Starting phenix.real_space_refine on Thu Sep 18 15:42:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmd_61598/09_2025/9jmd_61598_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmd_61598/09_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_61598/09_2025/9jmd_61598.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmd_61598/09_2025/9jmd_61598.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmd_61598/09_2025/9jmd_61598_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmd_61598/09_2025/9jmd_61598_trim.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.97, per 1000 atoms: 0.16 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: 1.39 Conformation dependent library (CDL) restraints added in 575.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.36 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: 3.19 Time building geometry restraints manager: 2.04 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: 0.960 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: 0.110 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.300 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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 : 7.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), 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 ARG 0.014 0.001 ARG E 160 TYR 0.024 0.001 TYR E 190 PHE 0.029 0.002 PHE E 239 TRP 0.012 0.001 TRP R 250 HIS 0.006 0.001 HIS R 315 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9337) covalent geometry : angle 0.73494 (12674) SS BOND : bond 0.00953 ( 2) SS BOND : angle 2.09798 ( 4) hydrogen bonds : bond 0.13762 ( 437) hydrogen bonds : angle 6.16002 ( 1245) *********************** 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 : 0.468 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: A 353 MET cc_start: 0.8129 (ttm) cc_final: 0.7888 (ttt) REVERT: B 19 LEU cc_start: 0.8848 (mt) cc_final: 0.8509 (mt) REVERT: R 111 CYS cc_start: 0.6182 (t) cc_final: 0.5897 (t) outliers start: 8 outliers final: 6 residues processed: 330 average time/residue: 1.0914 time to fit residues: 385.5777 Evaluate side-chains 209 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 203 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3805 r_free = 0.3805 target = 0.133650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.091032 restraints weight = 39603.104| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.92 r_work: 0.3052 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3417 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= 0.241 Angle : 0.652 6.382 12678 Z= 0.344 Chirality : 0.042 0.194 1447 Planarity : 0.008 0.201 1587 Dihedral : 7.536 89.471 1515 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 3.98 % Allowed : 29.18 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.25), residues: 1131 helix: 1.40 (0.27), residues: 408 sheet: -0.17 (0.29), residues: 284 loop : -0.87 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 236 TYR 0.027 0.002 TYR E 190 PHE 0.021 0.002 PHE R 344 TRP 0.010 0.002 TRP R 99 HIS 0.005 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 9337) covalent geometry : angle 0.65153 (12674) SS BOND : bond 0.00531 ( 2) SS BOND : angle 1.73423 ( 4) hydrogen bonds : bond 0.04671 ( 437) hydrogen bonds : angle 4.82453 ( 1245) *********************** 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 253 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 0.492 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: A 294 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7949 (mp0) REVERT: B 103 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8169 (t) REVERT: B 202 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8225 (mmm-85) REVERT: B 219 ARG cc_start: 0.8356 (mmt90) cc_final: 0.8022 (mmt90) REVERT: B 330 MET cc_start: 0.8698 (mmt) cc_final: 0.8366 (mmm) REVERT: E 12 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8166 (mm110) REVERT: E 45 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7481 (mt-10) REVERT: E 197 SER cc_start: 0.9586 (t) cc_final: 0.9363 (t) REVERT: E 234 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7477 (mt-10) REVERT: E 235 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5984 (t80) REVERT: R 38 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8789 (tt) REVERT: R 147 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7023 (ptt-90) REVERT: R 182 ASP cc_start: 0.7227 (t70) cc_final: 0.6686 (m-30) REVERT: R 241 GLN cc_start: 