Starting phenix.real_space_refine on Tue Apr 29 23:00:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bue_44907/04_2025/9bue_44907.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bue_44907/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bue_44907/04_2025/9bue_44907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bue_44907/04_2025/9bue_44907.map" model { file = "/net/cci-nas-00/data/ceres_data/9bue_44907/04_2025/9bue_44907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bue_44907/04_2025/9bue_44907.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 5.73, per 1000 atoms: 0.64 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.90 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: 2.44 Time building geometry restraints manager: 2.72 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.080 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (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 TRP 0.029 0.001 TRP R 79 HIS 0.003 0.000 HIS A 357 PHE 0.015 0.001 PHE R 119 TYR 0.024 0.001 TYR R 98 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.25458 ( 437) hydrogen bonds : angle 7.34970 ( 1266) SS BOND : bond 0.00145 ( 7) SS BOND : angle 0.77992 ( 14) covalent geometry : bond 0.00289 ( 9202) covalent geometry : angle 0.57339 (12478) 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 : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7282 (ttp-110) REVERT: B 42 ARG cc_start: 0.6199 (ttt180) cc_final: 0.5566 (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: 0.6945 (tpt) REVERT: R 213 ARG cc_start: 0.6404 (tpt-90) cc_final: 0.5767 (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: 0.7625 (tm-30) REVERT: R 410 LYS cc_start: 0.6817 (ptmt) cc_final: 0.6533 (pttm) outliers start: 4 outliers final: 4 residues processed: 194 average time/residue: 0.2912 time to fit residues: 72.0140 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 : 0.934 ------------------------------------------------------------------------------- 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 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.0010 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.0970 chunk 100 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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** R 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145512 restraints weight = 11365.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149012 restraints weight = 8040.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.151358 restraints weight = 5931.105| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9210 Z= 0.122 Angle : 0.527 5.919 12492 Z= 0.291 Chirality : 0.041 0.185 1391 Planarity : 0.004 0.063 1595 Dihedral : 4.563 67.277 1253 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.84 % Allowed : 16.93 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1126 helix: 1.80 (0.25), residues: 440 sheet: 0.35 (0.34), residues: 231 loop : -0.49 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 169 HIS 0.004 0.001 HIS R 223 PHE 0.022 0.001 PHE R 161 TYR 0.021 0.001 TYR R 98 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 437) hydrogen bonds : angle 4.91291 ( 1266) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.61693 ( 14) covalent geometry : bond 0.00248 ( 9202) covalent geometry : angle 0.52648 (12478) Misc. bond : bond 0.00078 ( 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: 27 poor density : 195 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: A 17 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8378 (mttm) REVERT: A 333 ARG cc_start: 0.7834 (tpt170) cc_final: 0.7382 (tpt170) REVERT: B 6 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6535 (pp30) REVERT: B 30 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7780 (tt) REVERT: B 42 ARG cc_start: 0.6163 (ttt180) cc_final: 0.5489 (ptm160) REVERT: B 210 LEU cc_start: 0.8448 (tp) cc_final: 0.8202 (tp) REVERT: G 50 LEU cc_start: 0.8648 (mt) cc_final: 0.8447 (mp) REVERT: R 137 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.6804 (m-10) REVERT: R 157 SER cc_start: 0.8854 (p) cc_final: 0.8496 (m) REVERT: R 187 MET cc_start: 0.7201 (tpp) cc_final: 0.6675 (tpt) REVERT: R 213 ARG cc_start: 0.6513 (tpt-90) cc_final: 0.5811 (ptm160) REVERT: R 276 ILE cc_start: 0.7741 (mm) cc_final: 0.7526 (mt) REVERT: R 397 GLU cc_start: 0.8401 (pm20) cc_final: 0.8128 (pm20) REVERT: R 410 LYS cc_start: 0.7313 (ptmt) cc_final: 0.6982 (pttm) outliers start: 27 outliers final: 15 residues processed: 212 average time/residue: 0.2717 time to fit residues: 74.7083 Evaluate side-chains 196 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 30 LEU 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 G residue 54 VAL Chi-restraints excluded: chain N residue 60 TYR 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 93 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 100 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 84 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.143392 restraints weight = 11553.