Starting phenix.real_space_refine on Wed Sep 17 13:56:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bue_44907/09_2025/9bue_44907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bue_44907/09_2025/9bue_44907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bue_44907/09_2025/9bue_44907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bue_44907/09_2025/9bue_44907.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bue_44907/09_2025/9bue_44907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bue_44907/09_2025/9bue_44907.map" } resolution = 3.6 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= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5717 2.51 5 N 1575 2.21 5 O 1647 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 9002 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1890 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 233 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 28} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2875 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 16, 'TRANS': 349} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 250 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 5, 'ARG:plan': 4, 'ASP:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 9002 At special positions: 0 Unit cell: (79.12, 98.9, 151.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1647 8.00 N 1575 7.00 C 5717 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 277.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 41.6% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.785A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.613A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.585A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.535A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.693A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.804A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 53 through 56 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 21 Processing helix chain 'R' and resid 39 through 62 Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.800A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 removed outlier: 3.879A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.882A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL R 203 " --> pdb=" O ILE R 199 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL R 205 " --> pdb=" O HIS R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 removed outlier: 3.659A pdb=" N ARG R 214 " --> pdb=" O GLU R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.755A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL R 249 " --> pdb=" O HIS R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 267 through 285 removed outlier: 3.935A pdb=" N LEU R 271 " --> pdb=" O TRP R 267 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL R 272 " --> pdb=" O GLY R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.947A pdb=" N LEU R 291 " --> pdb=" O ASN R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 331 Proline residue: R 304 - end of helix removed outlier: 3.526A pdb=" N MET R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG R 328 " --> pdb=" O VAL R 324 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 removed outlier: 4.076A pdb=" N TYR R 338 " --> pdb=" O GLU R 334 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LEU R 339 " --> pdb=" O SER R 335 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS R 340 " --> pdb=" O HIS R 336 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 413 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 4.043A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.716A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.057A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.600A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.649A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.816A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.761A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.612A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 11 through 12 removed outlier: 8.718A pdb=" N VAL N 12 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N THR N 125 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR N 94 " --> pdb=" O THR N 122 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL N 124 " --> pdb=" O ALA N 92 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 19 through 23 removed outlier: 3.897A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP N 73 " --> pdb=" O THR N 78 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.738A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2901 1.34 - 1.46: 1510 1.46 - 1.58: 4703 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 