0.7714 (pm20) cc_final: 0.7497 (pm20) REVERT: R 298 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7966 (mtp180) REVERT: R 368 LYS cc_start: 0.9172 (ttmm) cc_final: 0.8843 (tptt) outliers start: 39 outliers final: 15 residues processed: 238 average time/residue: 1.1202 time to fit residues: 285.3908 Evaluate side-chains 212 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 38 LEU 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 98 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 235 ASN B 264 GLN E 179 GLN R 128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.133551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.091157 restraints weight = 39319.250| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.91 r_work: 0.3014 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9339 Z= 0.183 Angle : 0.608 6.678 12678 Z= 0.315 Chirality : 0.041 0.172 1447 Planarity : 0.005 0.068 1587 Dihedral : 6.632 57.945 1507 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 3.37 % Allowed : 30.20 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.25), residues: 1131 helix: 1.66 (0.27), residues: 410 sheet: -0.08 (0.29), residues: 282 loop : -0.85 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 236 TYR 0.025 0.001 TYR E 190 PHE 0.018 0.001 PHE R 344 TRP 0.008 0.001 TRP R 99 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9337) covalent geometry : angle 0.60735 (12674) SS BOND : bond 0.00279 ( 2) SS BOND : angle 1.23528 ( 4) hydrogen bonds : bond 0.04209 ( 437) hydrogen bonds : angle 4.54532 ( 1245) *********************** 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 227 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.462 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 52 GLN cc_start: 0.8089 (tp40) cc_final: 0.7839 (tp40) REVERT: A 53 MET cc_start: 0.8400 (mmp) cc_final: 0.7914 (mmt) REVERT: A 294 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7942 (mp0) REVERT: A 316 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8041 (p) REVERT: B 15 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: B 20 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8406 (mtmm) REVERT: B 103 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8243 (t) REVERT: B 202 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.8255 (mmm-85) REVERT: B 219 ARG cc_start: 0.8422 (mmt90) cc_final: 0.8117 (mmt90) REVERT: B 330 MET cc_start: 0.8774 (mmt) cc_final: 0.8499 (mmm) REVERT: E 12 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8173 (mm110) REVERT: E 17 ARG cc_start: 0.7544 (tpp80) cc_final: 0.7007 (ttt-90) REVERT: E 18 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8231 (ttmm) REVERT: E 45 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7519 (mt-10) REVERT: E 153 GLU cc_start: 0.8382 (tp30) cc_final: 0.8127 (tm-30) REVERT: E 197 SER cc_start: 0.9610 (t) cc_final: 0.9375 (t) REVERT: E 223 ASP cc_start: 0.8687 (m-30) cc_final: 0.8466 (m-30) REVERT: E 234 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7976 (mt-10) REVERT: E 235 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.6053 (t80) REVERT: R 111 CYS cc_start: 0.8207 (t) cc_final: 0.7938 (t) REVERT: R 147 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6990 (ptt-90) REVERT: R 163 TRP cc_start: 0.8093 (OUTLIER) cc_final: 0.5871 (m-10) REVERT: R 182 ASP cc_start: 0.7055 (t70) cc_final: 0.6638 (m-30) REVERT: R 241 GLN cc_start: 0.7695 (pm20) cc_final: 0.7491 (pm20) REVERT: R 298 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7968 (mtp180) outliers start: 33 outliers final: 9 residues processed: 215 average time/residue: 1.1472 time to fit residues: 264.2564 Evaluate side-chains 197 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 210 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain R residue 38 LEU 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 298 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** 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 = 0.3803 r_free = 0.3803 target = 0.130930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.090879 restraints weight = 39967.214| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.76 r_work: 0.3003 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9339 Z= 0.188 Angle : 0.587 5.713 12678 Z= 0.305 Chirality : 0.040 0.175 1447 Planarity : 0.005 0.070 1587 Dihedral : 6.431 58.079 1506 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 3.98 % Allowed : 28.88 