Starting phenix.real_space_refine on Thu Jul 2 19:42:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.map" model { file = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2026/7arh_11882.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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 50 5.16 5 C 6159 2.51 5 N 1692 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9649 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1671 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 8, 'TRANS': 216} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1721 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 216} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'Z41': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.77, per 1000 atoms: 0.18 Number of scatterers: 9649 At special positions: 0 Unit cell: (85.176, 90.246, 154.128, 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 50 16.00 O 1748 8.00 N 1692 7.00 C 6159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 340.5 milliseconds 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 8 sheets defined 41.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 8 through 12 removed outlier: 3.870A pdb=" N LEU C 11 " --> pdb=" O PHE C 8 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG C 12 " --> pdb=" O ILE C 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 8 through 12' Processing helix chain 'C' and resid 22 through 28 removed outlier: 4.013A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 59 removed outlier: 3.767A pdb=" N ILE C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET C 48 " --> pdb=" O VAL C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.652A pdb=" N ASP C 136 " --> pdb=" O LYS C 133 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 133 through 137' Processing helix chain 'C' and resid 148 through 155 removed outlier: 3.919A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.804A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.048A pdb=" N ASP C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 252 " --> pdb=" O TRP C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 252' Processing helix chain 'C' and resid 256 through 271 removed outlier: 3.650A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C 266 " --> pdb=" O MET C 262 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 292 removed outlier: 3.690A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C 284 " --> pdb=" O PHE C 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.765A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.506A pdb=" N MET C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 339 removed outlier: 3.618A pdb=" N VAL C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 removed outlier: 3.709A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.695A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.727A pdb=" N ILE E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 59 removed outlier: 3.697A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 87 removed outlier: 3.725A pdb=" N HIS E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.766A pdb=" N PHE E 132 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 133' Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 239 through 243 removed outlier: 3.529A pdb=" N GLY E 242 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 243 " --> pdb=" O ASP E 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 243' Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 260 through 270 removed outlier: 3.663A pdb=" N ILE E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E 269 " --> pdb=" O ILE E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 removed outlier: 3.676A pdb=" N VAL E 277 " --> pdb=" O TYR E 273 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 292 Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.785A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP E 297 " --> pdb=" O MET E 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 292 through 297' Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.814A pdb=" N ILE E 302 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 317 removed outlier: 3.540A pdb=" N ILE E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 341 removed outlier: 3.571A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY E 327 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 357 removed outlier: 3.763A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E 355 " --> pdb=" O TRP E 351 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY E 357 " --> pdb=" O GLU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 395 removed outlier: 3.756A pdb=" N VAL E 380 " --> pdb=" O HIS E 376 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 403 removed outlier: 3.519A pdb=" N ALA E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 removed outlier: 3.570A pdb=" N LEU F 54 " --> pdb=" O THR F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 removed outlier: 4.283A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 83 through 88' Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.940A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.796A pdb=" N GLY F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 125 removed outlier: 4.331A pdb=" N ASN F 123 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER F 124 