BOND : bond 0.00715 ( 3) SS BOND : angle 1.28982 ( 6) hydrogen bonds : bond 0.04447 ( 369) hydrogen bonds : angle 5.39665 ( 1050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9034 (tttt) REVERT: A 26 ASP cc_start: 0.9044 (t0) cc_final: 0.8770 (t0) REVERT: B 59 TYR cc_start: 0.8708 (m-80) cc_final: 0.8322 (m-80) REVERT: B 183 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7384 (t-90) REVERT: B 215 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7723 (mp0) REVERT: B 217 MET cc_start: 0.8137 (ppp) cc_final: 0.7651 (ppp) REVERT: H 42 GLU cc_start: 0.8085 (pp20) cc_final: 0.7880 (pp20) REVERT: H 43 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8553 (mmtm) REVERT: R 115 TYR cc_start: 0.6128 (m-80) cc_final: 0.5834 (m-80) REVERT: R 175 ILE cc_start: 0.9179 (tp) cc_final: 0.8944 (mm) REVERT: R 423 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7625 (t80) REVERT: R 445 ASN cc_start: 0.8861 (t0) cc_final: 0.8560 (t0) outliers start: 18 outliers final: 11 residues processed: 209 average time/residue: 0.0957 time to fit residues: 27.4936 Evaluate side-chains 183 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.0870 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN ** B 311 HIS ** 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 = 0.3494 r_free = 0.3494 target = 0.090554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.074851 restraints weight = 24341.214| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.19 r_work: 0.3076 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8772 Z= 0.155 Angle : 0.665 15.447 11887 Z= 0.347 Chirality : 0.044 0.199 1345 Planarity : 0.003 0.046 1497 Dihedral : 4.984 52.937 1195 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 2.24 % Allowed : 15.60 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.14 (0.26), residues: 1072 helix: 1.79 (0.29), residues: 344 sheet: 0.24 (0.32), residues: 267 loop : -1.34 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 206 TYR 0.020 0.001 TYR R 235 PHE 0.025 0.001 PHE R 387 TRP 0.027 0.001 TRP R 402 HIS 0.009 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8769) covalent geometry : angle 0.66430 (11881) SS BOND : bond 0.00847 ( 3) SS BOND : angle 1.19992 ( 6) hydrogen bonds : bond 0.04021 ( 369) hydrogen bonds : angle 5.09134 ( 1050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.312 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 25 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8825 (tm-30) REVERT: A 26 ASP cc_start: 0.9021 (t0) cc_final: 0.8734 (m-30) REVERT: A 187 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8109 (tm-30) REVERT: A 244 MET cc_start: 0.7992 (mmp) cc_final: 0.7430 (mmp) REVERT: A 246 GLU cc_start: 0.8194 (tp30) cc_final: 0.7949 (tp30) REVERT: B 59 TYR cc_start: 0.8725 (m-80) cc_final: 0.8293 (m-80) REVERT: B 61 MET cc_start: 0.9292 (ppp) cc_final: 0.9047 (ppp) REVERT: B 183 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7461 (t-90) REVERT: B 215 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7716 (mp0) REVERT: B 217 MET cc_start: 0.8163 (ppp) cc_final: 0.7588 (ppp) REVERT: H 39 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8147 (tm-30) REVERT: H 42 GLU cc_start: 0.8174 (pp20) cc_final: 0.7902 (pp20) REVERT: H 43 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8530 (mmtm) REVERT: R 115 TYR cc_start: 0.6073 (m-80) cc_final: 0.5749 (m-80) REVERT: R 175 ILE cc_start: 0.9199 (tp) cc_final: 0.8977 (mm) REVERT: R 402 TRP cc_start: 0.8296 (m100) cc_final: 0.8005 (m100) REVERT: R 423 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7534 (t80) REVERT: R 445 ASN cc_start: 0.8840 (t0) cc_final: 0.8561 (t0) outliers start: 21 outliers final: 15 residues processed: 203 average time/residue: 0.1001 time to fit residues: 27.8300 Evaluate side-chains 181 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 56 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 256 ASN A 305 GLN A 347 ASN ** B 311 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.092420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.076864 restraints weight = 24718.809| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.18 r_work: 0.3122 