Starting phenix.real_space_refine on Tue Dec 31 19:08:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xz5_33525/12_2024/7xz5_33525_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xz5_33525/12_2024/7xz5_33525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xz5_33525/12_2024/7xz5_33525.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xz5_33525/12_2024/7xz5_33525.map" model { file = "/net/cci-nas-00/data/ceres_data/7xz5_33525/12_2024/7xz5_33525_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xz5_33525/12_2024/7xz5_33525_neut_trim.cif" } resolution = 3.1 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= -0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 5243 2.51 5 N 1433 2.21 5 O 1534 1.98 5 H 8189 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16456 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 3910 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1909 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 4609 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LSC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.43, per 1000 atoms: 0.45 Number of scatterers: 16456 At special positions: 0 Unit cell: (100.674, 99.603, 116.739, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 1 15.00 O 1534 8.00 N 1433 7.00 C 5243 6.00 H 8189 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 78 " - pdb=" SG CYS R 155 " distance=2.04 Simple disulfide: pdb=" SG CYS R 251 " - pdb=" SG CYS R 254 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.519A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.985A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.112A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.623A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.824A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 2 through 36 removed outlier: 4.035A pdb=" N ILE R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 61 removed outlier: 3.995A pdb=" N PHE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 66 removed outlier: 3.500A pdb=" N GLN R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 109 removed outlier: 4.783A pdb=" N LEU R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 117 removed outlier: 3.550A pdb=" N LEU R 114 " --> pdb=" O PRO R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 143 Proline residue: R 140 - end of helix Processing helix chain 'R' and resid 162 through 172 removed outlier: 4.073A pdb=" N VAL R 166 " --> pdb=" O HIS R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 210 Processing helix chain 'R' and resid 221 through 251 removed outlier: 3.932A pdb=" N VAL R 229 " --> pdb=" O ARG R 225 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU R 236 " --> pdb=" O GLY R 232 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TRP R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 256 through 261 removed outlier: 3.789A pdb=" N GLU R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 279 removed outlier: 3.774A pdb=" N LEU R 267 " --> pdb=" O TYR R 263 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU R 273 " --> pdb=" O VAL R 269 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.719A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.614A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.699A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.473A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.376A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.091A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.356A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.923A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.046A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1251 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: 5.67 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6948 1.03 - 1.23: 1279 1.23 - 1.42: 3757 1.42 - 1.62: 4552 1.62 - 1.82: 81 Bond restraints: 16617 Sorted by residual: bond pdb=" ND1 HIS R 162 " pdb=" CE1 HIS R 162 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.67e+01 bond pdb=" CE1 HIS R 164 " pdb=" NE2 HIS R 164 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.66e+01 bond pdb=" CD2 HIS R 164 " pdb=" NE2 HIS R 164 " ideal model delta sigma weight residual 1.374 1.287 0.087 1.10e-02 8.26e+03 6.29e+01 bond pdb=" CZ ARG R 103 " pdb=" NH2 ARG R 103 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.30e-02 5.92e+03 5.86e+01 bond pdb=" CZ ARG R 81 " pdb=" NH2 ARG R 81 " ideal model delta sigma weight residual 1.330 1.231 0.099 1.30e-02 5.92e+03 5.82e+01 ... (remaining 16612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 29118 5.05 - 10.11: 769 10.11 - 15.16: 8 15.16 - 20.22: 1 20.22 - 25.27: 1 Bond angle restraints: 29897 Sorted by residual: angle pdb=" N PRO N 100 " pdb=" CA PRO N 100 " pdb=" C PRO N 100 " ideal model delta sigma weight residual 113.78 127.83 -14.05 1.62e+00 3.81e-01 7.52e+01 angle pdb=" C21 LSC R 401 " pdb=" C22 LSC R 401 " pdb=" O23 LSC R 401 " ideal model delta sigma weight residual 108.44 133.71 -25.27 3.00e+00 1.11e-01 7.10e+01 angle pdb=" C LEU R 267 " pdb=" N GLY R 268 " pdb=" CA