9202 Sorted by residual: bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ARG A 228 " pdb=" CA ARG A 228 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.37e-02 5.33e+03 7.69e+00 bond pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.66e+00 bond pdb=" N THR P 30 " pdb=" CA THR P 30 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 6.99e+00 bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.91e+00 ... (remaining 9197 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 12325 2.33 - 4.66: 136 4.66 - 6.99: 14 6.99 - 9.32: 1 9.32 - 11.65: 2 Bond angle restraints: 12478 Sorted by residual: angle pdb=" CA PRO P 37 " pdb=" N PRO P 37 " pdb=" CD PRO P 37 " ideal model delta sigma weight residual 112.00 103.88 8.12 1.40e+00 5.10e-01 3.36e+01 angle pdb=" C PHE A 222 " pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " ideal model delta sigma weight residual 112.09 105.43 6.66 1.43e+00 4.89e-01 2.17e+01 angle pdb=" CA PRO R 86 " pdb=" N PRO R 86 " pdb=" CD PRO R 86 " ideal model delta sigma weight residual 112.00 106.50 5.50 1.40e+00 5.10e-01 1.55e+01 angle pdb=" C SER P 34 " pdb=" CA SER P 34 " pdb=" CB SER P 34 " ideal model delta sigma weight residual 116.63 112.43 4.20 1.16e+00 7.43e-01 1.31e+01 angle pdb=" O THR P 36 " pdb=" C THR P 36 " pdb=" N PRO P 37 " ideal model delta sigma weight residual 121.30 124.83 -3.53 1.03e+00 9.43e-01 1.17e+01 ... (remaining 12473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4748 17.89 - 35.77: 577 35.77 - 53.66: 113 53.66 - 71.55: 17 71.55 - 89.44: 7 Dihedral angle restraints: 5462 sinusoidal: 2116 harmonic: 3346 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 -177.56 -89.44 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 156.89 -63.89 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual 93.00 138.59 -45.59 1 1.00e+01 1.00e-02 2.88e+01 ... (remaining 5459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1196 0.057 - 0.114: 174 0.114 - 0.171: 17 0.171 - 0.228: 1 0.228 - 0.285: 3 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA PRO P 37 " pdb=" N PRO P 37 " pdb=" C PRO P 37 " pdb=" CB PRO P 37 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA PHE A 222 " pdb=" N PHE A 222 " pdb=" C PHE A 222 " pdb=" CB PHE A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ARG A 232 " pdb=" N ARG A 232 " pdb=" C ARG A 232 " pdb=" CB ARG A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1388 not shown) Planarity restraints: 1595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 85 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO R 86 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO R 86 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 86 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 332 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 327 " -0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 328 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 328 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 328 " -0.028 5.00e-02 4.00e+02 ... (remaining 1592 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 637 2.74 - 3.28: 9082 3.28 - 3.82: 14933 3.82 - 4.36: 17001 4.36 - 4.90: 29991 Nonbonded interactions: 71644 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" OE1 GLU B 130 " model vdw 2.212 3.040 nonbonded pdb=" N GLU R 397 " pdb=" OE1 GLU R 397 " model vdw 2.215 3.120 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.241 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.263 3.040 ... (remaining 71639 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 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 : 0.003 0.107 9210 Z= 0.198 Angle : 0.574 11.650 12492 Z= 0.334 Chirality : 0.042 0.285 1391 Planarity : 0.005 0.110 1595 Dihedral : 15.562 86.620 3273 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.42 % Allowed : 17.98 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.25), residues: 1126 helix: 1.21 (0.25), residues: 433 sheet: 0.32 (0.35), residues: 231 loop : -0.37 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.024 0.001 TYR R 98 PHE 0.015 0.001 PHE R 119 TRP 0.029 0.001 TRP R 79 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9202) covalent geometry : angle 0.57339 (12478) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.77992 ( 14) hydrogen bonds : bond 0.25458 ( 437) hydrogen bonds : angle 7.34970 ( 1266) Misc. bond : bond 0.10728 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7284 (ttp-110) REVERT: B 42 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5569 (ptm160) REVERT: B 333 ASP cc_start: 0.8272 (p0) cc_final: 0.7787 (p0) REVERT: R 187 MET cc_start: 0.7266 (tpp) cc_final: 0.6944 (tpt) REVERT: R 213 ARG cc_start: 0.6404 (tpt-90) cc_final: 0.5769 (ptm160) REVERT: R 229 MET cc_start: 0.7401 (tpp) cc_final: 0.7195 (tpp) REVERT: R 332 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7623 (tm-30) REVERT: R 410 LYS cc_start: 0.6817 (ptmt) cc_final: 0.6531 (pttm) outliers start: 4 outliers final: 4 residues processed: 194 average time/residue: 0.1306 time to fit residues: 32.4072 Evaluate side-chains 175 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 171 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain B residue 10 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN N 5 GLN R 194 ASN R 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.138295 restraints weight = 11650.