Starting phenix.real_space_refine on Mon Jun 16 01:33:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmd_61598/06_2025/9jmd_61598_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmd_61598/06_2025/9jmd_61598.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmd_61598/06_2025/9jmd_61598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmd_61598/06_2025/9jmd_61598.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmd_61598/06_2025/9jmd_61598_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmd_61598/06_2025/9jmd_61598_trim.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5837 2.51 5 N 1570 2.21 5 O 1678 1.98 5 H 8989 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18132 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5096 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3510 Classifications: {'peptide': 233} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 900 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 4668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4668 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 14, 'TRANS': 270} Chain breaks: 2 Chain: "R" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'CLR': 2, 'ZIT': 1} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Time building chain proxies: 9.11, per 1000 atoms: 0.50 Number of scatterers: 18132 At special positions: 0 Unit cell: (124.424, 91.464, 133.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 O 1678 8.00 N 1570 7.00 C 5837 6.00 H 8989 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 235 " distance=2.02 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: 4.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 38.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.612A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.602A pdb=" N ARG A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.141A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.591A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'E' and resid 52 through 55 removed outlier: 4.107A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.717A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'R' and resid 34 through 66 Proline residue: R 40 - end of helix Processing helix chain 'R' and resid 67 through 70 Processing helix chain 'R' and resid 71 through 89 removed outlier: 3.702A pdb=" N TYR R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.530A pdb=" N GLY R 118 " --> pdb=" O SER R 114 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLU R 119 " --> pdb=" O LEU R 115 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG R 142 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 168 removed outlier: 4.028A pdb=" N ALA R 160 " --> pdb=" O ARG R 156 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA R 164 " --> pdb=" O ALA R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 177 removed outlier: 3.873A pdb=" N LEU R 174 " --> pdb=" O ALA R 170 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE R 175 " --> pdb=" O GLY R 171 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL R 177 " --> pdb=" O PHE R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 231 removed outlier: 3.512A pdb=" N PHE R 231 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 241 through 252 removed outlier: 3.776A pdb=" N VAL R 247 " --> pdb=" O GLY R 243 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL R 251 " --> pdb=" O VAL R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 276 Proline residue: R 259 - end of helix removed outlier: 3.541A pdb=" N TYR R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY R 268 " --> pdb=" O SER R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 323 Proline residue: R 313 - end of helix removed outlier: 3.608A pdb=" N ILE R 319 " --> pdb=" O HIS R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 357 Proline residue: R 352 - end of helix Processing helix chain 'R' and resid 359 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.261A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.642A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 333 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU B 323 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 335 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.693A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.539A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.708A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 197 removed outlier: 