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG F 125 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 removed outlier: 3.800A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 removed outlier: 3.631A pdb=" N ALA F 139 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.537A pdb=" N GLU F 145 " --> pdb=" O ARG F 142 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU F 146 " --> pdb=" O PRO F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 146' Processing helix chain 'F' and resid 147 through 152 removed outlier: 4.017A pdb=" N ARG F 151 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 147 through 152' Processing helix chain 'F' and resid 182 through 195 removed outlier: 3.609A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU F 190 " --> pdb=" O GLN F 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.726A pdb=" N LYS F 210 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET F 212 " --> pdb=" O ALA F 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 207 through 212' Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.941A pdb=" N LEU D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 79 through 88 removed outlier: 3.994A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.969A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.712A pdb=" N ILE D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 115' Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.825A pdb=" N ALA D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.959A pdb=" N LEU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.564A pdb=" N GLU D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.530A pdb=" N ARG D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 182 removed outlier: 3.831A pdb=" N ASP D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'D' and resid 190 through 195 removed outlier: 3.572A pdb=" N LEU D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 90 through 96 removed outlier: 4.872A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP C 225 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TRP C 222 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 224 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.835A pdb=" N GLY C 112 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N MET C 201 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 115 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLU C 200 " --> pdb=" O GLY C 147 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY C 147 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU C 146 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG C 182 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 103 through 104 removed outlier: 3.553A pdb=" N LEU E 103 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE E 168 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE E 148 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU E 193 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE E 150 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 149 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LYS E 116 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 115 " --> pdb=" O PHE E 100 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS E 227 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA E 94 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA E 225 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLY E 223 " --> pdb=" O PRO E 96 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 252 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.572A pdb=" N LEU F 6 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AA6, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.722A pdb=" N GLY F 90 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ASP F 170 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N MET F 38 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL F 201 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET F 37 " --> pdb=" O ARG F 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 31 through 32 removed outlier: 3.931A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 89 through 92 removed outlier: 5.686A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ASP D 170 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE D 92 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 200 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N MET D 38 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N THR D 203 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N MET D 37 " --> pdb=" O ARG D 214 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.10 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: 3165 1.34 - 1.46: 1139 1.46 - 1.57: 5407 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9804 Sorted by residual: bond pdb=" C19 Z41 C 401 " pdb=" O3 Z41 C 401 " ideal model delta sigma weight residual 1.333 1.456 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C16 Z41 C 401 " pdb=" O2 Z41 C 401 " ideal model delta sigma weight residual 1.332 1.453 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C1 PLM V 201 " pdb=" C2 PLM V 201 " ideal model delta sigma weight residual 1.542 1.510 0.032 2.00e-02 2.50e+03 2.50e+00 bond pdb=" C1 PLM V 201 " pdb=" O2 PLM V 201 " ideal model delta sigma weight residual 1.249 1.220 0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" N THR D 62 " pdb=" CA THR D 