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8772 Z= 0.125 Angle : 0.652 14.467 11887 Z= 0.338 Chirality : 0.043 0.185 1345 Planarity : 0.003 0.046 1497 Dihedral : 4.918 53.256 1195 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 2.24 % Allowed : 17.52 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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 (0.26), residues: 1072 helix: 1.81 (0.29), residues: 344 sheet: 0.34 (0.32), residues: 280 loop : -1.31 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 206 TYR 0.010 0.001 TYR A 320 PHE 0.022 0.001 PHE R 387 TRP 0.018 0.001 TRP R 402 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8769) covalent geometry : angle 0.65137 (11881) SS BOND : bond 0.00678 ( 3) SS BOND : angle 1.01465 ( 6) hydrogen bonds : bond 0.03499 ( 369) hydrogen bonds : angle 4.85667 ( 1050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.281 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9395 (tmtt) cc_final: 0.9110 (tttp) REVERT: A 26 ASP cc_start: 0.9036 (t0) cc_final: 0.8776 (m-30) REVERT: B 183 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.7450 (t-90) REVERT: B 217 MET cc_start: 0.8192 (ppp) cc_final: 0.7589 (ppp) REVERT: H 3 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (pp30) REVERT: H 42 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7813 (pp20) REVERT: H 218 MET cc_start: 0.9101 (ttp) cc_final: 0.8901 (ttt) REVERT: R 83 GLN cc_start: 0.8980 (mp10) cc_final: 0.8696 (mp10) REVERT: R 115 TYR cc_start: 0.5976 (m-80) cc_final: 0.5638 (m-80) REVERT: R 175 ILE cc_start: 0.9202 (tp) cc_final: 0.8963 (mm) REVERT: R 423 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7565 (t80) REVERT: R 445 ASN cc_start: 0.8743 (t0) cc_final: 0.8506 (t0) outliers start: 21 outliers final: 13 residues processed: 198 average time/residue: 0.0937 time to fit residues: 25.8914 Evaluate side-chains 192 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 7 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 0.0040 chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075746 restraints weight = 24633.127| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.22 r_work: 0.3112 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8772 Z= 0.133 Angle : 0.648 13.245 11887 Z= 0.337 Chirality : 0.043 0.163 1345 Planarity : 0.003 0.046 1497 Dihedral : 4.879 54.240 1195 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.78 % Allowed : 17.63 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.29 (0.26), residues: 1072 helix: 1.89 (0.29), residues: 345 sheet: 0.38 (0.33), residues: 267 loop : -1.28 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 206 TYR 0.020 0.001 TYR R 156 PHE 0.022 0.001 PHE R 387 TRP 0.032 0.001 TRP R 402 HIS 0.008 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8769) covalent geometry : angle 0.64760 (11881) SS BOND : bond 0.00590 ( 3) SS BOND : angle 0.99760 ( 6) hydrogen bonds : bond 0.03454 ( 369) hydrogen bonds : angle 4.73465 ( 1050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.373 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 21 LYS cc_start: 0.9414 (tmtt) cc_final: 0.9098 (tttp) REVERT: A 244 MET cc_start: 0.7912 (mmp) cc_final: 0.7370 (mmp) REVERT: B 183 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7410 (t-90) REVERT: B 217 MET cc_start: 0.8222 (ppp) cc_final: 0.7603 (ppp) REVERT: G 25 ILE cc_start: 0.6428 (mp) cc_final: 0.6217 (mt) REVERT: H 39 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8128 (tm-30) REVERT: H 42 GLU cc_start: 0.8212 (pp20) cc_final: 0.7674 (pp20) REVERT: H 43 LYS cc_start: 0.8759 (mmtm) cc_final: 0.8284 (mmtm) REVERT: H 148 ARG cc_start: 0.6664 (tpp80) cc_final: 0.6454 (tpp80) REVERT: R 115 TYR cc_start: 0.6004 (m-80) cc_final: 0.5663 (m-80) REVERT: R 175 ILE cc_start: 0.9237 (tp) cc_final: 0.9009 (mm) REVERT: R 423 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7635 (t80) REVERT: R 445 ASN cc_start: 0.8729 (t0) cc_final: 0.8487 (t0) outliers start: 26 outliers final: 18 residues processed: 195 average time/residue: 0.0980 time to fit residues: 26.4382 Evaluate side-chains 196 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071635 restraints weight = 