4.051A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.518A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.541A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.612A pdb=" N SER E 70 " --> pdb=" O PHE E 79 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.832A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.499A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1245 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: 7.03 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 8961 1.02 - 1.22: 36 1.22 - 1.42: 3856 1.42 - 1.61: 5389 1.61 - 1.81: 84 Bond restraints: 18326 Sorted by residual: bond pdb=" C VAL R 316 " pdb=" O VAL R 316 " ideal model delta sigma weight residual 1.236 1.190 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" CA PHE R 314 " pdb=" C PHE R 314 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.32e-02 5.74e+03 1.61e+01 bond pdb=" CA PHE R 336 " pdb=" C PHE R 336 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.36e-02 5.41e+03 1.60e+01 bond pdb=" CA PRO R 313 " pdb=" CB PRO R 313 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.59e-02 3.96e+03 1.31e+01 bond pdb=" C LEU R 113 " pdb=" O LEU R 113 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.25e-02 6.40e+03 1.30e+01 ... (remaining 18321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 32604 2.49 - 4.98: 309 4.98 - 7.47: 26 7.47 - 9.96: 4 9.96 - 12.46: 1 Bond angle restraints: 32944 Sorted by residual: angle pdb=" N ILE R 338 " pdb=" CA ILE R 338 " pdb=" C ILE R 338 " ideal model delta sigma weight residual 111.00 102.97 8.03 1.09e+00 8.42e-01 5.43e+01 angle pdb=" N PRO R 313 " pdb=" CA PRO R 313 " pdb=" CB PRO R 313 " ideal model delta sigma weight residual 103.15 95.15 8.00 1.09e+00 8.42e-01 5.39e+01 angle pdb=" N PRO B 241 " pdb=" CA PRO B 241 " pdb=" CB PRO B 241 " ideal model delta sigma weight residual 103.39 96.77 6.62 1.08e+00 8.57e-01 3.76e+01 angle pdb=" CA PHE E 239 " pdb=" CB PHE E 239 " pdb=" CG PHE E 239 " ideal model delta sigma weight residual 113.80 119.64 -5.84 1.00e+00 1.00e+00 3.40e+01 angle pdb=" N ARG R 318 " pdb=" CA ARG R 318 " pdb=" C ARG R 318 " ideal model delta sigma weight residual 111.36 105.02 6.34 1.09e+00 8.42e-01 3.38e+01 ... (remaining 32939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 8109 23.98 - 47.96: 563 47.96 - 71.93: 118 71.93 - 95.91: 25 95.91 - 119.89: 3 Dihedral angle restraints: 8818 sinusoidal: 4862 harmonic: 3956 Sorted by residual: dihedral pdb=" CD ARG R 318 " pdb=" NE ARG R 318 " pdb=" CZ ARG R 318 " pdb=" NH1 ARG R 318 " ideal model delta sinusoidal sigma weight residual 0.00 82.37 -82.37 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS E 21 " pdb=" SG CYS E 21 " pdb=" SG CYS E 95 " pdb=" CB CYS E 95 " ideal model delta sinusoidal sigma weight residual 93.00 162.64 -69.64 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 235 " pdb=" CB CYS R 235 " ideal model delta sinusoidal sigma weight residual 93.00 156.43 -63.43 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 8815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1183 0.052 - 0.104: 196 0.104 - 0.156: 58 0.156 - 0.208: 7 0.208 - 0.260: 3 Chirality restraints: 1447 Sorted by residual: chirality pdb=" CB VAL R 57 " pdb=" CA VAL R 57 " pdb=" CG1 VAL R 57 " pdb=" CG2 VAL R 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL R 339 " pdb=" N VAL R 339 " pdb=" C VAL R 339 " pdb=" CB VAL R 339 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE R 320 " pdb=" CA ILE R 320 " pdb=" CG1 ILE R 320 " pdb=" CG2 ILE R 320 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1444 not shown) Planarity restraints: 2686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 318 " 1.438 9.50e-02 1.11e+02 5.56e-01 2.02e+03 pdb=" NE ARG R 318 " 0.164 2.00e-02 2.50e+03 pdb=" CZ ARG R 318 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG R 318 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG R 318 " -0.052 2.00e-02 2.50e+03 pdb="HH11 ARG R 318 " 0.555 2.00e-02 2.50e+03 pdb="HH12 ARG R 318 " -0.600 2.00e-02 2.50e+03 pdb="HH21 ARG R 318 " -0.116 2.00e-02 2.50e+03 pdb="HH22 ARG R 318 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 242 " 0.245 2.00e-02 2.50e+03 3.02e-01 1.37e+03 pdb=" CG ASN B 242 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN B 242 " -0.245 2.00e-02 2.50e+03 pdb=" ND2 ASN B 242 " 0.005 2.00e-02 2.50e+03 pdb="HD21 ASN B 242 " -0.456 2.00e-02 2.50e+03 pdb="HD22 ASN B 242 " 0.467 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 236 " 0.628 9.50e-02 1.11e+02 2.42e-01 3.73e+02 pdb=" NE ARG R 236 " 0.115 2.00e-02 2.50e+03 pdb=" CZ ARG R 236 