62 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.78e+00 ... (remaining 9799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12949 2.02 - 4.04: 232 4.04 - 6.06: 62 6.06 - 8.08: 14 8.08 - 10.10: 5 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C PRO D 61 " pdb=" N THR D 62 " pdb=" CA THR D 62 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C VAL C 130 " pdb=" N ASN C 131 " pdb=" CA ASN C 131 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C20 Z41 C 401 " pdb=" C19 Z41 C 401 " pdb=" O3 Z41 C 401 " ideal model delta sigma weight residual 110.49 120.47 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CA LEU E 129 " pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 118.44 123.05 -4.61 1.59e+00 3.96e-01 8.42e+00 angle pdb=" CA LEU D 206 " pdb=" CB LEU D 206 " pdb=" CG LEU D 206 " ideal model delta sigma weight residual 116.30 126.40 -10.10 3.50e+00 8.16e-02 8.33e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5490 17.79 - 35.57: 386 35.57 - 53.35: 60 53.35 - 71.14: 5 71.14 - 88.92: 8 Dihedral angle restraints: 5949 sinusoidal: 2364 harmonic: 3585 Sorted by residual: dihedral pdb=" CA GLN D 16 " pdb=" C GLN D 16 " pdb=" N GLU D 17 " pdb=" CA GLU D 17 " ideal model delta harmonic sigma weight residual 180.00 -158.35 -21.65 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CB GLU D 171 " pdb=" CG GLU D 171 " pdb=" CD GLU D 171 " pdb=" OE1 GLU D 171 " ideal model delta sinusoidal sigma weight residual 0.00 -88.92 88.92 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA SER D 19 " pdb=" C SER D 19 " pdb=" N VAL D 20 " pdb=" CA VAL D 20 " ideal model delta harmonic sigma weight residual 180.00 164.02 15.98 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 986 0.036 - 0.072: 393 0.072 - 0.109: 123 0.109 - 0.145: 45 0.145 - 0.181: 6 Chirality restraints: 1553 Sorted by residual: chirality pdb=" CA THR D 62 " pdb=" N THR D 62 " pdb=" C THR D 62 " pdb=" CB THR D 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.20e-01 chirality pdb=" CA THR E 346 " pdb=" N THR E 346 " pdb=" C THR E 346 " pdb=" CB THR E 346 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA THR C 126 " pdb=" N THR C 126 " pdb=" C THR C 126 " pdb=" CB THR C 126 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1550 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.038 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO E 347 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 126 " -0.035 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 127 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 127 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 127 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 61 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.55e+00 pdb=" C PRO D 61 " 0.033 2.00e-02 2.50e+03 pdb=" O PRO D 61 " -0.012 2.00e-02 2.50e+03 pdb=" N THR D 62 " -0.011 2.00e-02 2.50e+03 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3082 2.84 - 3.35: 7579 3.35 - 3.87: 14815 3.87 - 4.38: 16653 4.38 - 4.90: 28912 Nonbonded interactions: 71041 Sorted by model distance: nonbonded pdb=" O CYS F 12 " pdb=" OG SER F 63 " model vdw 2.324 3.040 nonbonded pdb=" O ASP C 123 " pdb=" OG1 THR C 126 " model vdw 2.340 3.040 nonbonded pdb=" O CYS D 12 " pdb=" OG SER D 63 " model vdw 2.368 3.040 nonbonded pdb=" O ALA F 120 " pdb=" OG SER F 124 " model vdw 2.376 3.040 nonbonded pdb=" O TYR E 382 " pdb=" OG1 THR E 386 " model vdw 2.382 3.040 ... (remaining 71036 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 3 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 or (resid 16 and (name N or name CA or name \ C or name O or name CB )) or resid 17 through 18 or (resid 19 through 21 and (n \ ame N or name CA or name C or name O or name CB )) or resid 22 or (resid 23 and \ (name N or name CA or name C or name O or name CB )) or resid 24 through 30 or ( \ resid 31 and (name N or name CA or name C or name O or name CB )) or resid 32 th \ rough 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) o \ r resid 37 through 54 or (resid 55 and (name N or name CA or name C or name O or \ name CB )) or resid 56 through 64 or (resid 65 and (name N or name CA or name C \ or name O or name CB )) or resid 66 through 170 or (resid 171 and (name N or na \ me CA or name C or name O or name CB )) or resid 172 through 176 or (resid 177 t \ hrough 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ through 193 or (resid 194 and (name N or name CA or name C or name O or name CB \ )) or resid 195 through 227)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 0.123 9806 Z= 0.191 Angle : 0.724 10.104 13262 Z= 0.357 Chirality : 0.046 0.181 1553 Planarity : 0.005 0.057 1698 Dihedral : 12.261 88.925 3641 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.20 % Allowed : 6.95 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.69 (0.16), residues: 1249 helix: -5.09 (0.05), residues: 447 sheet: -1.64 (0.42), residues: 132 loop : -3.33 (0.17), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 179 TYR 0.007 0.001 TYR C 199 PHE 0.010 0.001 PHE F 199 TRP 0.003 0.000 TRP E 138 HIS 0.003 0.000 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 9804) covalent geometry : angle 0.72398 / 0.36 (13262) hydrogen bonds : bond 0.36175 / 22.95 ( 249) hydrogen bonds : angle 11.14586 / 7.94 ( 714) Misc. bond : bond 0.07057 / 3.