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.146944 restraints weight = 8273.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.149417 restraints weight = 6082.729| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9210 Z= 0.108 Angle : 0.497 5.992 12492 Z= 0.272 Chirality : 0.041 0.161 1391 Planarity : 0.004 0.042 1595 Dihedral : 4.209 73.606 1246 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.68 % Allowed : 17.25 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1126 helix: 2.04 (0.25), residues: 445 sheet: 0.31 (0.34), residues: 228 loop : -0.48 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE B 199 TYR 0.025 0.001 TYR R 98 ARG 0.006 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 437) hydrogen bonds : angle 4.49138 ( 1266) SS BOND : bond 0.00214 ( 7) SS BOND : angle 0.58670 ( 14) covalent geometry : bond 0.00226 ( 9202) covalent geometry : angle 0.49682 (12478) Misc. bond : bond 0.00005 ( 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 225 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: A 314 GLU cc_start: 0.7026 (tm-30) cc_final: 0.6801 (tm-30) REVERT: B 42 ARG cc_start: 0.6210 (ttt180) cc_final: 0.5515 (ptm160) REVERT: B 234 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: G 9 ILE cc_start: 0.7291 (pt) cc_final: 0.6990 (tt) REVERT: R 137 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.6675 (m-10) REVERT: R 157 SER cc_start: 0.8796 (p) cc_final: 0.8561 (m) REVERT: R 187 MET cc_start: 0.7141 (tpp) cc_final: 0.6647 (tpt) REVERT: R 196 MET cc_start: 0.7745 (mtt) cc_final: 0.7506 (mtp) REVERT: R 213 ARG cc_start: 0.6546 (tpt-90) cc_final: 0.5822 (ptm160) REVERT: R 276 ILE cc_start: 0.7777 (mm) cc_final: 0.7536 (mt) REVERT: R 410 LYS cc_start: 0.7414 (ptmt) cc_final: 0.7065 (pttm) outliers start: 35 outliers final: 23 residues processed: 212 average time/residue: 0.2670 time to fit residues: 73.8665 Evaluate side-chains 205 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 214 VAL 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 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 173 THR 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 325 MET 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 107 CYS Chi-restraints excluded: chain N residue 122 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 324 VAL Chi-restraints excluded: chain R residue 361 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.0270 chunk 54 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.181236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141497 restraints weight = 11489.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144976 restraints weight = 8501.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146991 restraints weight = 6289.110| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9210 Z= 0.111 Angle : 0.505 5.895 12492 Z= 0.271 Chirality : 0.041 0.152 1391 Planarity : 0.003 0.039 1595 Dihedral : 4.243 74.183 1246 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.42 % Allowed : 17.14 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1126 helix: 2.16 (0.25), residues: 446 sheet: 0.17 (0.34), residues: 235 loop : -0.54 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.025 0.001 PHE R 161 TYR 0.026 0.001 TYR R 98 ARG 0.004 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 437) hydrogen bonds : angle 4.28248 ( 1266) SS BOND : bond 0.00163 ( 7) SS BOND : angle 0.66878 ( 14) covalent geometry : bond 0.00244 ( 9202) covalent geometry : angle 0.50467 (12478) Misc. bond : bond 0.00007 ( 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: 42 poor density : 182 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: A 314 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6713 (tm-30) REVERT: A 347 ARG cc_start: 0.7645 (ptp-110) cc_final: 0.7273 (ttp-170) REVERT: B 42 ARG cc_start: 0.6253 (ttt180) cc_final: 0.5491 (ptm160) REVERT: B 59 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: B 234 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8622 (m-80) REVERT: R 137 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6684 (m-10) REVERT: R 157 SER cc_start: 0.8773 (p) cc_final: 0.8535 (m) REVERT: R 187 MET cc_start: 0.7082 (tpp) cc_final: 0.6728 (tpt) REVERT: R 213 ARG cc_start: 0.6590 (tpt-90) cc_final: 0.5800 (ptm160) REVERT: R 397 GLU cc_start: 0.8369 (pm20) cc_final: 0.8131 (pm20) REVERT: R 410 LYS cc_start: 0.7485 (ptmt) cc_final: 0.7112 (pttm) outliers start: 42 outliers final: 