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.25), residues: 1131 helix: 1.70 (0.26), residues: 415 sheet: -0.07 (0.29), residues: 284 loop : -0.83 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 218 TYR 0.024 0.001 TYR E 190 PHE 0.017 0.001 PHE R 314 TRP 0.008 0.001 TRP R 250 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9337) covalent geometry : angle 0.58642 (12674) SS BOND : bond 0.00416 ( 2) SS BOND : angle 1.36692 ( 4) hydrogen bonds : bond 0.04013 ( 437) hydrogen bonds : angle 4.45549 ( 1245) *********************** 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 233 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.398 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: A 31 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8177 (mtm180) REVERT: A 32 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7917 (ttm-80) REVERT: A 52 GLN cc_start: 0.8161 (tp40) cc_final: 0.7852 (tp40) REVERT: A 53 MET cc_start: 0.8364 (mmp) cc_final: 0.7868 (mmt) REVERT: A 217 ASP cc_start: 0.8334 (t0) cc_final: 0.8016 (t0) REVERT: A 294 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7825 (mp0) REVERT: A 316 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.8023 (p) REVERT: B 202 ARG cc_start: 0.8458 (mmm-85) cc_final: 0.8256 (mmm-85) REVERT: B 219 ARG cc_start: 0.8445 (mmt90) cc_final: 0.8188 (mmt90) REVERT: B 330 MET cc_start: 0.8803 (mmt) cc_final: 0.8474 (mmm) REVERT: E 12 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8238 (mm110) REVERT: E 45 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7273 (mt-10) REVERT: E 197 SER cc_start: 0.9602 (OUTLIER) cc_final: 0.9292 (p) REVERT: E 223 ASP cc_start: 0.8766 (m-30) cc_final: 0.8480 (m-30) REVERT: E 234 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7923 (mt-10) REVERT: E 235 TYR cc_start: 0.6965 (OUTLIER) cc_final: 0.6117 (t80) REVERT: R 96 TYR cc_start: 0.8616 (t80) cc_final: 0.8365 (t80) REVERT: R 111 CYS cc_start: 0.8325 (t) cc_final: 0.8005 (t) REVERT: R 133 SER cc_start: 0.9163 (t) cc_final: 0.8886 (p) REVERT: R 147 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.7083 (ptt180) REVERT: R 182 ASP cc_start: 0.6924 (t70) cc_final: 0.6602 (m-30) REVERT: R 295 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7606 (tm-30) REVERT: R 298 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7947 (mtp180) REVERT: R 368 LYS cc_start: 0.9159 (ttmm) cc_final: 0.8844 (tptt) outliers start: 39 outliers final: 14 residues processed: 218 average time/residue: 1.1101 time to fit residues: 259.7648 Evaluate side-chains 201 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER 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 38 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 91 LEU Chi-restraints excluded: chain R residue 147 ARG 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 42 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 264 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN G 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089198 restraints weight = 39670.758| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.79 r_work: 0.2986 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4749 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= 0.173 Angle : 0.578 5.842 12678 Z= 0.300 Chirality : 0.040 0.167 1447 Planarity : 0.005 0.071 1587 Dihedral : 6.042 58.079 1504 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.06 % Allowed : 30.41 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1131 helix: 1.91 (0.26), residues: 409 sheet: 0.01 (0.29), residues: 281 loop : -0.75 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 218 TYR 0.024 0.001 TYR E 190 PHE 0.015 0.001 PHE R 344 TRP 0.007 0.001 TRP B 87 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 9337) covalent geometry : angle 0.57747 (12674) SS BOND : bond 0.00382 ( 2) SS BOND : angle 1.07698 ( 4) hydrogen bonds : bond 0.03895 ( 437) hydrogen bonds : angle 4.41244 ( 1245) *********************** 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 221 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.527 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: A 31 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8148 (mtm180) REVERT: A 32 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7850 (ttm-80) REVERT: A 53 MET cc_start: 0.8342 (mmp) cc_final: 0.7803 (mmt) REVERT: A 204 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.6481 (mp10) REVERT: A 217 ASP cc_start: 0.8329 (t0) cc_final: 0.8036 (t0) REVERT: A 294 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7849 (mp0) REVERT: A 316 SER cc_start: 0.8370 (OUTLIER) cc_final: 0.7953 (p) REVERT: A 337 GLU cc_start: 0.8128 (mp0) cc_final: 0.7823 (mp0) REVERT: B 15 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8247 (tm-30) REVERT: B 219 ARG cc_start: 0.8479 (mmt90) cc_final: 0.8256 (mmt90) REVERT: B 309 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8634 (mtm-85) REVERT: B 330 MET cc_start: 0.8794 (mmt) cc_final: 0.8494 (mmm) REVERT: E 12 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8237 (mm110) REVERT: E 45 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7286 (mt-10) REVERT: E 153 GLU cc_start: 0.8393 (tp30) cc_final: 0.8076 (tm-30) REVERT: E 197 SER cc_start: 0.9602 (OUTLIER) cc_final: 0.9313 (p) REVERT: E 235 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6139 (t80) REVERT: R 111 CYS cc_start: 0.8328 (t) cc_final: 0.7998 (t) REVERT: R 133 SER cc_start: 0.9162 (t) cc_final: 0.8879 (p) REVERT: R 147 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7092 (ptt180) REVERT: R 182 ASP cc_start: 0.6926 (t70) cc_final: 0.6596 (m-30) REVERT: R 295 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7591 (tm-30) REVERT: R 298 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7940 (mtp180) REVERT: R 322 ILE cc_start: 0.9498 (tp) cc_final: 0.9231 (pp) outliers start: 30 outliers final: 16 residues processed: 211 average time/residue: 1.1274 time to fit residues: 254.9662 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN 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 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 166 LEU 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 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 38 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 298 ARG Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3783 r_free = 0.3783 target = 0.129741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.088526 restraints weight = 39444.012| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.81 r_work: 0.2978 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9339 Z= 0.165 Angle : 0.574 6.466 12678 Z= 0.296 Chirality : 0.040 0.161 1447 Planarity : 0.004 0.071 1587 Dihedral : 5.951 57.963 1504 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.16 % Allowed : 30.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1131 helix: 2.00 (0.26), residues: 409 sheet: 0.12 (0.31), residues: 265 loop : -0.73 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 218 TYR 0.022 0.001 TYR E 190 PHE 0.014 0.001 PHE R 344 TRP 0.008 0.001 TRP B 174 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9337) covalent geometry : angle 0.57370 (12674) SS BOND : bond 0.00308 ( 2) SS BOND : angle 1.07598 ( 4) hydrogen bonds : bond 0.03803 ( 437) hydrogen bonds : angle 4.36770 ( 1245) *********************** 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 216 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 0.361 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: 0.8497 (ttm-80) cc_final: 0.8191 (mtm180) REVERT: A 52 GLN cc_start: 0.8118 (mm110) cc_final: 0.7865 (mm110) REVERT: A 53 MET cc_start: 0.8256 (mmp) cc_final: 0.7747 (mmt) REVERT: A 217 ASP cc_start: 0.8302 (t0) cc_final: 0.8025 (t0) REVERT: A 294 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7838 (mp0) REVERT: A 316 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.7914 (p) REVERT: A 337 GLU cc_start: 0.8145 (mp0) cc_final: 0.7838 (mp0) REVERT: B 15 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8281 (tm-30) REVERT: B 17 GLU cc_start: 0.8701 (tp30) cc_final: 0.8442 (tp30) REVERT: B 309 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8600 (mtm-85) REVERT: B 330 MET cc_start: 0.8798 (mmt) cc_final: 0.8486 (mmm) REVERT: E 12 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8265 (mm110) REVERT: E 45 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7321 (mt-10) REVERT: E 153 GLU cc_start: 0.8415 (tp30) cc_final: 0.8060 (tm-30) REVERT: E 197 SER cc_start: 0.9603 (OUTLIER) cc_final: 0.9326 (p) REVERT: E 235 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6122 (t80) REVERT: R 111 CYS cc_start: 0.8297 (t) cc_final: 0.7977 (t) REVERT: R 133 SER cc_start: 0.9176 (t) cc_final: 0.8926 (p) REVERT: R 182 ASP cc_start: 0.6855 (t70) cc_final: 0.6552 (m-30) REVERT: R 295 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7579 (tm-30) REVERT: R 298 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7990 (mtp180) outliers start: 31 outliers final: 16 residues processed: 203 average time/residue: 1.1621 time to fit residues: 252.9838 Evaluate side-chains 201 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 194 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 309 ARG 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 197 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 38 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.129188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088039 restraints weight = 39633.465| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.79 r_work: 0.2968 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: 0.7883 moved from start: 0.5079 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= 0.174 Angle : 0.576 7.936 12678 Z= 0.299 Chirality : 0.040 0.169 1447 Planarity : 0.005 0.072 1587 Dihedral : 5.865 57.930 1504 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.27 % Allowed : 30.51 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1131 helix: 2.14 (0.26), residues: 409 sheet: 0.12 (0.30), residues: 278 loop : -0.74 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 218 TYR 0.023 0.001 TYR E 190 PHE 0.013 0.001 PHE R 344 TRP 0.008 0.001 TRP B 174 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 9337) covalent geometry : angle 0.57607 (12674) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.11519 ( 4) hydrogen bonds : bond 0.03768 ( 437) hydrogen bonds : angle 4.33154 ( 1245) *********************** 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 212 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.522 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: 0.8455 (ttm-80) cc_final: 0.8169 (mtm180) REVERT: A 52 GLN cc_start: 0.8134 (mm110) cc_final: 0.7787 (mm-40) REVERT: A 53 MET cc_start: 0.8278 (mmp) cc_final: 0.7667 (mpt) REVERT: A 204 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6574 (mp10) REVERT: A 217 ASP cc_start: 0.8300 (t0) cc_final: 0.8042 (t0) REVERT: A 294 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7808 (mp0) REVERT: A 316 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 337 GLU cc_start: 0.8172 (mp0) cc_final: 0.7878 (mp0) REVERT: B 15 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: B 309 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8587 (mtm-85) REVERT: B 330 MET cc_start: 0.8769 (mmt) cc_final: 0.8466 (mmm) REVERT: E 12 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8312 (mm110) REVERT: E 45 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7297 (mt-10) REVERT: E 153 GLU cc_start: 0.8456 (tp30) cc_final: 0.8092 (tm-30) REVERT: E 197 SER cc_start: 0.9613 (OUTLIER) cc_final: 0.9347 (p) REVERT: E 235 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6155 (t80) REVERT: G 13 LYS cc_start: 0.8631 (tppt) cc_final: 0.8419 (tttp) REVERT: G 20 MET cc_start: 0.8701 (mmm) cc_final: 0.7351 (tmt) REVERT: R 182 ASP cc_start: 0.6843 (t70) cc_final: 0.6543 (m-30) REVERT: R 295 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7585 (tm-30) REVERT: R 298 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7990 (mtp180) outliers start: 32 outliers final: 17 residues processed: 200 average time/residue: 1.1369 time to fit residues: 244.3428 Evaluate side-chains 202 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN 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 194 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 309 ARG 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 197 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 38 LEU 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 335 TYR 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 80 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.129309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085268 restraints weight = 39407.671| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.96 r_work: 0.2952 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5168 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= 0.151 Angle : 0.564 5.467 12678 Z= 0.292 Chirality : 0.040 0.158 1447 Planarity : 0.005 0.071 1587 Dihedral : 5.762 57.843 1504 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.55 % Allowed : 30.