GLY R 268 " ideal model delta sigma weight residual 119.94 128.10 -8.16 1.11e+00 8.12e-01 5.41e+01 angle pdb=" CA PHE R 181 " pdb=" CB PHE R 181 " pdb=" CG PHE R 181 " ideal model delta sigma weight residual 113.80 121.13 -7.33 1.00e+00 1.00e+00 5.37e+01 angle pdb=" C ALA R 159 " pdb=" N VAL R 160 " pdb=" CA VAL R 160 " ideal model delta sigma weight residual 121.97 134.89 -12.92 1.80e+00 3.09e-01 5.15e+01 ... (remaining 29892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 7516 27.91 - 55.82: 271 55.82 - 83.73: 49 83.73 - 111.64: 6 111.64 - 139.55: 2 Dihedral angle restraints: 7844 sinusoidal: 4233 harmonic: 3611 Sorted by residual: dihedral pdb=" C TYR R 185 " pdb=" N TYR R 185 " pdb=" CA TYR R 185 " pdb=" CB TYR R 185 " ideal model delta harmonic sigma weight residual -122.60 -134.73 12.13 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C PHE R 138 " pdb=" N PHE R 138 " pdb=" CA PHE R 138 " pdb=" CB PHE R 138 " ideal model delta harmonic sigma weight residual -122.60 -134.28 11.68 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C GLU R 261 " pdb=" N GLU R 261 " pdb=" CA GLU R 261 " pdb=" CB GLU R 261 " ideal model delta harmonic sigma weight residual -122.60 -134.20 11.60 0 2.50e+00 1.60e-01 2.15e+01 ... (remaining 7841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 1100 0.140 - 0.281: 10 0.281 - 0.421: 16 0.421 - 0.562: 102 0.562 - 0.702: 61 Chirality restraints: 1289 Sorted by residual: chirality pdb=" CG LEU R 139 " pdb=" CB LEU R 139 " pdb=" CD1 LEU R 139 " pdb=" CD2 LEU R 139 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU R 167 " pdb=" CB LEU R 167 " pdb=" CD1 LEU R 167 " pdb=" CD2 LEU R 167 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" CG LEU R 77 " pdb=" CB LEU R 77 " pdb=" CD1 LEU R 77 " pdb=" CD2 LEU R 77 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 1286 not shown) Planarity restraints: 2465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 65 " -0.097 2.00e-02 2.50e+03 1.06e-01 1.67e+02 pdb=" CD GLN R 65 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN R 65 " 0.093 2.00e-02 2.50e+03 pdb=" NE2 GLN R 65 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN R 65 " 0.155 2.00e-02 2.50e+03 pdb="HE22 GLN R 65 " -0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 265 " -0.090 2.00e-02 2.50e+03 3.75e-02 5.63e+01 pdb=" CG TRP R 265 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP R 265 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 265 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP R 265 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 TRP R 265 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP R 265 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 265 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 265 " 0.025 2.00e-02 2.50e+03 pdb=" CH2 TRP R 265 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP R 265 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP R 265 " 0.048 2.00e-02 2.50e+03 pdb=" HE3 TRP R 265 " 0.027 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 265 " -0.073 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 265 " 0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP R 265 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 234 " 0.038 2.00e-02 2.50e+03 4.13e-02 5.13e+01 pdb=" CG PHE R 234 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE R 234 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE R 234 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE R 234 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE R 234 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE R 234 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE R 234 " -0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE R 234 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE R 234 " 0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE R 234 " -0.081 2.00e-02 2.50e+03 pdb=" HZ PHE R 234 " 0.031 2.00e-02 2.50e+03 ... (remaining 2462 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 870 2.19 - 2.79: 32990 2.79 - 3.40: 45187 3.40 - 4.00: 59077 4.00 - 4.60: 91879 Nonbonded interactions: 230003 Sorted by model distance: nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.590 2.450 nonbonded pdb=" OD1 ASP B 153 " pdb=" H ASN B 155 " model vdw 1.606 2.450 nonbonded pdb=" H GLN R 148 " pdb=" O VAL R 160 " model vdw 1.624 2.450 nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.634 2.450 nonbonded pdb=" O ALA R 235 " pdb=" HG1 THR R 239 " model vdw 1.634 2.450 ... (remaining 229998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 0.310 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 34.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 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 : 0.020 0.129 8428 Z= 1.300 Angle : 1.553 25.271 11401 Z= 1.011 Chirality : 0.210 0.702 1289 Planarity : 0.005 0.066 1450 Dihedral : 14.345 139.551 3062 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 8.