31 residues processed: 208 average time/residue: 0.2555 time to fit residues: 69.0437 Evaluate side-chains 209 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 218 ASN 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 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU 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 160 SER 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 325 MET Chi-restraints excluded: chain B residue 327 VAL 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 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 Chi-restraints excluded: chain R residue 361 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.173797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.134809 restraints weight = 11512.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138437 restraints weight = 7936.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.140603 restraints weight = 5988.587| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9210 Z= 0.151 Angle : 0.556 7.313 12492 Z= 0.296 Chirality : 0.042 0.148 1391 Planarity : 0.004 0.038 1595 Dihedral : 4.449 75.613 1246 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.73 % Allowed : 16.61 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1126 helix: 2.06 (0.25), residues: 447 sheet: -0.05 (0.33), residues: 237 loop : -0.72 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE B 253 TYR 0.024 0.002 TYR R 98 ARG 0.004 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 437) hydrogen bonds : angle 4.25008 ( 1266) SS BOND : bond 0.00161 ( 7) SS BOND : angle 0.90946 ( 14) covalent geometry : bond 0.00354 ( 9202) covalent geometry : angle 0.55531 (12478) Misc. bond : bond 0.00018 ( 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 218 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 314 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 347 ARG cc_start: 0.7587 (ptp-110) cc_final: 0.7249 (ttp-170) REVERT: B 30 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7809 (tt) REVERT: B 59 TYR cc_start: 0.8427 (OUTLIER) cc_final: 0.7504 (m-10) REVERT: B 172 GLU cc_start: 0.7483 (pt0) cc_final: 0.7174 (pt0) REVERT: B 234 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.8642 (m-80) REVERT: B 266 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6888 (t70) REVERT: R 137 PHE cc_start: 0.7602 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: R 157 SER cc_start: 0.8789 (p) cc_final: 0.8531 (m) REVERT: R 187 MET cc_start: 0.7110 (tpp) cc_final: 0.6780 (tpt) REVERT: R 213 ARG cc_start: 0.6588 (tpt-90) cc_final: 0.5924 (ptm160) REVERT: R 346 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6589 (mtp) REVERT: R 410 LYS cc_start: 0.7551 (ptmt) cc_final: 0.7206 (pttm) outliers start: 45 outliers final: 30 residues processed: 199 average time/residue: 0.2709 time to fit residues: 70.9844 Evaluate side-chains 202 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 218 ASN 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 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER 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 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 346 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.0470 chunk 50 optimal weight: 3.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- 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 B 75 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.134717 restraints weight = 11522.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138381 restraints weight = 7848.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140246 restraints weight = 5915.731| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9210 Z= 0.144 Angle : 0.548 6.434 12492 Z= 0.292 Chirality : 0.042 0.147 1391 Planarity : 0.004 0.037 1595 Dihedral : 4.502 76.063 1246 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.15 % Allowed : 17.35 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1126 helix: 2.06 (0.25), residues: 447 sheet: -0.17 (0.33), residues: 237 loop : -0.74 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.016 0.001 PHE N 68 TYR 0.022 0.001 TYR R 98 ARG 0.006 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 437) hydrogen bonds : angle 4.20289 ( 1266) SS BOND : bond 0.00152 ( 7) SS BOND : angle 0.94488 ( 14) covalent geometry : bond 0.00336 ( 9202) covalent geometry : angle 0.54761 (12478) Misc. bond : bond 0.00023 ( 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 221 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: A 308 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.6078 (mm) REVERT: B 30 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7804 (tt) REVERT: B 59 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7563 (m-10) REVERT: B 172 GLU