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.25), residues: 1131 helix: 2.30 (0.26), residues: 409 sheet: 0.24 (0.31), residues: 262 loop : -0.71 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 218 TYR 0.021 0.001 TYR E 190 PHE 0.013 0.001 PHE R 344 TRP 0.009 0.001 TRP B 174 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9337) covalent geometry : angle 0.56337 (12674) SS BOND : bond 0.00278 ( 2) SS BOND : angle 0.98105 ( 4) hydrogen bonds : bond 0.03692 ( 437) hydrogen bonds : angle 4.28965 ( 1245) *********************** 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 208 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.542 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: 0.8463 (ttm-80) cc_final: 0.8179 (mtm180) REVERT: A 52 GLN cc_start: 0.8110 (mm110) cc_final: 0.7776 (mm-40) REVERT: A 53 MET cc_start: 0.8225 (mmp) cc_final: 0.7651 (mpt) REVERT: A 217 ASP cc_start: 0.8322 (t0) cc_final: 0.8070 (t0) REVERT: A 294 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7819 (mp0) REVERT: A 316 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7857 (p) REVERT: A 337 GLU cc_start: 0.8188 (mp0) cc_final: 0.7887 (mp0) REVERT: B 309 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8634 (mtm-85) REVERT: B 330 MET cc_start: 0.8743 (mmt) cc_final: 0.8443 (mmm) REVERT: E 12 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8313 (mm110) REVERT: E 45 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7311 (mt-10) REVERT: E 153 GLU cc_start: 0.8484 (tp30) cc_final: 0.8111 (tm-30) REVERT: E 197 SER cc_start: 0.9616 (OUTLIER) cc_final: 0.9357 (p) REVERT: E 235 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6710 (m-80) REVERT: G 13 LYS cc_start: 0.8663 (tppt) cc_final: 0.8448 (tttp) REVERT: G 20 MET cc_start: 0.8692 (mmm) cc_final: 0.7300 (tmt) REVERT: R 182 ASP cc_start: 0.6863 (t70) cc_final: 0.6587 (m-30) REVERT: R 295 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7574 (tm-30) REVERT: R 298 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7992 (mtp180) outliers start: 25 outliers final: 17 residues processed: 197 average time/residue: 1.1814 time to fit residues: 250.2322 Evaluate side-chains 200 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 309 ARG 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 197 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 38 LEU 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 335 TYR 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 72 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085966 restraints weight = 39363.765| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.94 r_work: 0.2961 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9339 Z= 0.140 Angle : 0.567 6.067 12678 Z= 0.292 Chirality : 0.040 0.154 1447 Planarity : 0.005 0.071 1587 Dihedral : 5.617 57.640 1504 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.25), residues: 1131 helix: 2.39 (0.26), residues: 410 sheet: 0.19 (0.30), residues: 277 loop : -0.71 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 218 TYR 0.021 0.001 TYR E 190 PHE 0.012 0.001 PHE R 344 TRP 0.009 0.001 TRP B 174 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9337) covalent geometry : angle 0.56714 (12674) SS BOND : bond 0.00236 ( 2) SS BOND : angle 0.96337 ( 4) hydrogen bonds : bond 0.03615 ( 437) hydrogen bonds : angle 4.23506 ( 1245) *********************** 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 209 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.563 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: A 31 ARG cc_start: 0.8452 (ttm-80) cc_final: 0.8166 (mtm180) REVERT: A 52 GLN cc_start: 0.8102 (mm110) cc_final: 0.7842 (mm-40) REVERT: A 217 ASP cc_start: 0.8308 (t0) cc_final: 0.8072 (t0) REVERT: A 294 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7840 (mp0) REVERT: A 316 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7854 (p) REVERT: A 337 GLU cc_start: 0.8180 (mp0) cc_final: 0.7878 (mp0) REVERT: B 309 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8627 (mtm-85) REVERT: B 330 MET cc_start: 0.8733 (mmt) cc_final: 0.8436 (mmm) REVERT: E 12 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8322 (mm110) REVERT: E 45 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7300 (mt-10) REVERT: E 153 GLU cc_start: 0.8502 (tp30) cc_final: 0.8124 (tm-30) REVERT: E 197 SER cc_start: 0.9620 (t) cc_final: 0.9365 (p) REVERT: E 235 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6081 (t80) REVERT: G 20 MET cc_start: 0.8693 (mmm) cc_final: 0.7301 (tmt) REVERT: R 182 ASP cc_start: 0.6799 (t70) cc_final: 0.6577 (m-30) REVERT: R 295 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7562 (tm-30) REVERT: R 298 