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1036 helix: 1.59 (0.25), residues: 422 sheet: 1.31 (0.37), residues: 202 loop : 0.04 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP R 265 HIS 0.003 0.001 HIS B 91 PHE 0.036 0.004 PHE R 234 TYR 0.054 0.004 TYR R 257 ARG 0.011 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 263 TYR cc_start: 0.6750 (m-80) cc_final: 0.6415 (m-10) REVERT: R 298 LYS cc_start: 0.6378 (ttmm) cc_final: 0.5945 (mptt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.5659 time to fit residues: 125.7328 Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 255 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8428 Z= 0.225 Angle : 0.520 4.736 11401 Z= 0.283 Chirality : 0.040 0.137 1289 Planarity : 0.004 0.039 1450 Dihedral : 7.297 94.614 1169 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.56 % Allowed : 5.84 % Favored : 93.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.27), residues: 1036 helix: 2.61 (0.25), residues: 416 sheet: 1.00 (0.37), residues: 200 loop : 0.14 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 297 HIS 0.009 0.001 HIS R 255 PHE 0.020 0.002 PHE N 108 TYR 0.013 0.001 TYR A 339 ARG 0.002 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7668 (mtp) cc_final: 0.7410 (mtm) REVERT: R 263 TYR cc_start: 0.6595 (m-80) cc_final: 0.6312 (m-10) REVERT: R 298 LYS cc_start: 0.6373 (ttmm) cc_final: 0.5987 (mptt) outliers start: 5 outliers final: 5 residues processed: 148 average time/residue: 0.5592 time to fit residues: 108.2490 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8428 Z= 0.239 Angle : 0.512 5.943 11401 Z= 0.278 Chirality : 0.039 0.138 1289 Planarity : 0.004 0.042 1450 Dihedral : 6.832 85.114 1169 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.90 % Allowed : 7.30 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.27), residues: 1036 helix: 2.50 (0.25), residues: 416 sheet: 0.77 (0.37), residues: 204 loop : 0.05 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.002 PHE N 108 TYR 0.012 0.001 TYR A 339 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 21 MET cc_start: 0.7706 (mtp) cc_final: 0.7419 (mtm) REVERT: R 298 LYS cc_start: 0.6601 (ttmm) cc_final: 0.6271 (mptt) outliers start: 8 outliers final: 8 residues processed: 140 average time/residue: 0.5818 time to fit residues: 106.0673 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 8428 Z= 0.449 Angle : 0.630 7.722 11401 Z= 0.345 Chirality : 0.044 0.163 1289 Planarity : 0.006 0.083 1450 Dihedral : 7.143 82.693 1169 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.13 % Allowed : 8.75 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1036 helix: 1.76 (0.24), residues: 410 sheet: 0.49 (0.36), residues: 212 loop : -0.30 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.012 0.002 HIS A 357 PHE 0.027 0.002 PHE N 108 TYR 0.016 0.002 TYR R 185 ARG 0.005 0.001 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7390 (mtt-85) REVERT: A 248 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8382 (p) REVERT: G 21 MET cc_start: 0.7721 (mtp) cc_final: 0.7447 (mtm) REVERT: R 225 ARG cc_start: 0.7326 (ttp80) cc_final: 0.7111 (ttp-110) outliers start: 19 outliers final: 13 residues processed: 145 average time/residue: 0.5666 time to fit residues: 106.6711 Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 36 ASN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8428 Z= 0.270 Angle : 0.538 6.706 11401 Z= 0.292 Chirality : 0.040 0.137 1289 Planarity : 0.004 0.049 1450 Dihedral : 6.748 86.136 1169 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.02 % Allowed : 10.66 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.26), residues: 1036 helix: 1.90 (0.25), residues: 416 sheet: 0.48 (0.37), residues: 207 loop : -0.36 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE N 108 TYR 0.013 0.002 TYR A 37 ARG 0.003 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.7563 (mtm-85) REVERT: A 386 MET cc_start: 0.7100 (tmm) cc_final: 0.6840 (tmm) REVERT: G 21 MET cc_start: 0.7703 (mtp) cc_final: 0.7443 (mtm) REVERT: R 179 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7469 (mp) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.5808 time to fit residues: 102.1637 Evaluate side-chains 134 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.0970 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8428 Z= 0.225 Angle : 0.518 6.268 11401 Z= 0.280 Chirality : 0.039 0.136 1289 Planarity : 0.004 0.041 1450 Dihedral : 6.520 83.141 1169 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.68 % Allowed : 12.46 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1036 helix: 2.04 (0.25), residues: 416 sheet: 0.30 (0.36), residues: 212 loop : -0.38 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.017 0.001 PHE N 108 TYR 0.012 0.001 TYR A 37 ARG 0.003 0.000 ARG R 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7570 (mtm-85) REVERT: A 248 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8366 (p) REVERT: G 21 MET cc_start: 0.7698 (mtp) cc_final: 0.7437 (mtm) REVERT: R 179 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7449 (mp) outliers start: 15 outliers final: 12 residues processed: 137 average time/residue: 0.5651 time to fit residues: 100.6450 