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG R 236 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 236 " -0.025 2.00e-02 2.50e+03 pdb="HH11 ARG R 236 " -0.254 2.00e-02 2.50e+03 pdb="HH12 ARG R 236 " 0.207 2.00e-02 2.50e+03 pdb="HH21 ARG R 236 " -0.099 2.00e-02 2.50e+03 pdb="HH22 ARG R 236 " 0.002 2.00e-02 2.50e+03 ... (remaining 2683 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1272 2.20 - 2.80: 36775 2.80 - 3.40: 50450 3.40 - 4.00: 66462 4.00 - 4.60: 101494 Nonbonded interactions: 256453 Sorted by model distance: nonbonded pdb=" HZ2 LYS A 27 " pdb=" HE ARG A 31 " model vdw 1.598 2.100 nonbonded pdb="HH12 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.650 2.450 nonbonded pdb=" OD1 ASP B 200 " pdb=" H ASP B 200 " model vdw 1.666 2.450 nonbonded pdb=" OE2 GLU E 5 " pdb=" H CYS E 95 " model vdw 1.670 2.450 nonbonded pdb=" OG SER B 77 " pdb=" HE1 TRP B 87 " model vdw 1.672 2.450 ... (remaining 256448 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: 0.970 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: 0.280 Extract box with map and model: 0.750 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 41.180 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 : 0.004 0.082 9339 Z= 0.247 Angle : 0.736 12.456 12678 Z= 0.450 Chirality : 0.045 0.260 1447 Planarity : 0.016 0.489 1587 Dihedral : 16.967 119.889 3577 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 0.82 % Allowed : 26.12 % Favored : 73.06 % 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: 0.01 (0.25), residues: 1131 helix: 1.15 (0.27), residues: 396 sheet: -0.20 (0.28), residues: 293 loop : -0.81 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 250 HIS 0.006 0.001 HIS R 315 PHE 0.029 0.002 PHE E 239 TYR 0.024 0.001 TYR E 190 ARG 0.014 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.13762 ( 437) hydrogen bonds : angle 6.16002 ( 1245) SS BOND : bond 0.00953 ( 2) SS BOND : angle 2.09798 ( 4) covalent geometry : bond 0.00414 ( 9337) covalent geometry : angle 0.73494 (12674) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 331 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 323 time to evaluate : 1.538 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 MET cc_start: 0.8129 (ttm) cc_final: 0.7888 (ttt) REVERT: B 19 LEU cc_start: 0.8848 (mt) cc_final: 0.8595 (mt) REVERT: R 111 CYS cc_start: 0.6182 (t) cc_final: 0.5893 (t) outliers start: 8 outliers final: 6 residues processed: 330 average time/residue: 2.3481 time to fit residues: 832.8976 Evaluate side-chains 207 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 201 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain R residue 163 TRP Chi-restraints excluded: chain R residue 236 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 80 GLN B 235 ASN E 179 GLN R 74 ASN R 128 HIS R 351 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.135047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093280 restraints weight = 39593.428| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.89 r_work: 0.3049 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9339 Z= 0.236 Angle : 0.662 6.500 12678 Z= 0.346 Chirality : 0.042 0.197 1447 Planarity : 0.008 0.192 1587 Dihedral : 7.613 100.048 1515 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 4.18 % Allowed : 28.88 % Favored : 66.94 % 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: 0.17 (0.25), residues: 1131 helix: 1.41 (0.27), residues: 410 sheet: -0.23 (0.29), residues: 285 loop : -0.82 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 99 HIS 0.005 0.001 HIS B 230 PHE 0.020 0.002 PHE R 344 TYR 0.027 0.002 TYR E 190 ARG 0.012 0.001 ARG R 236 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 437) hydrogen bonds : angle 4.81262 ( 1245) SS BOND : bond 0.00613 ( 2) SS BOND : angle 1.58680 ( 4) covalent geometry : bond 0.00532 ( 9337) covalent geometry : angle 0.66111 (12674) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 1.665 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8258 (t) REVERT: B 219 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8027 (mmt90) REVERT: E 12 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8169 (mm110) REVERT: E 45 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7526 (mt-10) REVERT: E 88 GLU cc_start: 0.8272 (pp20) cc_final: 0.8069 (pp20) REVERT: E 197 SER cc_start: 0.9593 (t) cc_final: 0.9369 (t) REVERT: E 223 ASP cc_start: 0.8798 (m-30) cc_final: 0.8574 (m-30) REVERT: E 234 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7515 (mt-10) REVERT: E 235 