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 360 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 TYR cc_start: 0.8222 (m-10) cc_final: 0.8012 (m-80) REVERT: C 157 ASN cc_start: 0.8380 (t0) cc_final: 0.8044 (t0) REVERT: C 175 MET cc_start: 0.4499 (ppp) cc_final: 0.4133 (ppp) REVERT: C 195 GLU cc_start: 0.8358 (pp20) cc_final: 0.7944 (pp20) REVERT: C 292 GLU cc_start: 0.7886 (pp20) cc_final: 0.7468 (pp20) REVERT: C 293 LYS cc_start: 0.7197 (mttm) cc_final: 0.6946 (mttm) REVERT: C 312 MET cc_start: 0.7471 (ttt) cc_final: 0.7073 (ttp) REVERT: E 11 LEU cc_start: 0.6280 (mp) cc_final: 0.5698 (tt) REVERT: F 142 ARG cc_start: 0.7755 (tpp80) cc_final: 0.7514 (tpp80) REVERT: D 30 PHE cc_start: 0.7834 (t80) cc_final: 0.7492 (t80) REVERT: D 94 GLN cc_start: 0.7184 (pt0) cc_final: 0.6910 (pt0) REVERT: D 137 HIS cc_start: 0.8051 (p90) cc_final: 0.7721 (p-80) outliers start: 2 outliers final: 0 residues processed: 361 average time/residue: 0.0939 time to fit residues: 45.5841 Evaluate side-chains 239 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 79 GLN C 131 ASN C 204 ASN C 339 GLN E 174 ASN F 53 HIS F 96 HIS F 152 GLN D 10 ASN D 97 HIS D 152 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.157967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.119341 restraints weight = 16499.530| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.02 r_work: 0.3505 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9806 Z= 0.118 Angle : 0.579 8.004 13262 Z= 0.289 Chirality : 0.042 0.149 1553 Planarity : 0.005 0.046 1698 Dihedral : 4.344 52.420 1388 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.84 % Allowed : 17.03 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.18), residues: 1249 helix: -3.30 (0.16), residues: 445 sheet: -1.12 (0.43), residues: 142 loop : -2.80 (0.19), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 250 TYR 0.009 0.001 TYR E 258 PHE 0.009 0.001 PHE C 25 TRP 0.022 0.001 TRP C 246 HIS 0.007 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9804) covalent geometry : angle 0.57899 / 0.29 (13262) hydrogen bonds : bond 0.04260 / 2.76 ( 249) hydrogen bonds : angle 5.68578 / 4.05 ( 714) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 PHE cc_start: 0.7906 (t80) cc_final: 0.7637 (m-80) REVERT: C 195 GLU cc_start: 0.8683 (pp20) cc_final: 0.8177 (pp20) REVERT: C 292 GLU cc_start: 0.8691 (pp20) cc_final: 0.8351 (pp20) REVERT: C 293 LYS cc_start: 0.8124 (mttm) cc_final: 0.7822 (mttp) REVERT: C 312 MET cc_start: 0.8454 (ttt) cc_final: 0.7986 (ttm) REVERT: E 11 LEU cc_start: 0.6755 (mp) cc_final: 0.5765 (tt) REVERT: E 194 GLN cc_start: 0.8425 (tt0) cc_final: 0.8213 (mt0) REVERT: E 203 PHE cc_start: 0.7641 (t80) cc_final: 0.7254 (t80) REVERT: F 131 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8854 (mtmm) REVERT: F 219 ARG cc_start: 0.7306 (mmm160) cc_final: 0.7020 (ttp-110) REVERT: D 9 ASP cc_start: 0.8529 (p0) cc_final: 0.7903 (t0) REVERT: D 30 PHE cc_start: 0.8197 (t80) cc_final: 0.7865 (t80) REVERT: D 137 HIS cc_start: 0.8335 (p90) cc_final: 0.7897 (p-80) REVERT: D 179 ARG cc_start: 0.8377 (tpt90) cc_final: 0.8028 (tpt90) REVERT: D 206 LEU cc_start: 0.8625 (tp) cc_final: 0.8395 (tt) REVERT: D 212 MET cc_start: 0.7741 (tpp) cc_final: 0.6857 (tpp) REVERT: D 220 ASP cc_start: 0.8213 (t0) cc_final: 0.7970 (m-30) outliers start: 29 outliers final: 19 residues processed: 278 average time/residue: 0.0819 time to fit residues: 31.4692 Evaluate side-chains 241 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 68 optimal weight: 0.0870 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.1980 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 247 GLN C 301 GLN C 317 GLN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 HIS F 195 GLN D 137 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.147032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102939 restraints weight = 16419.178| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.16 r_work: 0.3286 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9806 Z= 0.150 Angle : 0.622 8.922 13262 Z= 0.306 Chirality : 0.042 0.139 1553 Planarity : 0.004 0.038 1698 Dihedral : 5.104 57.001 1388 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.40 % Allowed : 18.00 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.21), residues: 1249 helix: -1.74 (0.23), residues: 441 sheet: -1.21 (0.43), residues: 148 loop : -2.31 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 125 TYR 0.014 0.001 TYR E 258 PHE 0.017 0.002 PHE D 68 TRP 0.018 0.001 TRP C 246 HIS 0.012 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9804) covalent geometry : angle 0.62212 / 0.31 (13262) hydrogen bonds : bond 0.03618 / 2.39 ( 249) hydrogen bonds : angle 4.87136 / 3.43 ( 714) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6004 (mtt) cc_final: 0.5472 (mtt) REVERT: C 122 LYS cc_start: 0.8211 (tptp) cc_final: 0.8009 (tptp) REVERT: C 141 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8569 (mtmm) REVERT: C 148 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8210 (mm-30) REVERT: C 153 GLN cc_start: 0.8931 (pp30) cc_final: 0.8421 (pp30) REVERT: C 239 LYS cc_start: 0.8471 (tppt) cc_final: 0.8237 (tptp) REVERT: C 312 MET cc_start: 0.8704 (ttt) cc_final: 0.8503 (ttp) REVERT: E 161 LYS cc_start: 0.8527 (mmmm) cc_final: 0.8081 (ptpp) REVERT: E 203 PHE cc_start: 0.7743 (t80) cc_final: 0.7373 (t80) REVERT: E 325 