cc_start: 0.7612 (pt0) cc_final: 0.7224 (pt0) REVERT: B 190 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8532 (pt) REVERT: B 234 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: R 137 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7101 (m-10) REVERT: R 157 SER cc_start: 0.8754 (p) cc_final: 0.8550 (m) REVERT: R 187 MET cc_start: 0.7161 (tpp) cc_final: 0.6823 (tpt) REVERT: R 213 ARG cc_start: 0.6652 (tpt-90) cc_final: 0.5882 (ptm160) REVERT: R 410 LYS cc_start: 0.7606 (ptmt) cc_final: 0.7235 (pttm) outliers start: 49 outliers final: 35 residues processed: 203 average time/residue: 0.2603 time to fit residues: 69.5231 Evaluate side-chains 208 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 218 ASN 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 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU 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 160 SER Chi-restraints excluded: chain B residue 190 LEU 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 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 99 CYS Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 4 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 346 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 1.9990 chunk 18 optimal weight: 0.0370 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.174428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135251 restraints weight = 11761.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138123 restraints weight = 8111.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140423 restraints weight = 6373.034| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2830 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= 0.127 Angle : 0.545 6.760 12492 Z= 0.291 Chirality : 0.042 0.163 1391 Planarity : 0.004 0.039 1595 Dihedral : 4.501 76.806 1246 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 5.15 % Allowed : 17.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1126 helix: 2.10 (0.25), residues: 447 sheet: -0.21 (0.34), residues: 237 loop : -0.75 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE N 68 TYR 0.020 0.001 TYR R 98 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 437) hydrogen bonds : angle 4.17824 ( 1266) SS BOND : bond 0.00155 ( 7) SS BOND : angle 0.96480 ( 14) covalent geometry : bond 0.00294 ( 9202) covalent geometry : angle 0.54475 (12478) Misc. bond : bond 0.00011 ( 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 219 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 170 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: A 308 ILE cc_start: 0.6299 (OUTLIER) cc_final: 0.6065 (mm) REVERT: B 30 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 59 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 172 GLU cc_start: 0.7724 (pt0) cc_final: 0.7278 (pt0) REVERT: B 190 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8591 (pt) REVERT: B 234 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8646 (m-80) REVERT: R 137 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7107 (m-10) REVERT: R 157 SER cc_start: 0.8788 (p) cc_final: 0.8561 (m) REVERT: R 187 MET cc_start: 0.7197 (tpp) cc_final: 0.6908 (tpt) REVERT: R 213 ARG cc_start: 0.6734 (tpt-90) cc_final: 0.6075 (mmm160) REVERT: R 397 GLU cc_start: 0.8359 (pm20) cc_final: 0.8150 (pm20) REVERT: R 410 LYS cc_start: 0.7632 (ptmt) cc_final: 0.7282 (pttm) outliers start: 49 outliers final: 35 residues processed: 202 average time/residue: 0.2500 time to fit residues: 66.9777 Evaluate side-chains 208 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 218 ASN 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 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 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU 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 190 LEU 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 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 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 361 TRP 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: 5.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4050 r_free = 0.4050 target = 0.173156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134644 restraints weight = 11719.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138508 restraints weight = 7809.