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141849 restraints weight = 8022.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.143761 restraints weight = 6216.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.147055 restraints weight = 4883.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.147005 restraints weight = 4324.519| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9210 Z= 0.170 Angle : 0.569 6.175 12492 Z= 0.314 Chirality : 0.042 0.172 1391 Planarity : 0.004 0.067 1595 Dihedral : 4.754 70.380 1253 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.89 % Allowed : 16.40 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.73 (0.25), residues: 1126 helix: 1.65 (0.25), residues: 441 sheet: 0.22 (0.34), residues: 237 loop : -0.49 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 228 TYR 0.022 0.002 TYR R 98 PHE 0.023 0.002 PHE R 161 TRP 0.023 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9202) covalent geometry : angle 0.56858 (12478) SS BOND : bond 0.00188 ( 7) SS BOND : angle 0.79751 ( 14) hydrogen bonds : bond 0.05340 ( 437) hydrogen bonds : angle 4.95806 ( 1266) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: B 6 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6216 (pp30) REVERT: B 9 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: B 30 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7880 (tt) REVERT: B 42 ARG cc_start: 0.6277 (ttt180) cc_final: 0.5607 (ptm160) REVERT: B 59 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: R 137 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.7000 (m-10) REVERT: R 157 SER cc_start: 0.8807 (p) cc_final: 0.8429 (m) REVERT: R 187 MET cc_start: 0.7294 (tpp) cc_final: 0.6776 (tpt) REVERT: R 213 ARG cc_start: 0.6445 (tpt-90) cc_final: 0.5805 (ptm160) REVERT: R 410 LYS cc_start: 0.7299 (ptmt) cc_final: 0.7015 (pttm) outliers start: 37 outliers final: 20 residues processed: 208 average time/residue: 0.1189 time to fit residues: 32.0584 Evaluate side-chains 198 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 172 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain P residue 1 LYS Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 4 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN N 5 GLN R 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.179035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139303 restraints weight = 11653.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142789 restraints weight = 8315.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.145091 restraints weight = 6237.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147790 restraints weight = 4838.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147887 restraints weight = 4290.853| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9210 Z= 0.115 Angle : 0.515 6.177 12492 Z= 0.281 Chirality : 0.041 0.157 1391 Planarity : 0.004 0.044 1595 Dihedral : 4.346 73.317 1246 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.26 % Allowed : 17.77 % Favored : 78.97 % 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: 0.90 (0.26), residues: 1126 helix: 1.98 (0.25), residues: 442 sheet: 0.17 (0.34), residues: 237 loop : -0.52 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.028 0.001 TYR R 98 PHE 0.010 0.001 PHE B 199 TRP 0.021 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9202) covalent geometry : angle 0.51489 (12478) SS BOND : bond 0.00176 ( 7) SS BOND : angle 0.72901 ( 14) hydrogen bonds : bond 0.04196 ( 437) hydrogen bonds : angle 4.55925 ( 1266) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: A 347 ARG cc_start: 0.7600 (ptp-110) cc_final: 0.7275 (ttp-170) REVERT: B 6 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6438 (pp30) REVERT: B 42 ARG cc_start: 0.6292 (ttt180) cc_final: 0.5570 (ptm160) REVERT: B 59 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.7554 (m-10) REVERT: B 172 GLU cc_start: 0.7342 (pt0) cc_final: 0.7095 (pt0) REVERT: B 234 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: B 255 LEU cc_start: 0.9056 (mm) cc_final: 0.8693 (mp) REVERT: N 88 PRO cc_start: 0.8528 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: R 137 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: R 157 SER cc_start: 0.8756 (p) cc_final: 0.8498 (m) REVERT: R 187 MET cc_start: 0.7153 (tpp) cc_final: 0.6735 (tpt) REVERT: R 213 ARG cc_start: 0.6485 (tpt-90) cc_final: 0.5907 (ptm160) REVERT: R 410 LYS cc_start: 0.7337 (ptmt) cc_final: 0.7033 (pttm) outliers start: 31 outliers final: 17 residues processed: 207 average time/residue: 0.1270 time to fit residues: 34.0337 Evaluate side-chains 193 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 324 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 105 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.178656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.141171 restraints weight = 11688.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.143720 restraints weight = 8036.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146014 restraints weight = 5723.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.145923 restraints weight = 4719.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146306 restraints weight = 4670.273| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9210 Z= 0.113 Angle : 0.515 5.907 12492 Z= 0.280 Chirality : 0.041 0.156 1391 Planarity : 0.004 0.039 1595 Dihedral : 4.354 74.250 1246 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.63 % Allowed : 17.56 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.26), residues: 1126 helix: 2.11 (0.25), residues: 446 sheet: 0.15 (0.34), residues: 237 loop : -0.64 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 20 TYR 0.024 0.001 TYR R 98 PHE 0.024 0.001 PHE R 161 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9202) covalent geometry : angle 0.51479 (12478) SS BOND : bond 0.00160 ( 7) SS BOND : angle 0.76716 ( 14) hydrogen bonds : bond 0.03812 ( 437) hydrogen bonds : angle 4.38504 ( 1266) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6756 (mp0) REVERT: A 347 ARG cc_start: 0.7587 (ptp-110) cc_final: 0.7250 (ttp-170) REVERT: B 30 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7742 (tt) REVERT: B 42 ARG cc_start: 0.6324 (ttt180) cc_final: 0.5536 (ptm160) REVERT: B 59 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: B 172 GLU cc_start: 0.7632 (pt0) cc_final: 0.7265 (pt0) REVERT: B 234 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8592 (m-80) REVERT: B 266 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6904 (t70) REVERT: N 43 LYS cc_start: 0.6803 (mmmt) cc_final: 0.6599 (mmmt) REVERT: N 83 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.4863 (tpt) REVERT: R 137 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6998 (m-80) REVERT: R 157 SER cc_start: 0.8722 (p) cc_final: 0.8480 (m) REVERT: R 187 MET cc_start: 0.7087 (tpp) cc_final: 0.6735 (tpt) REVERT: R 213 ARG cc_start: 0.6626 (tpt-90) cc_final: 0.5833 (ptm160) REVERT: R 362 ARG cc_start: 0.7486 (ttt-90) cc_final: 0.7258 (ttt-90) REVERT: R 397 GLU cc_start: 0.8389 (pm20) cc_final: 0.8177 (pm20) REVERT: R 410 LYS cc_start: 0.7546 (ptmt) cc_final: 0.7162 (pttm) outliers start: 44 outliers final: 28 residues processed: 209 average time/residue: 0.1125 time to fit residues: 31.0991 Evaluate side-chains 207 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 1 LYS Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 361 TRP Chi-restraints excluded: chain R residue 367 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.177647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140247 restraints weight = 11650.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143184 restraints weight = 8021.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144820 restraints weight = 5993.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145242 restraints weight = 4751.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.145438 restraints weight = 4504.058| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9210 Z= 0.116 Angle : 0.523 8.761 12492 Z= 0.280 Chirality : 0.041 0.214 1391 Planarity : 0.003 0.038 1595 Dihedral : 4.380 75.011 1246 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.52 % Allowed : 17.88 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.26), residues: 1126 helix: 2.17 (0.25), residues: 446 sheet: 0.14 (0.34), residues: 235 loop : -0.70 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.021 0.001 TYR R 98 PHE 0.011 0.001 PHE B 199 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9202) covalent geometry : angle 0.52223 (12478) SS BOND : bond 0.00138 ( 7) SS BOND : angle 0.79203 ( 14) hydrogen bonds : bond 0.03626 ( 437) hydrogen bonds : angle 4.26155 ( 1266) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.6923 (tm-30) cc_final: 0.6662 (tm-30) REVERT: A 347 ARG cc_start: 0.7573 (ptp-110) cc_final: 0.7217 (ttp-170) REVERT: B 30 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7767 (tt) REVERT: B 59 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 172 GLU cc_start: 0.7684 (pt0) cc_final: 0.7284 (pt0) REVERT: B 234 PHE cc_start: 0.9090 (OUTLIER) cc_final: 0.8565 (m-80) REVERT: B 266 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6907 (t70) REVERT: R 137 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: R 157 SER cc_start: 0.8740 (p) cc_final: 0.8503 (m) REVERT: R 187 MET cc_start: 0.7130 (tpp) cc_final: 0.6795 (tpt) REVERT: R 213 ARG cc_start: 0.6633 (tpt-90) cc_final: 0.5880 (ptm160) REVERT: R 410 LYS cc_start: 0.7570 (ptmt) cc_final: 0.7188 (pttm) outliers start: 43 outliers final: 26 residues processed: 202 average time/residue: 0.1176 time to fit residues: 31.3773 Evaluate side-chains 194 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 75 GLN N 5 GLN R 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.171891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.133930 restraints weight = 11663.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136583 restraints weight = 8353.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138751 restraints weight = 5976.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.138777 restraints weight = 4763.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139195 restraints weight = 4928.375| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9210 Z= 0.162 Angle : 0.579 7.875 12492 Z= 0.309 Chirality : 0.043 0.164 1391 Planarity : 0.004 0.038 1595 Dihedral : 4.657 77.485 1246 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.10 % Allowed : 19.03 % Favored : 76.87 % 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: 0.71 (0.25), residues: 1126 helix: 2.05 (0.25), residues: 444 sheet: -0.23 (0.33), residues: 237 loop : -0.73 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 362 TYR 0.019 0.002 TYR R 98 PHE 0.017 0.002 PHE B 253 TRP 0.020 0.001 TRP R 79 HIS 0.009 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9202) covalent geometry : angle 0.57858 (12478) SS BOND : bond 0.00141 ( 7) SS BOND : angle 1.11447 ( 14) hydrogen bonds : bond 0.03982 ( 437) hydrogen bonds : angle 4.36267 ( 1266) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.6059 (mm) REVERT: B 30 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7805 (tt) REVERT: B 59 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: B 172 GLU cc_start: 0.7810 (pt0) cc_final: 0.7268 (pt0) REVERT: B 234 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8613 (m-80) REVERT: R 137 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: R 157 SER cc_start: 0.8763 (p) cc_final: 0.8558 (m) REVERT: R 187 MET cc_start: 0.7193 (tpp) cc_final: 0.6874 (tpt) REVERT: R 213 ARG cc_start: 0.6604 (tpt-90) cc_final: 0.5701 (ptm160) REVERT: R 359 PHE cc_start: 0.8048 (m-80) cc_final: 0.7577 (m-10) REVERT: R 410 LYS cc_start: 0.7665 (ptmt) cc_final: 0.7301 (pttm) outliers start: 39 outliers final: 31 residues processed: 196 average time/residue: 0.1241 time to fit residues: 31.8550 Evaluate side-chains 203 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 28 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 75 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.137057 restraints weight = 11608.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.139603 restraints weight = 8288.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.141522 restraints weight = 5970.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.142241 restraints weight = 4710.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.142513 restraints weight = 4520.220| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9210 Z= 0.118 Angle : 0.546 7.789 12492 Z= 0.291 Chirality : 0.042 0.161 1391 Planarity : 0.003 0.036 1595 Dihedral : 4.542 77.209 1246 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.42 % Allowed : 19.45 % Favored : 76.13 % 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: 0.79 (0.26), residues: 1126 helix: 2.08 (0.25), residues: 448 sheet: -0.13 (0.35), residues: 225 loop : -0.70 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.018 0.001 TYR R 98 PHE 0.010 0.001 PHE B 199 TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 9202) covalent geometry : angle 0.54554 (12478) SS BOND : bond 0.00154 ( 7) SS BOND : angle 0.94799 ( 14) hydrogen bonds : bond 0.03601 ( 437) hydrogen bonds : angle 4.25113 ( 1266) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6278 (OUTLIER) cc_final: 0.6011 (mm) REVERT: B 30 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7848 (tt) REVERT: B 59 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: B 172 GLU cc_start: 0.7824 (pt0) cc_final: 0.7292 (pt0) REVERT: B 234 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: R 137 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: R 157 SER cc_start: 0.8749 (p) cc_final: 0.8530 (m) REVERT: R 187 MET cc_start: 0.7211 (tpp) cc_final: 0.6908 (tpt) REVERT: R 213 ARG cc_start: 0.6612 (tpt-90) cc_final: 0.5709 (ptm160) REVERT: R 359 PHE cc_start: 0.8039 (m-80) cc_final: 0.7573 (m-10) REVERT: R 410 LYS cc_start: 0.7660 (ptmt) cc_final: 0.7300 (pttm) outliers start: 42 outliers final: 32 residues processed: 195 average time/residue: 0.1272 time to fit residues: 32.5562 Evaluate side-chains 198 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136361 restraints weight = 11611.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.139221 restraints weight = 7773.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141239 restraints weight = 5696.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141220 restraints weight = 4687.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141555 restraints weight = 4730.870| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9210 Z= 0.123 Angle : 0.550 7.458 12492 Z= 0.294 Chirality : 0.042 0.158 1391 Planarity : 0.004 0.040 1595 Dihedral : 3.925 18.022 1243 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.73 % Allowed : 19.35 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.26), residues: 1126 helix: 2.12 (0.25), residues: 448 sheet: -0.15 (0.35), residues: 225 loop : -0.73 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.017 0.001 TYR R 98 PHE 0.017 0.001 PHE N 68 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9202) covalent geometry : angle 0.54927 (12478) SS BOND : bond 0.00150 ( 7) SS BOND : angle 0.95862 ( 14) hydrogen bonds : bond 0.03534 ( 437) hydrogen bonds : angle 4.17994 ( 1266) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7895 (mtm110) REVERT: A 308 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6066 (mm) REVERT: B 6 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6023 (pm20) REVERT: B 30 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7819 (tt) REVERT: B 59 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.7628 (m-80) REVERT: B 172 GLU cc_start: 0.7827 (pt0) cc_final: 0.7294 (pt0) REVERT: B 234 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8562 (m-80) REVERT: R 137 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7323 (m-10) REVERT: R 157 SER cc_start: 0.8763 (p) cc_final: 0.8543 (m) REVERT: R 187 MET cc_start: 0.7141 (tpp) cc_final: 0.6917 (tpt) REVERT: R 359 PHE cc_start: 0.8025 (m-80) cc_final: 0.7585 (m-10) REVERT: R 410 LYS cc_start: 0.7727 (ptmt) cc_final: 0.7324 (pttm) outliers start: 45 outliers final: 33 residues processed: 192 average time/residue: 0.1302 time to fit residues: 32.3975 Evaluate side-chains 201 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.166393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127382 restraints weight = 11837.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130244 restraints weight = 8024.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132278 restraints weight = 6327.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.133880 restraints weight = 4992.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134147 restraints weight = 4599.766| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9210 Z= 0.201 Angle : 0.627 8.695 12492 Z= 0.333 Chirality : 0.045 0.157 1391 Planarity : 0.004 0.043 1595 Dihedral : 4.245 18.537 1243 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.84 % Allowed : 19.66 % Favored : 75.50 % 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: 0.49 (0.25), residues: 1126 helix: 1.94 (0.25), residues: 444 sheet: -0.44 (0.33), residues: 245 loop : -0.86 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 389 TYR 0.023 0.002 TYR N 32 PHE 0.021 0.002 PHE N 68 TRP 0.013 0.001 TRP R 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 9202) covalent geometry : angle 0.62556 (12478) SS BOND : bond 0.00233 ( 7) SS BOND : angle 1.26357 ( 14) hydrogen bonds : bond 0.04137 ( 437) hydrogen bonds : angle 4.40238 ( 1266) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 ILE cc_start: 0.6351 (OUTLIER) cc_final: 0.6081 (mm) REVERT: B 6 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6510 (pm20) REVERT: B 30 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7928 (tt) REVERT: B 59 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 172 GLU cc_start: 0.7966 (pt0) cc_final: 0.7383 (pt0) REVERT: B 234 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8582 (m-80) REVERT: R 137 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: R 187 MET cc_start: 0.7213 (tpp) cc_final: 0.6885 (tpt) REVERT: R 359 PHE cc_start: 0.8095 (m-80) cc_final: 0.7693 (m-10) REVERT: R 410 LYS cc_start: 0.7765 (ptmt) cc_final: 0.7412 (pttm) outliers start: 46 outliers final: 34 residues processed: 190 average time/residue: 0.1194 time to fit residues: 29.8000 Evaluate side-chains 199 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 1 LYS Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 397 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 6 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 408 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.168532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129780 restraints weight = 11704.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.132543 restraints weight = 7904.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.134575 restraints weight = 6057.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137927 restraints weight = 4891.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137847 restraints weight = 4155.168| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9210 Z= 0.146 Angle : 0.577 8.148 12492 Z= 0.307 Chirality : 0.043 0.158 1391 Planarity : 0.004 0.043 1595 Dihedral : 4.137 18.556 1243 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.42 % Allowed : 20.82 % Favored : 74.76 % 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: 0.54 (0.25), residues: 1126 helix: 2.04 (0.25), residues: 444 sheet: -0.50 (0.33), residues: 244 loop : -0.85 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.017 0.001 TYR R 98 PHE 0.018 0.001 PHE N 68 TRP 0.014 0.001 TRP R 118 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9202) covalent geometry : angle 0.57651 (12478) SS BOND : bond 0.00172 ( 7) SS BOND : angle 1.15665 ( 14) hydrogen bonds : bond 0.03783 ( 437) hydrogen bonds : angle 4.29973 ( 1266) Misc. bond : bond 0.00022 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7956 (mtm110) REVERT: A 308 ILE cc_start: 0.6410 (OUTLIER) cc_final: 0.6131 (mm) REVERT: B 6 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6127 (pm20) REVERT: B 30 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7964 (tt) REVERT: B 59 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: B 172 GLU cc_start: 0.7983 (pt0) cc_final: 0.7424 (pt0) REVERT: B 234 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8637 (m-80) REVERT: R 137 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: R 187 MET cc_start: 0.7254 (tpp) cc_final: 0.6950 (tpt) REVERT: R 359 PHE cc_start: 0.8100 (m-80) cc_final: 0.7767 (m-10) REVERT: R 410 LYS cc_start: 0.7713 (ptmt) cc_final: 0.7383 (pttm) outliers start: 42 outliers final: 36 residues processed: 188 average time/residue: 0.1194 time to fit residues: 29.7418 Evaluate side-chains 200 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 137 PHE Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 215 ASP Chi-restraints excluded: chain R residue 321 ARG Chi-restraints excluded: chain R residue 324 VAL Chi-restraints excluded: chain R residue 357 VAL Chi-restraints excluded: chain R residue 361 TRP Chi-restraints excluded: chain R residue 367 MET Chi-restraints excluded: chain R residue 397 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 82 optimal weight: 0.0040 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.172442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132684 restraints weight = 11678.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136014 restraints weight = 7930.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137926 restraints weight = 6063.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140464 restraints weight = 4840.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.140518 restraints weight = 4265.241| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9210 Z= 0.117 Angle : 0.561 7.260 12492 Z= 0.297 Chirality : 0.042 0.153 1391 Planarity : 0.004 0.043 1595 Dihedral : 4.026 18.475 1243 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.63 % Allowed : 20.72 % Favored : 74.66 % 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: 0.68 (0.26), residues: 1126 helix: 2.16 (0.25), residues: 446 sheet: -0.39 (0.34), residues: 230 loop : -0.82 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.017 0.001 TYR R 98 PHE 0.019 0.001 PHE R 161 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9202) covalent geometry : angle 0.55992 (12478) SS BOND : bond 0.00184 ( 7) SS BOND : angle 1.03473 ( 14) hydrogen bonds : bond 0.03513 ( 437) hydrogen bonds : angle 4.19555 ( 1266) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1597.10 seconds wall clock time: 28 minutes 25.94 seconds (1705.94 seconds total)