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8523 (mm) REVERT: F 131 LYS cc_start: 0.9230 (mtmm) cc_final: 0.8972 (mtmm) REVERT: F 185 PHE cc_start: 0.8297 (m-80) cc_final: 0.8008 (m-80) REVERT: F 212 MET cc_start: 0.7942 (mmm) cc_final: 0.6991 (mmt) REVERT: D 30 PHE cc_start: 0.8098 (t80) cc_final: 0.7640 (t80) REVERT: D 137 HIS cc_start: 0.8416 (p-80) cc_final: 0.7952 (p-80) REVERT: D 142 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7337 (mmt-90) REVERT: D 171 GLU cc_start: 0.8113 (tp30) cc_final: 0.7619 (tm-30) REVERT: D 212 MET cc_start: 0.7992 (tpp) cc_final: 0.7150 (tpp) outliers start: 45 outliers final: 27 residues processed: 284 average time/residue: 0.0850 time to fit residues: 33.5123 Evaluate side-chains 248 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 100 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 333 CYS Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 0.0060 chunk 48 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 112 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 317 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.148720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105654 restraints weight = 16475.353| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.15 r_work: 0.3322 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9806 Z= 0.097 Angle : 0.571 9.770 13262 Z= 0.274 Chirality : 0.041 0.145 1553 Planarity : 0.003 0.035 1698 Dihedral : 4.817 58.763 1388 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.74 % Allowed : 21.14 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.22), residues: 1249 helix: -0.96 (0.25), residues: 442 sheet: -0.88 (0.46), residues: 131 loop : -2.18 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 17 TYR 0.008 0.001 TYR E 258 PHE 0.017 0.001 PHE D 68 TRP 0.016 0.001 TRP C 246 HIS 0.009 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 ( 9804) covalent geometry : angle 0.57061 / 0.27 (13262) hydrogen bonds : bond 0.02654 / 1.78 ( 249) hydrogen bonds : angle 4.49904 / 3.17 ( 714) Misc. bond : bond 0.00023 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.5819 (mtt) cc_final: 0.5332 (mtt) REVERT: C 86 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8193 (mmtm) REVERT: C 118 ASP cc_start: 0.9104 (t0) cc_final: 0.8814 (t0) REVERT: C 141 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8571 (mtmm) REVERT: C 148 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8216 (mm-30) REVERT: C 153 GLN cc_start: 0.8904 (pp30) cc_final: 0.8463 (pp30) REVERT: C 160 ASP cc_start: 0.8223 (m-30) cc_final: 0.7996 (m-30) REVERT: C 317 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: E 22 MET cc_start: 0.7451 (ppp) cc_final: 0.6756 (ptt) REVERT: E 134 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: E 203 PHE cc_start: 0.7614 (t80) cc_final: 0.7332 (t80) REVERT: E 325 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8311 (mm) REVERT: F 38 MET cc_start: 0.6542 (tmm) cc_final: 0.6323 (tmm) REVERT: F 131 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8989 (mtmm) REVERT: D 9 ASP cc_start: 0.8517 (p0) cc_final: 0.7930 (t70) REVERT: D 30 PHE cc_start: 0.8106 (t80) cc_final: 0.7418 (t80) REVERT: D 137 HIS cc_start: 0.8446 (p-80) cc_final: 0.8148 (p-80) REVERT: D 141 HIS cc_start: 0.7775 (m170) cc_final: 0.7571 (m170) REVERT: D 142 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7387 (tpp80) REVERT: D 171 GLU cc_start: 0.8085 (tp30) cc_final: 0.7472 (tm-30) REVERT: D 212 MET cc_start: 0.7875 (tpp) cc_final: 0.7043 (mmt) outliers start: 28 outliers final: 15 residues processed: 241 average time/residue: 0.0821 time to fit residues: 27.2880 Evaluate side-chains 222 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.144356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099690 restraints weight = 16456.244| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.18 r_work: 0.3230 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9806 Z= 0.124 Angle : 0.584 9.587 13262 Z= 0.285 Chirality : 0.042 0.140 1553 Planarity : 0.003 0.035 1698 Dihedral : 5.085 58.605 1388 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.72 % Allowed : 21.43 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.23), residues: 1249 helix: -0.61 (0.25), residues: 456 sheet: -0.99 (0.42), residues: 152 loop : -1.96 (0.22), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.009 0.001 TYR E 258 PHE 0.017 0.001 PHE D 68 TRP 0.018 0.001 TRP E 138 HIS 0.005 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 9804) covalent geometry : angle 0.58384 / 0.29 (13262) hydrogen bonds : bond 0.02921 / 1.95 ( 249) hydrogen bonds : angle 4.35029 / 3.03 ( 714) Misc. bond : bond 0.00043 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6415 (mtt) cc_final: 0.5876 (mtt) REVERT: C 39 MET cc_start: 0.8937 (ttp) cc_final: 0.8681 (ttp) REVERT: C 148 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8194 (mm-30) REVERT: C 153 GLN cc_start: 0.8981 (pp30) cc_final: 0.8422 (pp30) REVERT: C 195 GLU cc_start: 0.8735 (pp20) cc_final: 0.8373 (pp20) REVERT: E 127 SER cc_start: 0.8943 (m) cc_final: 0.8611 (p) REVERT: E 134 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: E 203 PHE cc_start: 0.7953 (t80) cc_final: 0.7424 (t80) REVERT: E 325 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8387 (mm) REVERT: F 131 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8984 (mtmm) REVERT: F 185 PHE