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7988 (mtp180) outliers start: 23 outliers final: 17 residues processed: 201 average time/residue: 1.1209 time to fit residues: 242.6206 Evaluate side-chains 199 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 309 ARG 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 38 LEU 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 335 TYR Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.127115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082706 restraints weight = 39724.107| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.95 r_work: 0.2910 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9339 Z= 0.243 Angle : 0.611 5.985 12678 Z= 0.319 Chirality : 0.041 0.187 1447 Planarity : 0.005 0.070 1587 Dihedral : 5.767 58.198 1504 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.65 % Allowed : 31.02 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1131 helix: 2.24 (0.26), residues: 410 sheet: 0.17 (0.30), residues: 276 loop : -0.81 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 218 TYR 0.024 0.001 TYR E 190 PHE 0.016 0.001 PHE R 344 TRP 0.008 0.001 TRP A 248 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00558 ( 9337) covalent geometry : angle 0.61082 (12674) SS BOND : bond 0.00231 ( 2) SS BOND : angle 1.37052 ( 4) hydrogen bonds : bond 0.03966 ( 437) hydrogen bonds : angle 4.40233 ( 1245) ********************** 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 202 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.549 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: 0.8449 (ttm-80) cc_final: 0.8123 (mtm180) REVERT: A 52 GLN cc_start: 0.8087 (mm110) cc_final: 0.7759 (mm-40) REVERT: A 53 MET cc_start: 0.8201 (mmp) cc_final: 0.7649 (mpt) REVERT: A 204 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6548 (mp10) REVERT: A 217 ASP cc_start: 0.8384 (t0) cc_final: 0.8162 (t0) REVERT: A 294 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7839 (mp0) REVERT: A 316 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7924 (p) REVERT: B 330 MET cc_start: 0.8798 (mmt) cc_final: 0.8499 (mmm) REVERT: E 12 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8349 (mm110) REVERT: E 45 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7263 (mt-10) REVERT: E 98 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8939 (p) REVERT: E 159 CYS cc_start: 0.8941 (p) cc_final: 0.8661 (t) REVERT: E 197 SER cc_start: 0.9621 (OUTLIER) cc_final: 0.9361 (p) REVERT: E 235 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6297 (t80) REVERT: G 13 LYS cc_start: 0.8711 (tppt) cc_final: 0.8359 (tptp) REVERT: G 20 MET cc_start: 0.8656 (mmm) cc_final: 0.7270 (tmt) REVERT: R 182 ASP cc_start: 0.6872 (t70) cc_final: 0.6595 (m-30) REVERT: R 298 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7990 (mtp180) outliers start: 26 outliers final: 15 residues processed: 193 average time/residue: 1.1331 time to fit residues: 235.7470 Evaluate side-chains 194 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 GLN 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 166 LEU 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 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 38 LEU 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 335 TYR Chi-restraints excluded: chain R residue 357 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 78 optimal weight: 0.0980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.130331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.089102 restraints weight = 39224.608| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.78 r_work: 0.2996 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9339 Z= 0.110 Angle : 0.569 6.839 12678 Z= 0.292 Chirality : 0.040 0.154 1447 Planarity : 0.005 0.071 1587 Dihedral : 5.512 57.648 1504 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.25), residues: 1131 helix: 2.57 (0.26), residues: 404 sheet: 0.24 (0.30), residues: 273 loop : -0.65 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 218 TYR 0.020 0.001 TYR E 190 PHE 0.010 0.001 PHE R 344 TRP 0.013 0.001 TRP B 174 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9337) covalent geometry : angle 0.56840 (12674) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.84593 ( 4) hydrogen bonds : bond 0.03525 ( 437) hydrogen bonds : angle 4.20387 ( 1245) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8382.72 seconds wall clock time: 142 minutes 10.80 seconds (8530.80 seconds total)