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6030 (t80) REVERT: R 119 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7678 (mm-30) REVERT: R 147 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7042 (ptt-90) REVERT: R 298 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7988 (mtp180) REVERT: R 368 LYS cc_start: 0.9163 (ttmm) cc_final: 0.8846 (tptt) outliers start: 41 outliers final: 16 residues processed: 242 average time/residue: 2.8533 time to fit residues: 748.8171 Evaluate side-chains 210 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 163 TRP Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 298 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 6 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 GLN B 264 GLN E 179 GLN R 128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.134328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.092185 restraints weight = 39188.324| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.90 r_work: 0.3030 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9339 Z= 0.156 Angle : 0.585 5.962 12678 Z= 0.303 Chirality : 0.040 0.162 1447 Planarity : 0.005 0.068 1587 Dihedral : 6.590 57.652 1507 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.92 % Favored : 96.99 % Rotamer: Outliers : 3.16 % Allowed : 29.90 % Favored : 66.94 % 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: 0.40 (0.25), residues: 1131 helix: 1.69 (0.27), residues: 410 sheet: -0.06 (0.29), residues: 281 loop : -0.83 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 250 HIS 0.005 0.001 HIS A 324 PHE 0.025 0.001 PHE E 67 TYR 0.024 0.001 TYR E 190 ARG 0.007 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 437) hydrogen bonds : angle 4.52714 ( 1245) SS BOND : bond 0.00330 ( 2) SS BOND : angle 1.25524 ( 4) covalent geometry : bond 0.00356 ( 9337) covalent geometry : angle 0.58430 (12674) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 1.733 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8388 (pt0) REVERT: A 316 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8070 (p) REVERT: B 15 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: B 330 MET cc_start: 0.8711 (mmt) cc_final: 0.8406 (mmm) REVERT: E 12 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8156 (mm110) REVERT: E 18 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8234 (ttmm) REVERT: E 45 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7503 (mt-10) REVERT: E 153 GLU cc_start: 0.8367 (tp30) cc_final: 0.8115 (tm-30) REVERT: E 197 SER cc_start: 0.9613 (t) cc_final: 0.9290 (p) REVERT: E 223 ASP cc_start: 0.8876 (m-30) cc_final: 0.8581 (m-30) REVERT: E 234 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7915 (mt-10) REVERT: E 235 TYR cc_start: 0.6805 (OUTLIER) cc_final: 0.5933 (t80) REVERT: R 111 CYS cc_start: 0.8182 (t) cc_final: 0.7878 (t) REVERT: R 119 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7718 (mm-30) REVERT: R 135 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8244 (mm-30) REVERT: R 147 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7047 (ptt-90) REVERT: R 298 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7967 (mtp180) outliers start: 31 outliers final: 10 residues processed: 219 average time/residue: 2.7966 time to fit residues: 666.0255 Evaluate side-chains 198 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 163 TRP Chi-restraints excluded: chain R residue 298 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 89 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 99 optimal weight: 40.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.130351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.089786 restraints weight = 39862.162| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.78 r_work: 0.2984 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9339 Z= 0.225 Angle : 0.603 6.020 12678 Z= 0.315 Chirality : 0.041 0.183 1447 Planarity : 0.005 0.069 1587 Dihedral : 6.501 58.181 1506 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.08 % Allowed : 29.18 % Favored : 66.73 % 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: 0.42 (0.25), residues: 1131 helix: 1.80 (0.26), residues: 409 sheet: -0.10 (0.29), residues: 284 loop : -0.87 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 99 HIS 0.005 0.001 HIS E 34 PHE 0.018 0.001 PHE R 344 TYR 0.025 0.001 TYR E 190 ARG 0.006 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 437) hydrogen bonds : angle 4.47557 ( 1245) SS BOND : bond 0.00393 ( 2) SS BOND : angle 1.46721 ( 4) covalent geometry : bond 0.00498 ( 9337) covalent