cc_start: 0.8390 (m-80) cc_final: 0.7999 (m-80) REVERT: F 212 MET cc_start: 0.8203 (mmm) cc_final: 0.7206 (mmt) REVERT: D 30 PHE cc_start: 0.8164 (t80) cc_final: 0.7819 (t80) REVERT: D 137 HIS cc_start: 0.8426 (p-80) cc_final: 0.7982 (p-80) REVERT: D 141 HIS cc_start: 0.8042 (m170) cc_final: 0.7716 (m170) REVERT: D 142 ARG cc_start: 0.7981 (tpp80) cc_final: 0.7622 (tpp80) REVERT: D 171 GLU cc_start: 0.8025 (tp30) cc_final: 0.7233 (tm-30) REVERT: D 212 MET cc_start: 0.7819 (tpp) cc_final: 0.7591 (tpp) outliers start: 38 outliers final: 28 residues processed: 239 average time/residue: 0.0873 time to fit residues: 29.0376 Evaluate side-chains 236 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 233 ASN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097967 restraints weight = 16304.680| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.19 r_work: 0.3203 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9806 Z= 0.124 Angle : 0.574 10.116 13262 Z= 0.279 Chirality : 0.043 0.144 1553 Planarity : 0.003 0.036 1698 Dihedral : 5.072 58.466 1388 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.50 % Allowed : 21.33 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.23), residues: 1249 helix: -0.18 (0.26), residues: 457 sheet: -0.98 (0.42), residues: 152 loop : -1.92 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 139 TYR 0.009 0.001 TYR E 258 PHE 0.018 0.001 PHE D 68 TRP 0.016 0.001 TRP E 138 HIS 0.004 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 ( 9804) covalent geometry : angle 0.57422 / 0.28 (13262) hydrogen bonds : bond 0.02789 / 1.87 ( 249) hydrogen bonds : angle 4.28481 / 2.97 ( 714) Misc. bond : bond 0.00046 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6573 (mtt) cc_final: 0.6026 (mtt) REVERT: C 39 MET cc_start: 0.8988 (ttp) cc_final: 0.8747 (ttp) REVERT: C 148 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8302 (mm-30) REVERT: C 153 GLN cc_start: 0.9025 (pp30) cc_final: 0.8824 (pt0) REVERT: C 195 GLU cc_start: 0.8774 (pp20) cc_final: 0.8506 (pp20) REVERT: E 127 SER cc_start: 0.8964 (m) cc_final: 0.8625 (p) REVERT: E 134 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: E 325 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8391 (mm) REVERT: E 332 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8923 (mm) REVERT: F 11 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8204 (mm) REVERT: F 131 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8994 (mtmm) REVERT: F 185 PHE cc_start: 0.8417 (m-80) cc_final: 0.8076 (m-80) REVERT: F 212 MET cc_start: 0.8105 (mmm) cc_final: 0.7169 (mmt) REVERT: F 219 ARG cc_start: 0.7581 (mmm160) cc_final: 0.7288 (ttm110) REVERT: D 30 PHE cc_start: 0.8135 (t80) cc_final: 0.7724 (t80) REVERT: D 123 ASN cc_start: 0.8991 (m-40) cc_final: 0.8743 (p0) REVERT: D 137 HIS cc_start: 0.8466 (p-80) cc_final: 0.8025 (p90) REVERT: D 141 HIS cc_start: 0.8223 (m170) cc_final: 0.7835 (m170) REVERT: D 142 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7798 (ttm170) REVERT: D 212 MET cc_start: 0.7883 (tpp) cc_final: 0.7602 (tpp) outliers start: 46 outliers final: 29 residues processed: 235 average time/residue: 0.0810 time to fit residues: 26.6436 Evaluate side-chains 228 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 27 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 34 optimal weight: 0.0050 chunk 118 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 0.0970 chunk 19 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 97 HIS ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.146227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102342 restraints weight = 16132.571| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.17 r_work: 0.3271 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9806 Z= 0.091 Angle : 0.559 10.192 13262 Z= 0.271 Chirality : 0.042 0.137 1553 Planarity : 0.003 0.037 1698 Dihedral : 4.712 55.849 1388 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.33 % Allowed : 22.11 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.24), residues: 1249 helix: 0.03 (0.26), residues: 467 sheet: -0.76 (0.46), residues: 136 loop : -1.93 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 139 TYR 0.008 0.001 TYR E 258 PHE 0.016 0.001 PHE D 68 TRP 0.017 0.001 TRP C 246 HIS 0.004 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 9804) covalent geometry : angle 0.55918 / 0.27 (13262) hydrogen bonds : bond 0.02272 / 1.54 ( 249) hydrogen bonds : angle 4.05071 / 2.79 ( 714) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6316 (mtt) cc_final: 0.5795 (mtt) REVERT: C 123 ASP cc_start: 0.8001 (t70) cc_final: 0.7671 (t0) REVERT: C 148 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8267 (mm-30) REVERT: C 195 GLU cc_start: 0.8684 (pp20) cc_final: 0.8470 (pp20) REVERT: E 69 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8364 (mt-10) REVERT: E 127 SER cc_start: 0.8978 (m) cc_final: 0.8568 (p) REVERT: E 178 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6561 (ptmm) REVERT: E 180 MET cc_start: 0.4314 (mtm) cc_final: 0.4112 (mtm) REVERT: E 325 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8320 (mm) REVERT: E 332 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8885 (mm) REVERT: E 409 ARG cc_start: 0.8355 (tpt90) cc_final: 0.8121 (mmm160) REVERT: F 11 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8227 (mm) REVERT: F 37 MET cc_start: 