24454.411| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.17 r_work: 0.3023 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8772 Z= 0.249 Angle : 0.730 11.467 11887 Z= 0.382 Chirality : 0.045 0.157 1345 Planarity : 0.004 0.047 1497 Dihedral : 5.384 56.175 1195 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.95 % Allowed : 18.27 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: -0.05 (0.26), residues: 1072 helix: 1.56 (0.28), residues: 346 sheet: 0.18 (0.33), residues: 268 loop : -1.44 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 206 TYR 0.013 0.002 TYR H 178 PHE 0.021 0.002 PHE R 387 TRP 0.022 0.002 TRP R 402 HIS 0.007 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8769) covalent geometry : angle 0.72990 (11881) SS BOND : bond 0.00954 ( 3) SS BOND : angle 1.24143 ( 6) hydrogen bonds : bond 0.04323 ( 369) hydrogen bonds : angle 5.01535 ( 1050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.356 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9131 (t0) cc_final: 0.8756 (t0) REVERT: A 351 CYS cc_start: 0.8136 (t) cc_final: 0.7919 (p) REVERT: B 57 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7594 (mmtp) REVERT: B 183 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7518 (t-90) REVERT: H 3 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7975 (pp30) REVERT: H 42 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: H 43 LYS cc_start: 0.8753 (mmtm) cc_final: 0.8053 (mmtm) REVERT: R 60 LEU cc_start: 0.9015 (mt) cc_final: 0.8580 (tt) REVERT: R 175 ILE cc_start: 0.9238 (tp) cc_final: 0.9033 (mm) REVERT: R 239 LYS cc_start: 0.8894 (tptt) cc_final: 0.8529 (mmtt) REVERT: R 423 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7664 (t80) REVERT: R 445 ASN cc_start: 0.8804 (t0) cc_final: 0.8579 (t0) outliers start: 37 outliers final: 27 residues processed: 189 average time/residue: 0.0974 time to fit residues: 25.4065 Evaluate side-chains 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 394 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 0.0010 chunk 10 optimal weight: 6.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 311 HIS ** 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 = 0.3456 r_free = 0.3456 target = 0.088447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072791 restraints weight = 24792.426| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.15 r_work: 0.3040 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8772 Z= 0.191 Angle : 0.711 11.543 11887 Z= 0.368 Chirality : 0.045 0.232 1345 Planarity : 0.003 0.048 1497 Dihedral : 5.314 56.780 1195 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 3.53 % Allowed : 19.87 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.00 (0.26), residues: 1072 helix: 1.56 (0.28), residues: 347 sheet: 0.36 (0.32), residues: 277 loop : -1.52 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.012 0.001 TYR R 156 PHE 0.022 0.001 PHE R 387 TRP 0.021 0.001 TRP R 402 HIS 0.015 0.002 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8769) covalent geometry : angle 0.71062 (11881) SS BOND : bond 0.00857 ( 3) SS BOND : angle 1.13963 ( 6) hydrogen bonds : bond 0.03985 ( 369) hydrogen bonds : angle 4.90523 ( 1050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 0.377 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.9054 (mmp80) cc_final: 0.8621 (mmp80) REVERT: B 57 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7496 (mmtp) REVERT: B 183 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: H 3 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7998 (pp30) REVERT: H 39 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8464 (tm-30) REVERT: H 42 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8229 (pp20) REVERT: R 60 LEU cc_start: 0.8993 (mt) cc_final: 0.8569 (tt) REVERT: R 239 LYS cc_start: 0.8899 (tptt) cc_final: 0.8524 (mmtt) REVERT: R 402 TRP cc_start: 0.8394 (m100) cc_final: 0.8128 (m100) REVERT: R 423 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7702 (t80) REVERT: R 445 ASN cc_start: 0.8814 (t0) cc_final: 0.8596 (t0) outliers start: 33 outliers final: 22 residues processed: 188 average time/residue: 0.0933 time to fit residues: 24.6434 Evaluate