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Chi-restraints excluded: chain R residue 274 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.0970 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8428 Z= 0.182 Angle : 0.489 5.830 11401 Z= 0.262 Chirality : 0.039 0.133 1289 Planarity : 0.004 0.038 1450 Dihedral : 6.270 89.500 1169 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.46 % Allowed : 13.36 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.27), residues: 1036 helix: 2.25 (0.25), residues: 416 sheet: 0.41 (0.36), residues: 205 loop : -0.34 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE N 108 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7343 (t0) cc_final: 0.6980 (t0) REVERT: A 248 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 386 MET cc_start: 0.7070 (tmm) cc_final: 0.6800 (tmm) REVERT: B 188 MET cc_start: 0.8437 (mmm) cc_final: 0.8158 (mmm) REVERT: B 327 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8475 (p) REVERT: G 21 MET cc_start: 0.7701 (mtp) cc_final: 0.7442 (mtm) outliers start: 13 outliers final: 8 residues processed: 141 average time/residue: 0.5992 time to fit residues: 109.2826 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8428 Z= 0.309 Angle : 0.541 6.837 11401 Z= 0.293 Chirality : 0.041 0.141 1289 Planarity : 0.005 0.048 1450 Dihedral : 6.396 81.218 1169 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.80 % Allowed : 13.13 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1036 helix: 2.05 (0.25), residues: 412 sheet: 0.20 (0.36), residues: 216 loop : -0.39 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 357 PHE 0.023 0.002 PHE N 108 TYR 0.014 0.002 TYR R 185 ARG 0.009 0.001 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8360 (p) REVERT: B 327 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8478 (p) REVERT: G 21 MET cc_start: 0.7761 (mtp) cc_final: 0.7504 (mtm) REVERT: R 179 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7444 (mp) outliers start: 16 outliers final: 11 residues processed: 139 average time/residue: 0.5802 time to fit residues: 104.4711 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 23 THR Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 125 CYS Chi-restraints excluded: chain R residue 179 LEU Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8428 Z= 0.133 Angle : 0.467 4.909 11401 Z= 0.248 Chirality : 0.038 0.132 1289 Planarity : 0.003 0.048 1450 Dihedral : 6.072 87.218 1169 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.67 % Allowed : 14.14 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.27), residues: 1036 helix: 2.30 (0.25), residues: 424 sheet: 0.46 (0.37), residues: 202 loop : -0.34 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS R 204 PHE 0.010 0.001 PHE R 181 TYR 0.009 0.001 TYR A 37 ARG 0.009 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7315 (t0) cc_final: 0.6979 (t0) REVERT: B 188 MET cc_start: 0.8389 (mmm) cc_final: 0.8107 (mmm) REVERT: G 21 MET cc_start: 0.7707 (mtp) cc_final: 0.7449 (mtm) outliers start: 6 outliers final: 6 residues processed: 139 average time/residue: 0.5759 time to fit residues: 103.7954 Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8428 Z= 0.221 Angle : 0.501 5.830 11401 Z= 0.268 Chirality : 0.039 0.133 1289 Planarity : 0.004 0.046 1450 Dihedral : 6.090 80.474 1169 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.90 % Allowed : 14.25 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.27), residues: 1036 helix: 2.38 (0.25), residues: 412 sheet: 0.34 (0.36), residues: 212 loop : -0.31 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE N 108 TYR 0.013 0.001 TYR A 37 ARG 0.010 0.000 ARG G 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.377 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.7347 (t0) cc_final: 0.7006 (t0) REVERT: A 248 VAL cc_start: 0.8673 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 188 MET cc_start: 0.8461 (mmm) cc_final: 0.8177 (mmm) REVERT: G 21 MET cc_start: 0.7715 (mtp) cc_final: 0.7455 (mtm) REVERT: R 225 ARG cc_start: 0.7382 (ttp80) cc_final: 0.7043 (ttp-110) outliers start: 8 outliers final: 6 residues processed: 136 average time/residue: 0.5664 time to fit residues: 100.1507 Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 265 TRP Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109501 restraints weight = 28097.751| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.12 r_work: 0.3110 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8428 Z= 0.186 Angle : 0.491 5.582 11401 Z= 0.262 Chirality : 0.039 0.132 1289 Planarity : 0.004 0.047 1450 Dihedral : 6.017 79.542 1169 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.90 % Allowed : 14.25 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1036 helix: 2.25 (0.25), residues: 424 sheet: 0.32 (0.36), residues: 208 loop : -0.29 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE N 108 TYR 0.011 0.001 TYR A 37 ARG 0.010 0.000 ARG G 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3972.56 seconds wall clock time: 72 minutes 13.92 seconds (4333.92 seconds total)