Starting phenix.real_space_refine on Tue Sep 24 18:29:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/09_2024/7ejk_31162_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/09_2024/7ejk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/09_2024/7ejk_31162.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/09_2024/7ejk_31162.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/09_2024/7ejk_31162_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ejk_31162/09_2024/7ejk_31162_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.189 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 5.44, per 1000 atoms: 0.63 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: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.89 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: 2.35 Time building geometry restraints manager: 2.80 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: 1.230 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.550 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- 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 8769 Z= 0.345 Angle : 0.773 13.116 11881 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 : 12.36 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 (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: -0.01 (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 TRP 0.028 0.001 TRP R 402 HIS 0.004 0.001 HIS R 446 PHE 0.024 0.001 PHE R 427 TYR 0.007 0.001 TYR H 178 ARG 0.011 0.000 ARG R 450 *********************** 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 fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 0.986 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: 0.2360 time to fit residues: 67.1811 Evaluate side-chains 166 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 90 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 256 ASN A 305 GLN A 331 ASN A 347 ASN B 239 ASN B 268 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8769 Z= 0.218 Angle : 0.702 15.663 11881 Z= 0.369 Chirality : 0.045 0.172 1345 Planarity : 0.004 0.044 1497 Dihedral : 4.958 52.188 1197 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.80 % Rotamer: Outliers : 1.92 % Allowed : 12.18 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.13 (0.26), residues: 1072 helix: 1.83 (0.29), residues: 341 sheet: 0.29 (0.32), residues: 260 loop : -1.37 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 402 HIS 0.009 0.001 HIS A 189 PHE 0.026 0.002 PHE R 387 TYR 0.017 0.002 TYR R 156 ARG 0.008 0.001 ARG A 206 *********************** 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 fitting. rotamer outliers: 18 poor density : 200 time to evaluate : 0.965 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: 0.9244 (tmtt) cc_final: 0.8890 (tttt) REVERT: B 59 TYR cc_start: 0.8498 (m-80) cc_final: 0.8004 (m-80) REVERT: B 75 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8278 (mm-40) REVERT: B 78 LYS cc_start: 0.9056 (mttm) cc_final: 0.8789 (mmtm) REVERT: B 183 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7306 (t-90) REVERT: B 215 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7603 (mp0) REVERT: B 217 MET cc_start: 0.7955 (ppp) cc_final: 0.7439 (ppp) REVERT: H 43 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8353 (mmtm) REVERT: R 115 TYR cc_start: 0.6073 (m-80) cc_final: 0.5783 (m-80) REVERT: R 175 ILE cc_start: 0.9144 (tp) cc_final: 0.8909 (mm) REVERT: R 423 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.7663 (t80) REVERT: R 445 ASN cc_start: 0.8752 (t0) cc_final: 0.8488 (t0) outliers start: 18 outliers final: 11 residues processed: 209 average time/residue: 0.2061 time to fit residues: 58.7935 Evaluate side-chains 182 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 169 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8769 Z= 0.186 Angle : 0.646 10.155 11881 Z= 0.340 Chirality : 0.044 0.164 1345 Planarity : 0.003 0.046 1497 Dihedral : 4.870 52.803 1195 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 2.24 % Allowed : 15.71 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.20 (0.26), residues: 1072 helix: 1.85 (0.29), residues: 344 sheet: 0.30 (0.32), residues: 266 loop : -1.32 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 402 HIS 0.009 0.001 HIS A 189 PHE 0.023 0.001 PHE R 387 TYR 0.019 0.001 TYR R 235 ARG 0.006 0.000 ARG A 206 *********************** 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 217 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.101 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8556 (tm-30) REVERT: A 187 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 210 LYS cc_start: 0.8993 (pttm) cc_final: 0.8664 (pttm) REVERT: A 244 MET cc_start: 0.7839 (mmp) cc_final: 0.7279 (mmp) REVERT: A 246 GLU cc_start: 0.7935 (tp30) cc_final: 0.7674 (tp30) REVERT: B 61 MET cc_start: 0.9086 (ppp) cc_final: 0.8824 (ppp) REVERT: B 183 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7399 (t-90) REVERT: B 215 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7628 (mp0) REVERT: B 217 MET cc_start: 0.7996 (ppp) cc_final: 0.7406 (ppp) REVERT: G 25 ILE cc_start: 0.6327 (mp) cc_final: 0.6108 (mt) REVERT: R 115 TYR cc_start: 0.5962 (m-80) cc_final: 0.5635 (m-80) REVERT: R 175 ILE cc_start: 0.9146 (tp) cc_final: 0.8914 (mm) REVERT: R 402 TRP cc_start: 0.8053 (m100) cc_final: 0.7762 (m100) REVERT: R 409 TYR cc_start: 0.8248 (m-80) cc_final: 0.8037 (m-80) REVERT: R 423 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7549 (t80) REVERT: R 445 ASN cc_start: 0.8695 (t0) cc_final: 0.8467 (t0) outliers start: 21 outliers final: 16 residues processed: 206 average time/residue: 0.2082 time to fit residues: 57.9813 Evaluate side-chains 192 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 286 LEU 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 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 96 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8769 Z= 0.331 Angle : 0.708 8.969 11881 Z= 0.375 Chirality : 0.045 0.160 1345 Planarity : 0.004 0.047 1497 Dihedral : 5.290 54.276 1195 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 3.31 % Allowed : 17.09 % 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 (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: 0.05 (0.26), residues: 1072 helix: 1.74 (0.29), residues: 343 sheet: 0.31 (0.32), residues: 264 loop : -1.47 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 402 HIS 0.008 0.001 HIS A 189 PHE 0.023 0.002 PHE R 387 TYR 0.012 0.002 TYR A 303 ARG 0.007 0.001 ARG A 206 *********************** 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 210 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 0.907 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: B 183 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7451 (t-90) REVERT: B 215 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7689 (mp0) REVERT: H 39 GLN cc_start: 0.8589 (tm-30) cc_final: 0.7808 (tm-30) REVERT: H 208 GLU cc_start: 0.7795 (pt0) cc_final: 0.6500 (pt0) REVERT: H 218 MET cc_start: 0.8995 (ttp) cc_final: 0.8791 (ttt) REVERT: R 175 ILE cc_start: 0.9188 (tp) cc_final: 0.8969 (mm) REVERT: R 239 LYS cc_start: 0.8689 (mmtp) cc_final: 0.8409 (mmtt) REVERT: R 402 TRP cc_start: 0.8220 (m100) cc_final: 0.8018 (m100) REVERT: R 423 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7636 (t80) REVERT: R 445 ASN cc_start: 0.8685 (t0) cc_final: 0.8471 (t0) outliers start: 31 outliers final: 23 residues processed: 196 average time/residue: 0.1998 time to fit residues: 53.6656 Evaluate side-chains 191 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 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 311 HIS 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 H residue 119 VAL Chi-restraints excluded: chain H residue 214 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 88 optimal weight: 0.4980 chunk 71 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8769 Z= 0.187 Angle : 0.662 9.558 11881 Z= 0.346 Chirality : 0.043 0.160 1345 Planarity : 0.003 0.047 1497 Dihedral : 5.153 54.466 1195 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 3.21 % Allowed : 18.16 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.15 (0.26), residues: 1072 helix: 1.83 (0.29), residues: 343 sheet: 0.35 (0.32), residues: 267 loop : -1.42 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 402 HIS 0.016 0.001 HIS A 189 PHE 0.022 0.001 PHE R 387 TYR 0.012 0.001 TYR R 156 ARG 0.007 0.000 ARG A 206 *********************** 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 fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 0.937 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. REVERT: A 244 MET cc_start: 0.7730 (mmp) cc_final: 0.7215 (mmp) REVERT: B 183 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7406 (t-90) REVERT: B 296 VAL cc_start: 0.9333 (t) cc_final: 0.9131 (m) REVERT: H 3 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7811 (pp30) REVERT: H 39 GLN cc_start: 0.8598 (tm-30) cc_final: 0.7814 (tm-30) REVERT: H 91 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8146 (t) REVERT: R 175 ILE cc_start: 0.9195 (tp) cc_final: 0.8977 (mm) REVERT: R 423 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7664 (t80) outliers start: 30 outliers final: 17 residues processed: 195 average time/residue: 0.1909 time to fit residues: 51.7711 Evaluate side-chains 191 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 183 HIS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 75 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8769 Z= 0.387 Angle : 0.746 9.052 11881 Z= 0.393 Chirality : 0.046 0.165 1345 Planarity : 0.004 0.049 1497 Dihedral : 5.472 56.364 1195 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 4.06 % Allowed : 18.70 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.12 (0.26), residues: 1072 helix: 1.55 (0.28), residues: 345 sheet: 0.15 (0.32), residues: 274 loop : -1.55 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 402 HIS 0.007 0.001 HIS A 189 PHE 0.022 0.002 PHE R 387 TYR 0.013 0.002 TYR H 178 ARG 0.006 0.001 ARG A 206 *********************** 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 204 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 0.953 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: 0.9097 (t0) cc_final: 0.8767 (t0) REVERT: A 206 ARG cc_start: 0.8943 (mmp80) cc_final: 0.8682 (mmp80) REVERT: A 244 MET cc_start: 0.7720 (mmp) cc_final: 0.7227 (mmp) REVERT: B 57 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7262 (mmtp) REVERT: B 183 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7451 (t-90) REVERT: B 296 VAL cc_start: 0.9357 (t) cc_final: 