side-chains 190 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 84 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 423 PHE Chi-restraints excluded: chain R residue 447 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 8.9990 chunk 77 optimal weight: 0.2980 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 311 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.091391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075721 restraints weight = 24173.002| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.17 r_work: 0.3101 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8772 Z= 0.129 Angle : 0.690 14.511 11887 Z= 0.355 Chirality : 0.044 0.183 1345 Planarity : 0.003 0.049 1497 Dihedral : 4.993 57.628 1195 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 3.53 % Allowed : 19.66 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 1072 helix: 1.79 (0.29), residues: 347 sheet: 0.44 (0.32), residues: 287 loop : -1.44 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.017 0.001 TYR R 156 PHE 0.017 0.001 PHE R 387 TRP 0.020 0.001 TRP R 402 HIS 0.010 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8769) covalent geometry : angle 0.68944 (11881) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.00303 ( 6) hydrogen bonds : bond 0.03289 ( 369) hydrogen bonds : angle 4.61950 ( 1050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.325 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9096 (t0) cc_final: 0.8787 (t0) REVERT: A 206 ARG cc_start: 0.9031 (mmp80) cc_final: 0.8635 (mmp80) REVERT: B 57 LYS cc_start: 0.7551 (mmtp) cc_final: 0.7226 (mmtp) REVERT: B 59 TYR cc_start: 0.8872 (m-80) cc_final: 0.8615 (m-80) REVERT: B 183 HIS cc_start: 0.7809 (OUTLIER) cc_final: 0.7452 (t-90) REVERT: H 3 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8011 (pp30) REVERT: H 39 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8470 (tm-30) REVERT: H 42 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: H 43 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8206 (mmtm) REVERT: H 91 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8123 (t) REVERT: R 60 LEU cc_start: 0.8925 (mt) cc_final: 0.8513 (tt) REVERT: R 423 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7711 (t80) outliers start: 33 outliers final: 18 residues processed: 204 average time/residue: 0.1005 time to fit residues: 27.9945 Evaluate side-chains 196 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 6.9990 chunk 60 optimal weight: 0.0270 chunk 94 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS A 205 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.089846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.074060 restraints weight = 24610.941| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.18 r_work: 0.3070 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8772 Z= 0.166 Angle : 0.740 15.728 11887 Z= 0.382 Chirality : 0.045 0.169 1345 Planarity : 0.004 0.069 1497 Dihedral : 5.139 58.817 1195 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer: Outliers : 2.56 % Allowed : 21.37 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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 (0.26), residues: 1072 helix: 1.79 (0.28), residues: 343 sheet: 0.43 (0.32), residues: 288 loop : -1.39 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 349 TYR 0.028 0.001 TYR R 156 PHE 0.017 0.001 PHE R 387 TRP 0.047 0.002 TRP R 402 HIS 0.021 0.002 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8769) covalent geometry : angle 0.73641 (11881) SS BOND : bond 0.00715 ( 3) SS BOND : angle 3.33542 ( 6) hydrogen bonds : bond 0.03520 ( 369) hydrogen bonds : angle 4.72620 ( 1050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.357 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9099 (t0) cc_final: 0.8804 (t0) REVERT: B 57 LYS cc_start: 0.7771 (mmtp) cc_final: 0.7237 (mmtp) REVERT: B 183 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7473 (t-90) REVERT: G 48 ASP cc_start: 0.8665 (p0) cc_final: 0.8343 (p0) REVERT: H 39 GLN cc_start: 0.8795 (tm-30) cc_final: 0.8465 (tm-30) REVERT: H 42 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8259 (pp20) REVERT: H 91 