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140528 restraints weight = 5536.524| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9210 Z= 0.128 Angle : 0.545 6.849 12492 Z= 0.289 Chirality : 0.042 0.159 1391 Planarity : 0.004 0.036 1595 Dihedral : 3.893 18.328 1243 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 5.26 % Allowed : 18.30 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.26), residues: 1126 helix: 2.09 (0.25), residues: 448 sheet: -0.27 (0.34), residues: 237 loop : -0.75 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.032 0.001 PHE R 161 TYR 0.021 0.001 TYR R 98 ARG 0.006 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 437) hydrogen bonds : angle 4.11794 ( 1266) SS BOND : bond 0.00154 ( 7) SS BOND : angle 0.97584 ( 14) covalent geometry : bond 0.00296 ( 9202) covalent geometry : angle 0.54415 (12478) Misc. bond : bond 0.00019 ( 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 216 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: A 308 ILE cc_start: 0.6291 (OUTLIER) cc_final: 0.6057 (mm) REVERT: B 6 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6245 (pm20) REVERT: B 30 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7822 (tt) REVERT: B 59 TYR cc_start: 0.8439 (OUTLIER) cc_final: 0.7595 (m-10) REVERT: B 172 GLU cc_start: 0.7734 (pt0) cc_final: 0.7261 (pt0) REVERT: B 190 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8597 (pt) REVERT: B 234 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: R 137 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7218 (m-10) REVERT: R 157 SER cc_start: 0.8790 (p) cc_final: 0.8560 (m) REVERT: R 187 MET cc_start: 0.7206 (tpp) cc_final: 0.6909 (tpt) REVERT: R 213 ARG cc_start: 0.6589 (tpt-90) cc_final: 0.5982 (mmm160) REVERT: R 359 PHE cc_start: 0.7905 (m-10) cc_final: 0.7557 (m-10) REVERT: R 397 GLU cc_start: 0.8360 (pm20) cc_final: 0.8147 (pm20) REVERT: R 410 LYS cc_start: 0.7674 (ptmt) cc_final: 0.7331 (pttm) outliers start: 50 outliers final: 40 residues processed: 196 average time/residue: 0.2539 time to fit residues: 67.0004 Evaluate side-chains 210 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 218 ASN 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 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 69 LEU 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 190 LEU 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 46 LYS 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 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 165 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 361 TRP 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 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.0020 chunk 80 optimal weight: 2.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.178108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140733 restraints weight = 11714.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143545 restraints weight = 8202.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145146 restraints weight = 6110.965| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9210 Z= 0.111 Angle : 0.533 8.305 12492 Z= 0.284 Chirality : 0.041 0.157 1391 Planarity : 0.004 0.038 1595 Dihedral : 3.844 18.048 1243 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.26 % Allowed : 18.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1126 helix: 2.15 (0.25), residues: 448 sheet: -0.18 (0.34), residues: 235 loop : -0.70 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 79 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.001 PHE N 68 TYR 0.021 0.001 TYR R 98 ARG 0.009 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03397 ( 437) hydrogen bonds : angle 4.06937 ( 1266) SS BOND : bond 0.00169 ( 7) SS BOND : angle 0.92945 ( 14) covalent geometry : bond 0.00246 ( 9202) covalent geometry : angle 0.53242 (12478) Misc. bond : bond 0.00012 ( 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 216 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 166 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: A 20 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7846 (mtm110) REVERT: A 308 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6078 (mm) REVERT: B 6 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6218 (pm20) REVERT: B 30 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7718 (tt) REVERT: B 59 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7548 (m-10) REVERT: B 172 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7275 (pt0) REVERT: B 190 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8604 (pt) REVERT: B 234 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8619 (m-80) REVERT: R 137 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: R 157 SER cc_start: 0.8791 (p) cc_final: 0.8563 (m) REVERT: R 187 MET cc_start: 0.7170 (tpp) cc_final: 0.6909 (tpt) REVERT: R 213 ARG cc_start: 0.6673 (tpt-90) cc_final: 0.6040 (mmm160) REVERT: R 359 PHE cc_start: 0.7887 (m-10) cc_final: 0.7505 (m-10) REVERT: R 410 LYS cc_start: 0.7713 (ptmt) cc_final: 0.7361 (pttm) outliers start: 50 outliers final: 34 residues processed: 197 average time/residue: 0.2697 time to fit residues: 70.8828 Evaluate side-chains 207 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 218 ASN 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 69 LEU 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 172 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU 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 5 GLN 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 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 324 VAL Chi-restraints excluded: chain R residue 361 TRP Chi-restraints excluded: chain R residue 367 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN R 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140222 restraints weight = 11788.