0.9147 (m) REVERT: H 3 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7854 (pp30) REVERT: H 39 GLN cc_start: 0.8611 (tm-30) cc_final: 0.7660 (tm-30) REVERT: R 423 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7737 (t80) outliers start: 38 outliers final: 28 residues processed: 189 average time/residue: 0.2026 time to fit residues: 53.5677 Evaluate side-chains 192 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 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 311 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 25 ILE 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 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 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 11 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 87 optimal weight: 0.0020 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 347 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8769 Z= 0.185 Angle : 0.696 10.239 11881 Z= 0.360 Chirality : 0.045 0.241 1345 Planarity : 0.003 0.049 1497 Dihedral : 5.159 56.760 1195 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.48 % Favored : 95.43 % Rotamer: Outliers : 3.31 % Allowed : 19.76 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1072 helix: 1.79 (0.28), residues: 347 sheet: 0.28 (0.31), residues: 291 loop : -1.53 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP R 402 HIS 0.006 0.001 HIS A 189 PHE 0.021 0.001 PHE R 387 TYR 0.012 0.001 TYR A 320 ARG 0.012 0.000 ARG H 148 *********************** 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 214 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 1.546 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8911 (mmp80) cc_final: 0.8685 (mmp80) REVERT: A 244 MET cc_start: 0.7841 (mmp) cc_final: 0.7192 (mmp) REVERT: B 57 LYS cc_start: 0.7402 (mmtp) cc_final: 0.6993 (mmtp) REVERT: B 59 TYR cc_start: 0.8717 (m-80) cc_final: 0.8330 (m-80) REVERT: B 183 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7419 (t-90) REVERT: G 48 ASP cc_start: 0.8704 (p0) cc_final: 0.8409 (p0) REVERT: H 3 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7805 (pp30) REVERT: H 39 GLN cc_start: 0.8647 (tm-30) cc_final: 0.7723 (tm-30) REVERT: H 91 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8072 (t) REVERT: R 60 LEU cc_start: 0.8861 (mt) cc_final: 0.8452 (tt) REVERT: R 152 GLN cc_start: 0.8051 (mp10) cc_final: 0.7826 (mp10) REVERT: R 423 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7731 (t80) outliers start: 31 outliers final: 19 residues processed: 196 average time/residue: 0.2091 time to fit residues: 56.7710 Evaluate side-chains 193 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 LEU 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 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 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 228 ILE Chi-restraints excluded: chain R residue 423 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 93 optimal weight: 0.2980 chunk 98 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8769 Z= 0.189 Angle : 0.691 9.700 11881 Z= 0.358 Chirality : 0.044 0.172 1345 Planarity : 0.004 0.055 1497 Dihedral : 5.063 58.188 1195 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 3.31 % Allowed : 21.15 % 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 (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: 0.12 (0.26), residues: 1072 helix: 1.83 (0.28), residues: 347 sheet: 0.25 (0.31), residues: 293 loop : -1.53 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP R 402 HIS 0.007 0.001 HIS A 189 PHE 0.019 0.001 PHE R 387 TYR 0.026 0.001 TYR R 156 ARG 0.013 0.000 ARG A 349 *********************** 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 211 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 180 time to evaluate : 0.976 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8901 (mmp80) cc_final: 0.8672 (mmp80) REVERT: B 57 LYS cc_start: 0.7503 (mmtp) cc_final: 0.7062 (mmtp) REVERT: B 59 TYR cc_start: 0.8752 (m-80) cc_final: 0.8397 (m-80) REVERT: B 183 HIS cc_start: 0.7665 (OUTLIER) cc_final: 0.7427 (t-90) REVERT: G 48 ASP cc_start: 0.8669 (p0) cc_final: 0.8361 (p0) REVERT: H 3 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7818 (pp30) REVERT: H 39 GLN cc_start: 0.8623 (tm-30) cc_final: 0.7666 (tm-30) REVERT: H 91 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8106 (t) REVERT: R 60 LEU cc_start: 0.8836 (mt) cc_final: 0.8431 (tt) REVERT: R 152 GLN cc_start: 0.8061 (mp10) cc_final: 0.7836 (mp10) REVERT: R 239 LYS cc_start: 0.8800 (tptt) cc_final: 0.8434 (mmtt) REVERT: R 423 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7719 (t80) outliers start: 31 outliers final: 20 residues processed: 198 average time/residue: 0.2037 time to fit residues: 54.9932 Evaluate side-chains 194 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 170 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 LEU 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 255 LEU 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 63 THR 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 145 ASP Chi-restraints excluded: chain R residue 228 ILE 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 90 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8769 Z= 0.206 Angle : 0.714 10.340 11881 Z= 0.369 Chirality : 0.044 0.169 1345 