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8202 (t) REVERT: H 128 MET cc_start: 0.8761 (mmm) cc_final: 0.8473 (mmt) REVERT: R 60 LEU cc_start: 0.8922 (mt) cc_final: 0.8511 (tt) REVERT: R 239 LYS cc_start: 0.8895 (tptt) cc_final: 0.8561 (mmtt) REVERT: R 423 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7693 (t80) outliers start: 24 outliers final: 19 residues processed: 188 average time/residue: 0.0977 time to fit residues: 25.1542 Evaluate side-chains 195 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 ASP Chi-restraints excluded: chain R residue 228 ILE Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 311 HIS ** 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 = 0.3503 r_free = 0.3503 target = 0.091046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075287 restraints weight = 24285.655| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.17 r_work: 0.3099 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8772 Z= 0.136 Angle : 0.734 16.108 11887 Z= 0.377 Chirality : 0.045 0.176 1345 Planarity : 0.004 0.050 1497 Dihedral : 5.078 59.373 1195 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 2.78 % Allowed : 21.69 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.24 (0.26), residues: 1072 helix: 1.83 (0.28), residues: 343 sheet: 0.46 (0.32), residues: 282 loop : -1.41 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 349 TYR 0.024 0.001 TYR R 156 PHE 0.016 0.001 PHE R 387 TRP 0.030 0.001 TRP R 402 HIS 0.013 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8769) covalent geometry : angle 0.73331 (11881) SS BOND : bond 0.00582 ( 3) SS BOND : angle 1.89955 ( 6) hydrogen bonds : bond 0.03317 ( 369) hydrogen bonds : angle 4.63434 ( 1050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.386 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9096 (t0) cc_final: 0.8800 (t0) REVERT: A 189 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6873 (p90) REVERT: B 57 LYS cc_start: 0.7546 (mmtp) cc_final: 0.7309 (mmtp) REVERT: B 183 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7435 (t-90) REVERT: G 48 ASP cc_start: 0.8717 (p0) cc_final: 0.8419 (p0) REVERT: H 39 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8016 (tm-30) REVERT: H 42 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7548 (pp20) REVERT: H 43 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8278 (mmtm) REVERT: H 91 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8180 (t) REVERT: R 60 LEU cc_start: 0.8925 (mt) cc_final: 0.8522 (tt) REVERT: R 83 GLN cc_start: 0.9008 (mp10) cc_final: 0.8786 (mp10) REVERT: R 239 LYS cc_start: 0.8859 (tptt) cc_final: 0.8521 (mmtt) REVERT: R 423 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7700 (t80) outliers start: 26 outliers final: 19 residues processed: 193 average time/residue: 0.0914 time to fit residues: 24.3597 Evaluate side-chains 197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 120 TRP Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 311 HIS ** 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 = 0.3488 r_free = 0.3488 target = 0.090386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074633 restraints weight = 24600.874| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.17 r_work: 0.3083 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8772 Z= 0.155 Angle : 0.740 15.606 11887 Z= 0.378 Chirality : 0.045 0.167 1345 Planarity : 0.004 0.056 1497 Dihedral : 5.087 59.686 1195 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 2.78 % Allowed : 21.79 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.24 (0.26), residues: 1072 helix: 1.83 (0.28), residues: 343 sheet: 0.39 (0.32), residues: 289 loop : -1.38 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 349 TYR 0.020 0.001 TYR R 156 PHE 0.017 0.001 PHE R 387 TRP 0.030 0.001 TRP R 402 HIS 0.015 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8769) covalent geometry : angle 0.73965 (11881) SS BOND : bond 0.00681 ( 3) SS BOND : angle 1.63284 ( 6) hydrogen bonds : bond 0.03403 ( 369) hydrogen bonds : angle 4.65654 ( 1050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2029.56 seconds wall clock time: 35 minutes 43.59 seconds (2143.59 seconds total)