0.5102 (mmt) cc_final: 0.4890 (mmp) REVERT: F 131 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8954 (mtmm) REVERT: F 185 PHE cc_start: 0.8331 (m-80) cc_final: 0.8106 (m-80) REVERT: F 212 MET cc_start: 0.8084 (mmm) cc_final: 0.7094 (mmt) REVERT: F 219 ARG cc_start: 0.7696 (mmm160) cc_final: 0.7381 (ttm110) REVERT: D 9 ASP cc_start: 0.8532 (p0) cc_final: 0.7779 (t0) REVERT: D 30 PHE cc_start: 0.8147 (t80) cc_final: 0.7804 (t80) REVERT: D 123 ASN cc_start: 0.8944 (m-40) cc_final: 0.8636 (p0) REVERT: D 137 HIS cc_start: 0.8462 (p-80) cc_final: 0.8007 (p-80) REVERT: D 141 HIS cc_start: 0.8133 (m170) cc_final: 0.7711 (m170) REVERT: D 142 ARG cc_start: 0.8037 (tpp80) cc_final: 0.7786 (ttm170) REVERT: D 170 ASP cc_start: 0.8250 (t0) cc_final: 0.7976 (t0) REVERT: D 171 GLU cc_start: 0.8215 (tp30) cc_final: 0.7666 (tm-30) REVERT: D 212 MET cc_start: 0.7829 (tpp) cc_final: 0.7523 (tpp) outliers start: 34 outliers final: 22 residues processed: 246 average time/residue: 0.0859 time to fit residues: 29.2131 Evaluate side-chains 220 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 120 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 0.3980 chunk 88 optimal weight: 0.0000 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 153 GLN E 134 GLN E 181 GLN E 286 ASN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.145420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102078 restraints weight = 16415.122| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.29 r_work: 0.3244 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9806 Z= 0.092 Angle : 0.564 10.814 13262 Z= 0.272 Chirality : 0.042 0.133 1553 Planarity : 0.003 0.039 1698 Dihedral : 4.732 58.909 1388 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.03 % Allowed : 22.99 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.24), residues: 1249 helix: 0.27 (0.26), residues: 467 sheet: -0.91 (0.45), residues: 142 loop : -1.84 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 139 TYR 0.007 0.001 TYR E 258 PHE 0.018 0.001 PHE D 68 TRP 0.016 0.001 TRP C 246 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 ( 9804) covalent geometry : angle 0.56431 / 0.27 (13262) hydrogen bonds : bond 0.02279 / 1.55 ( 249) hydrogen bonds : angle 3.95502 / 2.71 ( 714) Misc. bond : bond 0.00024 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6421 (mtt) cc_final: 0.5841 (mtt) REVERT: C 148 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8242 (mm-30) REVERT: C 195 GLU cc_start: 0.8697 (pp20) cc_final: 0.8479 (pp20) REVERT: C 291 MET cc_start: 0.8782 (mmp) cc_final: 0.8102 (mtt) REVERT: E 127 SER cc_start: 0.8969 (m) cc_final: 0.8621 (p) REVERT: E 178 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.6582 (ptmm) REVERT: E 181 GLN cc_start: 0.7825 (mm110) cc_final: 0.7383 (pm20) REVERT: E 325 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8340 (mm) REVERT: E 332 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8910 (mm) REVERT: E 409 ARG cc_start: 0.8333 (tpt90) cc_final: 0.8103 (mmm160) REVERT: F 11 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8207 (mm) REVERT: F 212 MET cc_start: 0.8097 (mmm) cc_final: 0.7090 (mmt) REVERT: F 219 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7334 (ttm110) REVERT: D 9 ASP cc_start: 0.8578 (p0) cc_final: 0.7807 (t0) REVERT: D 30 PHE cc_start: 0.8155 (t80) cc_final: 0.7799 (t80) REVERT: D 123 ASN cc_start: 0.8992 (m-40) cc_final: 0.8667 (p0) REVERT: D 137 HIS cc_start: 0.8425 (p-80) cc_final: 0.7928 (p-80) REVERT: D 141 HIS cc_start: 0.8170 (m170) cc_final: 0.7730 (m170) REVERT: D 142 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7782 (ttm170) REVERT: D 171 GLU cc_start: 0.8123 (tp30) cc_final: 0.7375 (tm-30) REVERT: D 212 MET cc_start: 0.7760 (tpp) cc_final: 0.7164 (tpp) outliers start: 31 outliers final: 24 residues processed: 223 average time/residue: 0.0722 time to fit residues: 22.8215 Evaluate side-chains 222 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.142290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097172 restraints weight = 16298.971| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.19 r_work: 0.3190 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9806 Z= 0.116 Angle : 0.595 11.127 13262 Z= 0.286 Chirality : 0.043 0.149 1553 Planarity : 0.003 0.040 1698 Dihedral : 5.036 59.309 1388 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.13 % Allowed : 23.09 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.24), residues: 1249 helix: 0.41 (0.26), residues: 469 sheet: -0.91 (0.45), residues: 140 loop : -1.68 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 139 TYR 0.008 0.001 TYR E 258 PHE 0.017 0.001 PHE D 68 TRP 0.015 0.001 TRP C 246 HIS 0.004 0.001 HIS F 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 9804) covalent geometry : angle 0.59510 / 0.29 (13262) hydrogen bonds : bond 0.02630 / 1.76 ( 249) hydrogen bonds : angle 4.03393 / 2.77 ( 714) Misc. bond : bond 0.00043 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6658 (mtt) cc_final: 0.6076 (mtt) REVERT: C 122 LYS cc_start: 0.8288 (tppt) cc_final: 0.7962 (tptp) REVERT: C 123 ASP cc_start: 0.8270 (t70) cc_final: 0.7830 (t70) REVERT: C 195 GLU cc_start: 0.8698 (pp20) cc_final: 0.8496 (pp20) REVERT: C 237 GLN cc_start: 0.8343 (mp10) cc_final: 0.8095 (pm20) REVERT: C 291 MET cc_start: 0.8726 (mmp) cc_final: 0.8054 (mtt) REVERT: E 127 SER