geometry : angle 0.60245 (12674) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.434 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8155 (mtm180) REVERT: A 53 MET cc_start: 0.8346 (mmp) cc_final: 0.7861 (mmt) REVERT: A 217 ASP cc_start: 0.8363 (t0) cc_final: 0.8051 (t0) REVERT: A 235 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8376 (pt0) REVERT: A 316 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.7982 (p) REVERT: B 15 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: E 12 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8244 (mm110) REVERT: E 45 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7415 (mt-10) REVERT: E 197 SER cc_start: 0.9595 (OUTLIER) cc_final: 0.9290 (p) REVERT: E 222 GLU cc_start: 0.8724 (pm20) cc_final: 0.8513 (pm20) REVERT: E 223 ASP cc_start: 0.8850 (m-30) cc_final: 0.8529 (m-30) REVERT: E 234 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7994 (mt-10) REVERT: E 235 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6166 (t80) REVERT: R 111 CYS cc_start: 0.8347 (t) cc_final: 0.8009 (t) REVERT: R 119 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7740 (mm-30) REVERT: R 133 SER cc_start: 0.9148 (t) cc_final: 0.8872 (p) REVERT: R 147 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.7033 (ptt180) REVERT: R 295 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7603 (tm-30) REVERT: R 298 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (mtp180) outliers start: 40 outliers final: 13 residues processed: 213 average time/residue: 2.5761 time to fit residues: 595.6141 Evaluate side-chains 200 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 298 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN E 179 GLN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.091754 restraints weight = 39532.502| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.76 r_work: 0.3025 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9339 Z= 0.116 Angle : 0.564 5.840 12678 Z= 0.290 Chirality : 0.039 0.148 1447 Planarity : 0.005 0.071 1587 Dihedral : 6.010 57.649 1504 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.76 % Allowed : 31.02 % Favored : 66.22 % 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: 0.66 (0.25), residues: 1131 helix: 2.00 (0.26), residues: 409 sheet: 0.04 (0.29), residues: 281 loop : -0.76 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 99 HIS 0.004 0.001 HIS E 34 PHE 0.013 0.001 PHE R 344 TYR 0.021 0.001 TYR E 190 ARG 0.007 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 437) hydrogen bonds : angle 4.35973 ( 1245) SS BOND : bond 0.00317 ( 2) SS BOND : angle 1.05183 ( 4) covalent geometry : bond 0.00267 ( 9337) covalent geometry : angle 0.56369 (12674) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 1.521 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8189 (mtm180) REVERT: A 217 ASP cc_start: 0.8290 (t0) cc_final: 0.8002 (t0) REVERT: A 235 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (pt0) REVERT: A 316 SER cc_start: 0.8356 (t) cc_final: 0.7973 (p) REVERT: B 15 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: B 309 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8632 (mtm-85) REVERT: E 12 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8222 (mm110) REVERT: E 45 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7293 (mt-10) REVERT: E 153 GLU cc_start: 0.8415 (tp30) cc_final: 0.8100 (tm-30) REVERT: E 197 SER cc_start: 0.9603 (t) cc_final: 0.9306 (p) REVERT: E 222 GLU cc_start: 0.8729 (pm20) cc_final: 0.8524 (pm20) REVERT: E 235 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.5951 (t80) REVERT: R 111 CYS cc_start: 0.8268 (t) cc_final: 0.7958 (t) REVERT: R 133 SER cc_start: 0.9185 (t) cc_final: 0.8907 (p) REVERT: R 295 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7547 (tm-30) REVERT: R 298 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7954 (mtp180) REVERT: R 322 ILE cc_start: 0.9504 (tp) cc_final: 0.9229 (pp) REVERT: R 368 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8825 (tptt) outliers start: 27 outliers final: 8 residues processed: 206 average time/residue: 2.3177 time to fit residues: 514.3100 Evaluate side-chains 195 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 163 TRP Chi-restraints excluded: chain R residue 298 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 86 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 81 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 21 ASN B 264 GLN E 179 GLN G 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094308 