Planarity : 0.004 0.049 1497 Dihedral : 5.103 59.103 1195 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.13 % Favored : 94.78 % Rotamer: Outliers : 2.78 % Allowed : 21.58 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.18 (0.26), residues: 1072 helix: 1.88 (0.28), residues: 344 sheet: 0.29 (0.31), residues: 293 loop : -1.48 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP R 402 HIS 0.008 0.001 HIS A 189 PHE 0.019 0.001 PHE R 387 TYR 0.020 0.001 TYR R 156 ARG 0.013 0.001 ARG A 349 *********************** 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 206 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 0.896 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8904 (mmp80) cc_final: 0.8656 (mmp80) REVERT: B 57 LYS cc_start: 0.7522 (mmtp) cc_final: 0.7135 (mmtp) REVERT: B 59 TYR cc_start: 0.8736 (m-80) cc_final: 0.8406 (m-80) REVERT: B 183 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7378 (t-90) REVERT: G 25 ILE cc_start: 0.6109 (mp) cc_final: 0.5846 (mt) REVERT: G 48 ASP cc_start: 0.8608 (p0) cc_final: 0.8311 (p0) REVERT: H 91 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (t) REVERT: R 60 LEU cc_start: 0.8804 (mt) cc_final: 0.8408 (tt) REVERT: R 160 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7727 (mmt90) REVERT: R 239 LYS cc_start: 0.8804 (tptt) cc_final: 0.8436 (mmtt) REVERT: R 423 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7735 (t80) outliers start: 26 outliers final: 19 residues processed: 193 average time/residue: 0.2097 time to fit residues: 54.9272 Evaluate side-chains 198 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 202 VAL 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 255 LEU 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 22 CYS Chi-restraints excluded: chain H residue 63 THR 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 145 ASP 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 62 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 0.0270 chunk 52 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 overall best weight: 0.7450 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8769 Z= 0.191 Angle : 0.746 17.383 11881 Z= 0.380 Chirality : 0.045 0.185 1345 Planarity : 0.004 0.055 1497 Dihedral : 5.090 59.928 1195 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 2.35 % Allowed : 22.44 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % 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: 0.21 (0.26), residues: 1072 helix: 1.83 (0.28), residues: 349 sheet: 0.39 (0.32), residues: 287 loop : -1.47 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 402 HIS 0.007 0.001 HIS A 189 PHE 0.017 0.001 PHE R 387 TYR 0.021 0.001 TYR R 156 ARG 0.012 0.000 ARG A 349 ********************** 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 208 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 1.011 Fit side-chains TARDY: cannot create tardy model for: "TYR A 354 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 206 ARG cc_start: 0.8890 (mmp80) cc_final: 0.8658 (mmp80) REVERT: B 57 LYS cc_start: 0.7407 (mmtp) cc_final: 0.7036 (mmtp) REVERT: B 59 TYR cc_start: 0.8723 (m-80) cc_final: 0.8429 (m-80) REVERT: G 25 ILE cc_start: 0.6025 (mp) cc_final: 0.5754 (mt) REVERT: G 48 ASP cc_start: 0.8686 (p0) cc_final: 0.8372 (p0) REVERT: H 39 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8358 (tm-30) REVERT: H 91 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8062 (t) REVERT: R 60 LEU cc_start: 0.8797 (mt) cc_final: 0.8410 (tt) REVERT: R 152 GLN cc_start: 0.7948 (mp10) cc_final: 0.7703 (mp10) REVERT: R 160 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7723 (mmt90) REVERT: R 239 LYS cc_start: 0.8816 (tptt) cc_final: 0.8445 (mmtt) REVERT: R 423 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7748 (t80) outliers start: 22 outliers final: 19 residues processed: 198 average time/residue: 0.2147 time to fit residues: 57.3763 Evaluate side-chains 198 residues out of total 936 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 177 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 343 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 300 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 63 THR 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 145 ASP 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 26 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3460 r_free = 0.3460 target = 0.088694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073184 restraints weight = 24356.437| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.10 r_work: 0.3050 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8769 Z= 0.320 Angle : 0.795 15.998 11881 Z= 0.407 Chirality : 0.047 0.272 1345 Planarity : 0.004 0.053 1497 Dihedral : 5.342 58.904 1195 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 2.67 % Allowed : 22.54 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 1.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1072 helix: 1.75 (0.28), residues: 345 sheet: 0.29 (0.32), residues: 285 loop : -1.46 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 402 HIS 0.011 0.002 HIS A 189 PHE 0.019 0.002 PHE R 387 TYR 0.013 0.001 TYR R 156 ARG 0.013 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.13 seconds wall clock time: 39 minutes 11.90 seconds (2351.90 seconds total)