cc_start: 0.8900 (m) cc_final: 0.8554 (p) REVERT: E 325 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8330 (mm) REVERT: E 409 ARG cc_start: 0.8319 (tpt90) cc_final: 0.8095 (mmm160) REVERT: F 11 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8218 (mm) REVERT: F 37 MET cc_start: 0.5468 (mmp) cc_final: 0.5146 (mmp) REVERT: F 212 MET cc_start: 0.8307 (mmm) cc_final: 0.7141 (mmp) REVERT: F 219 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7430 (ttm110) REVERT: D 9 ASP cc_start: 0.8460 (p0) cc_final: 0.7755 (t0) REVERT: D 30 PHE cc_start: 0.8100 (t80) cc_final: 0.7740 (t80) REVERT: D 94 GLN cc_start: 0.7849 (pt0) cc_final: 0.6501 (tt0) REVERT: D 123 ASN cc_start: 0.9015 (m-40) cc_final: 0.8706 (p0) REVERT: D 137 HIS cc_start: 0.8489 (p-80) cc_final: 0.8025 (p90) REVERT: D 141 HIS cc_start: 0.8322 (m170) cc_final: 0.7874 (m170) REVERT: D 142 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7880 (ttm170) REVERT: D 171 GLU cc_start: 0.8151 (tp30) cc_final: 0.7435 (tm-30) REVERT: D 212 MET cc_start: 0.7833 (tpp) cc_final: 0.7286 (tpp) outliers start: 32 outliers final: 21 residues processed: 225 average time/residue: 0.0886 time to fit residues: 28.2860 Evaluate side-chains 218 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.0010 chunk 44 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 115 optimal weight: 0.2980 chunk 85 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.143741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.099108 restraints weight = 16189.053| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 3.11 r_work: 0.3227 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9806 Z= 0.100 Angle : 0.603 11.673 13262 Z= 0.286 Chirality : 0.042 0.137 1553 Planarity : 0.003 0.044 1698 Dihedral : 4.857 59.748 1388 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.64 % Allowed : 23.87 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1249 helix: 0.50 (0.26), residues: 479 sheet: -1.00 (0.41), residues: 160 loop : -1.69 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 179 TYR 0.007 0.001 TYR E 258 PHE 0.019 0.001 PHE D 68 TRP 0.017 0.001 TRP E 138 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 9804) covalent geometry : angle 0.60258 / 0.29 (13262) hydrogen bonds : bond 0.02407 / 1.62 ( 249) hydrogen bonds : angle 3.97268 / 2.71 ( 714) Misc. bond : bond 0.00025 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2498 Ramachandran restraints generated. 1249 Oldfield, 0 Emsley, 1249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 291 MET cc_start: 0.8628 (mmp) cc_final: 0.8123 (mtt) REVERT: E 22 MET cc_start: 0.7497 (ppp) cc_final: 0.7187 (ptt) REVERT: E 25 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8094 (tt) REVERT: E 123 GLU cc_start: 0.7714 (pp20) cc_final: 0.7028 (pp20) REVERT: E 127 SER cc_start: 0.8985 (m) cc_final: 0.8607 (p) REVERT: E 181 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7565 (pm20) REVERT: E 203 PHE cc_start: 0.8029 (t80) cc_final: 0.7616 (t80) REVERT: E 325 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8299 (mm) REVERT: E 409 ARG cc_start: 0.8263 (tpt90) cc_final: 0.8039 (mmm160) REVERT: F 11 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8207 (mm) REVERT: F 37 MET cc_start: 0.5610 (mmp) cc_final: 0.5237 (mmp) REVERT: F 212 MET cc_start: 0.8288 (mmm) cc_final: 0.7094 (mmp) REVERT: F 219 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7340 (ttm110) REVERT: D 9 ASP cc_start: 0.8375 (p0) cc_final: 0.7610 (t0) REVERT: D 30 PHE cc_start: 0.8083 (t80) cc_final: 0.7693 (t80) REVERT: D 94 GLN cc_start: 0.7836 (pt0) cc_final: 0.6576 (tt0) REVERT: D 123 ASN cc_start: 0.8970 (m-40) cc_final: 0.8653 (p0) REVERT: D 137 HIS cc_start: 0.8448 (p-80) cc_final: 0.7924 (p-80) REVERT: D 141 HIS cc_start: 0.8283 (m170) cc_final: 0.7829 (m170) REVERT: D 142 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7898 (ttm170) REVERT: D 170 ASP cc_start: 0.8322 (t0) cc_final: 0.7986 (t0) REVERT: D 171 GLU cc_start: 0.8057 (tp30) cc_final: 0.7467 (tm-30) REVERT: D 212 MET cc_start: 0.7821 (tpp) cc_final: 0.7292 (tpp) outliers start: 27 outliers final: 22 residues processed: 229 average time/residue: 0.0938 time to fit residues: 30.4053 Evaluate side-chains 228 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.143718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099160 restraints weight = 16286.675| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 3.15 r_work: 0.3218 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9806 Z= 0.106 Angle : 0.630 11.864 13262 Z= 0.302 Chirality : 0.042 0.147 1553 Planarity : 0.003 0.045 1698 Dihedral : 4.846 58.708 1388 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.45 % Allowed : 24.85 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.24), residues: 1249 helix: 0.65 (0.26), residues: 467 sheet: -1.06 (0.41), residues: 162 loop : -1.71 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 15 TYR 0.009 0.001 TYR D 15 PHE 0.017 0.001 PHE D 68 TRP 0.016 0.001 TRP C 246 HIS 0.003 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9804) covalent geometry : angle 0.63002 / 0.30 (13262) hydrogen bonds : bond 0.02482 / 1.67 ( 249) hydrogen bonds : angle 3.99140 / 2.73 ( 714) Misc. bond : bond 0.00028 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.34 seconds wall clock time: 38 minutes 7.56 seconds (2287.56 seconds total)