restraints weight = 39415.698| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.73 r_work: 0.3042 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9339 Z= 0.112 Angle : 0.553 6.492 12678 Z= 0.283 Chirality : 0.039 0.139 1447 Planarity : 0.005 0.070 1587 Dihedral : 5.749 57.192 1504 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.65 % Allowed : 31.43 % Favored : 65.92 % 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: 0.88 (0.25), residues: 1131 helix: 2.24 (0.26), residues: 409 sheet: 0.19 (0.30), residues: 265 loop : -0.70 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 99 HIS 0.004 0.001 HIS E 34 PHE 0.011 0.001 PHE R 344 TYR 0.019 0.001 TYR E 190 ARG 0.008 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 437) hydrogen bonds : angle 4.22457 ( 1245) SS BOND : bond 0.00324 ( 2) SS BOND : angle 0.91143 ( 4) covalent geometry : bond 0.00256 ( 9337) covalent geometry : angle 0.55297 (12674) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 1.406 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8223 (mtm180) REVERT: A 52 GLN cc_start: 0.8137 (tp40) cc_final: 0.7914 (tp40) REVERT: A 53 MET cc_start: 0.8344 (mmp) cc_final: 0.7777 (mmt) REVERT: A 204 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6660 (mp10) REVERT: A 217 ASP cc_start: 0.8254 (t0) cc_final: 0.7973 (t0) REVERT: A 316 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.7943 (p) REVERT: B 15 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: B 275 ILE cc_start: 0.9014 (pt) cc_final: 0.8739 (mm) REVERT: E 12 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8237 (mm110) REVERT: E 45 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7263 (mt-10) REVERT: E 153 GLU cc_start: 0.8420 (tp30) cc_final: 0.8053 (tm-30) REVERT: E 197 SER cc_start: 0.9614 (t) cc_final: 0.9329 (p) REVERT: E 222 GLU cc_start: 0.8762 (pm20) cc_final: 0.8512 (pm20) REVERT: E 235 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.5764 (t80) REVERT: R 111 CYS cc_start: 0.8263 (t) cc_final: 0.7947 (t) REVERT: R 119 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7726 (mm-30) REVERT: R 133 SER cc_start: 0.9190 (t) cc_final: 0.8908 (p) REVERT: R 295 GLN cc_start: 0.7771 (tm-30) cc_final: 0.7520 (tm-30) REVERT: R 298 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7972 (mtp180) REVERT: R 368 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8806 (tptt) outliers start: 26 outliers final: 11 residues processed: 209 average time/residue: 2.1936 time to fit residues: 495.8532 Evaluate side-chains 195 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 298 ARG Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.130291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.089560 restraints weight = 39582.138| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.77 r_work: 0.2989 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9339 Z= 0.188 Angle : 0.588 7.739 12678 Z= 0.303 Chirality : 0.040 0.167 1447 Planarity : 0.005 0.072 1587 Dihedral : 5.766 57.207 1504 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.55 % Allowed : 31.73 % Favored : 65.71 % 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: 0.83 (0.25), residues: 1131 helix: 2.24 (0.25), residues: 409 sheet: 0.09 (0.30), residues: 283 loop : -0.74 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 99 HIS 0.004 0.001 HIS E 167 PHE 0.014 0.001 PHE R 344 TYR 0.022 0.001 TYR E 190 ARG 0.010 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 437) hydrogen bonds : angle 4.29741 ( 1245) SS BOND : bond 0.00253 ( 2) SS BOND : angle 1.16751 ( 4) covalent geometry : bond 0.00428 ( 9337) covalent geometry : angle 0.58777 (12674) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.627 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8194 (mtm180) REVERT: A 52 GLN cc_start: 0.8202 (tp40) cc_final: 0.7992 (tp40) REVERT: A 53 MET cc_start: 0.8321 (mmp) cc_final: 0.7747 (mmt) REVERT: A 204 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6570 (mp10) REVERT: A 217 ASP cc_start: 0.8262 (t0) cc_final: 0.7992 (t0) REVERT: A 316 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 15 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: B 19 LEU cc_start: 0.7836 (mt) cc_final: 0.7222 (mt) REVERT: E 12 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8270 (mm110) REVERT: E 45 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7264 (mt-10) REVERT: E 153 GLU cc_start: 0.8457 (tp30) cc_final: 0.8090 (tm-30) REVERT: E 197 SER cc_start: 0.9613 (t) cc_final: 0.9342 (p) REVERT: E 235 