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.142625 restraints weight = 8044.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144900 restraints weight = 5874.226| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 9210 Z= 0.202 Angle : 0.910 59.198 12492 Z= 0.529 Chirality : 0.042 0.205 1391 Planarity : 0.005 0.116 1595 Dihedral : 3.836 18.070 1243 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 5.05 % Allowed : 19.45 % Favored : 75.50 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1126 helix: 2.16 (0.25), residues: 448 sheet: -0.15 (0.34), residues: 235 loop : -0.71 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 79 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE A 222 TYR 0.020 0.001 TYR R 98 ARG 0.010 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 437) hydrogen bonds : angle 4.06567 ( 1266) SS BOND : bond 0.00164 ( 7) SS BOND : angle 0.92913 ( 14) covalent geometry : bond 0.00399 ( 9202) covalent geometry : angle 0.90976 (12478) Misc. bond : bond 0.00014 ( 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 212 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: A 20 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7844 (mtm110) REVERT: A 308 ILE cc_start: 0.6330 (OUTLIER) cc_final: 0.6076 (mm) REVERT: B 30 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7730 (tt) REVERT: B 59 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7545 (m-10) REVERT: B 172 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7262 (pt0) REVERT: B 190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8607 (pt) REVERT: B 234 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8620 (m-80) REVERT: R 137 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7005 (m-10) REVERT: R 157 SER cc_start: 0.8795 (p) cc_final: 0.8571 (m) REVERT: R 187 MET cc_start: 0.7185 (tpp) cc_final: 0.6918 (tpt) REVERT: R 213 ARG cc_start: 0.6672 (tpt-90) cc_final: 0.5732 (ptm160) REVERT: R 359 PHE cc_start: 0.7874 (m-10) cc_final: 0.7492 (m-10) REVERT: R 410 LYS cc_start: 0.7716 (ptmt) cc_final: 0.7361 (pttm) outliers start: 48 outliers final: 37 residues processed: 195 average time/residue: 0.2919 time to fit residues: 75.1980 Evaluate side-chains 207 residues out of total 1001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 218 ASN 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 30 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 69 LEU 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 172 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 190 LEU 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 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 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 361 TRP Chi-restraints excluded: chain R residue 367 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** 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 = 0.4071 r_free = 0.4071 target = 0.175254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.138432 restraints weight = 11608.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.141684 restraints weight = 8019.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143173 restraints weight = 5820.785| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 9210 Z= 0.202 Angle : 0.910 59.198 12492 Z= 0.529 Chirality : 0.042 0.205 1391 Planarity : 0.005 0.116 1595 Dihedral : 3.836 18.070 1243 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.84 % Allowed : 19.56 % Favored : 75.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1126 helix: 2.16 (0.25), residues: 448 sheet: -0.15 (0.34), residues: 235 loop : -0.71 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 79 HIS 0.004 0.001 HIS A 220 PHE 0.012 0.001 PHE A 222 TYR 0.020 0.001 TYR R 98 ARG 0.010 0.000 ARG R 328 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 437) hydrogen bonds : angle 4.06567 ( 1266) SS BOND : bond 0.00164 ( 7) SS BOND : angle 0.92913 ( 14) covalent geometry : bond 0.00399 ( 9202) covalent geometry : angle 0.90976 (12478) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3540.65 seconds wall clock time: 63 minutes 40.78 seconds (3820.78 seconds total)