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: G 13 LYS cc_start: 0.8651 (tppt) cc_final: 0.8433 (tttp) REVERT: G 20 MET cc_start: 0.8664 (mmm) cc_final: 0.7228 (tmt) REVERT: R 99 TRP cc_start: 0.8159 (m100) cc_final: 0.7745 (m100) REVERT: R 111 CYS cc_start: 0.8258 (t) cc_final: 0.7922 (t) REVERT: R 295 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7603 (tm-30) REVERT: R 298 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7993 (mtp180) REVERT: R 335 TYR cc_start: 0.9051 (m-80) cc_final: 0.8632 (m-10) outliers start: 25 outliers final: 15 residues processed: 197 average time/residue: 2.2254 time to fit residues: 473.1368 Evaluate side-chains 199 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 298 ARG Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090015 restraints weight = 39485.593| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.80 r_work: 0.2996 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9339 Z= 0.139 Angle : 0.569 5.884 12678 Z= 0.292 Chirality : 0.040 0.151 1447 Planarity : 0.005 0.073 1587 Dihedral : 5.631 56.871 1504 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.45 % Allowed : 31.53 % Favored : 66.02 % 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 (0.25), residues: 1131 helix: 2.41 (0.25), residues: 409 sheet: 0.26 (0.31), residues: 262 loop : -0.69 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 99 HIS 0.004 0.001 HIS E 34 PHE 0.012 0.001 PHE R 106 TYR 0.020 0.001 TYR E 190 ARG 0.010 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 437) hydrogen bonds : angle 4.21194 ( 1245) SS BOND : bond 0.00269 ( 2) SS BOND : angle 0.93706 ( 4) covalent geometry : bond 0.00320 ( 9337) covalent geometry : angle 0.56871 (12674) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.423 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8163 (mtm180) REVERT: A 52 GLN cc_start: 0.8155 (tp40) cc_final: 0.7934 (tp40) REVERT: A 53 MET cc_start: 0.8309 (mmp) cc_final: 0.7764 (mmt) REVERT: A 204 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: A 217 ASP cc_start: 0.8265 (t0) cc_final: 0.8015 (t0) REVERT: A 316 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7858 (p) REVERT: E 12 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8282 (mm110) REVERT: E 45 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7243 (mt-10) REVERT: E 153 GLU cc_start: 0.8483 (tp30) cc_final: 0.8098 (tm-30) REVERT: E 197 SER cc_start: 0.9614 (OUTLIER) cc_final: 0.9349 (p) REVERT: E 235 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5958 (t80) REVERT: G 13 LYS cc_start: 0.8620 (tppt) cc_final: 0.8404 (tttp) REVERT: G 19 LYS cc_start: 0.8266 (mtpm) cc_final: 0.8046 (mtmm) REVERT: G 20 MET cc_start: 0.8597 (mmm) cc_final: 0.7121 (tmt) REVERT: R 295 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7543 (tm-30) REVERT: R 298 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7977 (mtp180) REVERT: R 335 TYR cc_start: 0.9051 (m-80) cc_final: 0.8636 (m-10) outliers start: 24 outliers final: 13 residues processed: 196 average time/residue: 2.2734 time to fit residues: 482.2744 Evaluate side-chains 195 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 298 ARG Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.085245 restraints weight = 39141.345| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.96 r_work: 0.2956 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9339 Z= 0.167 Angle : 0.583 5.663 12678 Z= 0.300 Chirality : 0.040 0.161 1447 Planarity : 0.005 0.073 1587 Dihedral : 5.578 56.967 1504 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.14 % Allowed : 31.84 % Favored : 66.02 % 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: 0.99 (0.25), residues: 1131 helix: 2.40 (0.25), residues: 409 sheet: 0.26 (0.30), residues: 276 loop : -0.75 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 99 HIS 0.004 0.001 HIS E 167 PHE 0.013 0.001 PHE R 344 TYR 0.021 0.001 TYR E 190 ARG 0.010 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 437) hydrogen bonds : angle 4.24312 ( 1245) SS BOND : bond 0.00193 ( 2) SS BOND : angle 1.04625 ( 4) covalent geometry : bond 0.00383 ( 9337) covalent geometry : angle 0.58289 (12674) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 181 time to evaluate : 1.487 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8160 (mtm180) REVERT: A 52 GLN cc_start: 0.8139 (tp40) cc_final: 0.7930 (tp40) REVERT: A 53 MET cc_start: 0.8266 (mmp) cc_final: 0.7996 (tpp) REVERT: A 204 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6551 (mp10) REVERT: A 217 ASP cc_start: 0.8281 (t0) cc_final: 0.8042 (t0) REVERT: A 316 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7868 (p) REVERT: E 12 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8304 (mm110) REVERT: E 45 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7302 (mt-10) REVERT: E 153 GLU cc_start: 0.8482 (tp30) cc_final: 0.8092 (tm-30) REVERT: E 197 SER cc_start: 0.9619 (t) cc_final: 0.9361 (p) REVERT: E 235 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6078 (t80) REVERT: G 19 LYS cc_start: 0.8241 (mtpm) cc_final: 0.8004 (mtmm) REVERT: G 20 MET cc_start: 0.8603 (mmm) cc_final: 0.7169 (tmt) REVERT: R 135 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8170 (mt-10) REVERT: R 295 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7578 (tm-30) REVERT: R 298 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7997 (mtp180) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 2.2158 time to fit residues: 469.5286 Evaluate side-chains 196 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.127865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083418 restraints weight = 39534.079| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.95 r_work: 0.2924 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9339 Z= 0.219 Angle : 0.611 6.918 12678 Z= 0.317 Chirality : 0.041 0.177 1447 Planarity : 0.005 0.072 1587 Dihedral : 5.662 57.256 1504 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.35 % Allowed : 31.53 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.25), residues: 1131 helix: 2.28 (0.25), residues: 410 sheet: 0.32 (0.30), residues: 274 loop : -0.84 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 99 HIS 0.005 0.001 HIS E 34 PHE 0.016 0.001 PHE R 344 TYR 0.023 0.001 TYR E 190 ARG 0.012 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 437) hydrogen bonds : angle 4.34378 ( 1245) SS BOND : bond 0.00177 ( 2) SS BOND : angle 1.21487 ( 4) covalent geometry : bond 0.00501 ( 9337) covalent geometry : angle 0.61106 (12674) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 135 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 1.536 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8152 (mtm180) REVERT: A 53 MET cc_start: 0.8241 (mmp) cc_final: 0.7949 (tpp) REVERT: A 204 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: A 217 ASP cc_start: 0.8374 (t0) cc_final: 0.8150 (t0) REVERT: A 316 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7913 (p) REVERT: E 12 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8324 (mm110) REVERT: E 45 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7291 (mt-10) REVERT: E 197 SER cc_start: 0.9620 (OUTLIER) cc_final: 0.9358 (p) REVERT: E 235 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6233 (t80) REVERT: G 13 LYS cc_start: 0.8725 (tppt) cc_final: 0.8373 (tptp) REVERT: G 19 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7971 (mtmm) REVERT: G 20 MET cc_start: 0.8624 (mmm) cc_final: 0.7200 (tmt) REVERT: R 135 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8144 (mt-10) REVERT: R 295 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7624 (tm-30) REVERT: R 298 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7998 (mtp180) outliers start: 23 outliers final: 12 residues processed: 194 average time/residue: 2.1977 time to fit residues: 460.8825 Evaluate side-chains 195 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 298 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.128899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087344 restraints weight = 39394.087| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.79 r_work: 0.2966 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9339 Z= 0.155 Angle : 0.591 6.032 12678 Z= 0.304 Chirality : 0.040 0.161 1447 Planarity : 0.005 0.073 1587 Dihedral : 5.538 57.232 1504 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.94 % Allowed : 31.94 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.25), residues: 1131 helix: 2.41 (0.25), residues: 404 sheet: 0.32 (0.30), residues: 274 loop : -0.75 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 99 HIS 0.004 0.001 HIS E 34 PHE 0.013 0.001 PHE R 344 TYR 0.018 0.001 TYR E 190 ARG 0.012 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 437) hydrogen bonds : angle 4.29576 ( 1245) SS BOND : bond 0.00237 ( 2) SS BOND : angle 0.94717 ( 4) covalent geometry : bond 0.00360 ( 9337) covalent geometry : angle 0.59101 (12674) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17716.52 seconds wall clock time: 305 minutes 11.80 seconds (18311.80 seconds total)