Starting phenix.real_space_refine on Wed Mar 4 01:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7arh_11882/03_2026/7arh_11882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arh_11882/03_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_11882/03_2026/7arh_11882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arh_11882/03_2026/7arh_11882.map" model { file = "/net/cci-nas-00/data/ceres_data/7arh_11882/03_2026/7arh_11882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arh_11882/03_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-5986/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 2 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: 2.62, per 1000 atoms: 0.27 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: 0.92 Conformation dependent library (CDL) restraints added in 450.4 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: 1.35 Time building geometry restraints manager: 1.21 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: 5494 17.79 - 35.57: 386 35.57 - 53.35: 60 53.35 - 71.14: 7 71.14 - 88.92: 8 Dihedral angle restraints: 5955 sinusoidal: 2370 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 5952 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.410 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 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 : 12.333 88.925 3647 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 covalent geometry : bond 0.00321 ( 9804) covalent geometry : angle 0.72398 (13262) hydrogen bonds : bond 0.36175 ( 249) hydrogen bonds : angle 11.14586 ( 714) Misc. bond : bond 0.07057 ( 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 : 0.367 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: 0.1151 time to fit residues: 55.2371 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 : 0.359 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4166 r_free = 0.4166 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.119876 restraints weight = 16474.338| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.06 r_work: 0.3507 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9806 Z= 0.116 Angle : 0.577 8.051 13262 Z= 0.288 Chirality : 0.042 0.153 1553 Planarity : 0.005 0.046 1698 Dihedral : 4.870 60.092 1394 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.74 % Allowed : 16.83 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.19 (0.18), residues: 1249 helix: -3.32 (0.16), residues: 445 sheet: -1.14 (0.43), residues: 142 loop : -2.80 (0.19), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 179 TYR 0.008 0.001 TYR E 258 PHE 0.009 0.001 PHE E 329 TRP 0.022 0.001 TRP C 246 HIS 0.007 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9804) covalent geometry : angle 0.57730 (13262) hydrogen bonds : bond 0.04387 ( 249) hydrogen bonds : angle 5.73017 ( 714) Misc. bond : bond 0.00036 ( 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 289 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 261 time to evaluate : 0.400 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: 0.7924 (t80) cc_final: 0.7679 (m-80) REVERT: C 195 GLU cc_start: 0.8669 (pp20) cc_final: 0.8163 (pp20) REVERT: C 292 GLU cc_start: 0.8683 (pp20) cc_final: 0.8350 (pp20) REVERT: C 293 LYS cc_start: 0.8085 (mttm) cc_final: 0.7789 (mttp) REVERT: C 312 MET cc_start: 0.8450 (ttt) cc_final: 0.7986 (ttm) REVERT: E 11 LEU cc_start: 0.6748 (mp) cc_final: 0.5783 (tt) REVERT: E 203 PHE cc_start: 0.7600 (t80) cc_final: 0.7221 (t80) REVERT: F 131 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8846 (mtmm) REVERT: F 219 ARG cc_start: 0.7305 (mmm160) cc_final: 0.7017 (ttp-110) REVERT: D 9 ASP cc_start: 0.8548 (p0) cc_final: 0.7906 (t0) REVERT: D 30 PHE cc_start: 0.8204 (t80) cc_final: 0.7892 (t80) REVERT: D 137 HIS cc_start: 0.8326 (p90) cc_final: 0.7892 (p-80) REVERT: D 141 HIS cc_start: 0.7417 (m170) cc_final: 0.7132 (m170) REVERT: D 179 ARG cc_start: 0.8387 (tpt90) cc_final: 0.8058 (tpt90) REVERT: D 206 LEU cc_start: 0.8620 (tp) cc_final: 0.8390 (tt) REVERT: D 212 MET cc_start: 0.7609 (tpp) cc_final: 0.6657 (tpp) REVERT: D 220 ASP cc_start: 0.8211 (t0) cc_final: 0.7961 (m-30) outliers start: 28 outliers final: 18 residues processed: 277 average time/residue: 0.1001 time to fit residues: 38.0876 Evaluate side-chains 245 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 18 optimal weight: 0.4980 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 68 optimal weight: 0.1980 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 301 GLN C 317 GLN F 141 HIS D 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.149410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105642 restraints weight = 16404.064| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.18 r_work: 0.3325 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9806 Z= 0.131 Angle : 0.600 8.674 13262 Z= 0.294 Chirality : 0.042 0.142 1553 Planarity : 0.003 0.037 1698 Dihedral : 5.346 59.797 1394 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.01 % Allowed : 18.20 % Favored : 77.79 % 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: -3.01 (0.21), residues: 1249 helix: -1.77 (0.23), residues: 444 sheet: -0.80 (0.45), residues: 136 loop : -2.46 (0.20), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 125 TYR 0.013 0.001 TYR E 258 PHE 0.019 0.001 PHE D 68 TRP 0.018 0.001 TRP C 246 HIS 0.005 0.001 HIS F 141 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9804) covalent geometry : angle 0.59956 (13262) hydrogen bonds : bond 0.03464 ( 249) hydrogen bonds : angle 4.89768 ( 714) Misc. bond : bond 0.00028 ( 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 286 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.5850 (mtt) cc_final: 0.5302 (mtt) REVERT: C 141 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8559 (mtmm) REVERT: C 153 GLN cc_start: 0.8828 (pp30) cc_final: 0.8610 (pp30) REVERT: C 239 LYS cc_start: 0.8452 (tppt) cc_final: 0.8216 (tptp) REVERT: C 312 MET cc_start: 0.8736 (ttt) cc_final: 0.8535 (ttp) REVERT: E 161 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8047 (ptpp) REVERT: E 203 PHE cc_start: 0.7708 (t80) cc_final: 0.7416 (t80) REVERT: E 325 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8669 (mm) REVERT: F 128 GLU cc_start: 0.8121 (pm20) cc_final: 0.7808 (pm20) REVERT: F 131 LYS cc_start: 0.9247 (mtmm) cc_final: 0.8927 (mtmm) REVERT: D 30 PHE cc_start: 0.8095 (t80) cc_final: 0.7613 (t80) REVERT: D 137 HIS cc_start: 0.8395 (p90) cc_final: 0.7786 (p-80) REVERT: D 141 HIS cc_start: 0.7972 (m170) cc_final: 0.7641 (m170) REVERT: D 142 ARG cc_start: 0.7930 (tpp80) cc_final: 0.7603 (mmt-90) REVERT: D 171 GLU cc_start: 0.8177 (tp30) cc_final: 0.7494 (tm-30) REVERT: D 212 MET cc_start: 0.7913 (tpp) cc_final: 0.6944 (tpp) outliers start: 41 outliers final: 24 residues processed: 273 average time/residue: 0.0979 time to fit residues: 37.2273 Evaluate side-chains 245 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 48 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN F 152 GLN D 180 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.148876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106036 restraints weight = 16484.603| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 3.15 r_work: 0.3330 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4767 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= 0.101 Angle : 0.569 10.372 13262 Z= 0.275 Chirality : 0.041 0.130 1553 Planarity : 0.003 0.035 1698 Dihedral : 5.279 58.882 1394 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.74 % Allowed : 20.94 % Favored : 76.32 % 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: -2.49 (0.22), residues: 1249 helix: -1.12 (0.24), residues: 458 sheet: -0.33 (0.49), residues: 114 loop : -2.35 (0.21), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 17 TYR 0.009 0.001 TYR E 258 PHE 0.018 0.001 PHE D 68 TRP 0.016 0.001 TRP C 246 HIS 0.005 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9804) covalent geometry : angle 0.56939 (13262) hydrogen bonds : bond 0.02746 ( 249) hydrogen bonds : angle 4.47082 ( 714) Misc. bond : bond 0.00025 ( 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 258 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.5893 (mtt) cc_final: 0.5394 (mtt) REVERT: C 86 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8159 (mmtm) REVERT: C 118 ASP cc_start: 0.9100 (t0) cc_final: 0.8801 (t0) REVERT: C 141 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8556 (mtmm) REVERT: C 148 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7935 (mm-30) REVERT: C 153 GLN cc_start: 0.8912 (pp30) cc_final: 0.8448 (pp30) REVERT: C 160 ASP cc_start: 0.8204 (m-30) cc_final: 0.7960 (m-30) REVERT: C 189 THR cc_start: 0.8155 (m) cc_final: 0.7712 (m) REVERT: C 317 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8537 (mp10) REVERT: E 139 ARG cc_start: 0.8705 (mpp80) cc_final: 0.8439 (mtm-85) REVERT: E 161 LYS cc_start: 0.8459 (mmmm) cc_final: 0.8073 (ptpp) REVERT: E 203 PHE cc_start: 0.7598 (t80) cc_final: 0.7185 (t80) REVERT: E 276 MET cc_start: 0.8665 (mmt) cc_final: 0.8465 (mmt) REVERT: E 325 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8461 (mm) REVERT: F 131 LYS cc_start: 0.9208 (mtmm) cc_final: 0.9001 (mtmm) REVERT: F 219 ARG cc_start: 0.7544 (mmm160) cc_final: 0.7244 (ttm110) REVERT: D 9 ASP cc_start: 0.8514 (p0) cc_final: 0.7897 (t70) REVERT: D 30 PHE cc_start: 0.8103 (t80) cc_final: 0.7459 (t80) REVERT: D 137 HIS cc_start: 0.8414 (p90) cc_final: 0.7865 (p-80) REVERT: D 141 HIS cc_start: 0.8105 (m170) cc_final: 0.7778 (m170) REVERT: D 212 MET cc_start: 0.7880 (tpp) cc_final: 0.6914 (mmt) outliers start: 28 outliers final: 18 residues processed: 249 average time/residue: 0.1036 time to fit residues: 35.6501 Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 317 GLN 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.0070 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.146443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.102826 restraints weight = 16459.588| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.21 r_work: 0.3268 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9806 Z= 0.109 Angle : 0.568 9.472 13262 Z= 0.277 Chirality : 0.042 0.142 1553 Planarity : 0.003 0.035 1698 Dihedral : 5.369 59.680 1394 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.52 % Allowed : 21.92 % 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: -2.05 (0.23), residues: 1249 helix: -0.67 (0.25), residues: 459 sheet: -0.62 (0.44), residues: 138 loop : -2.07 (0.22), residues: 652 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 0.018 0.001 PHE D 68 TRP 0.015 0.001 TRP C 246 HIS 0.006 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9804) covalent geometry : angle 0.56777 (13262) hydrogen bonds : bond 0.02701 ( 249) hydrogen bonds : angle 4.31265 ( 714) Misc. bond : bond 0.00032 ( 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 254 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8221 (mmtm) REVERT: C 148 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8005 (mm-30) REVERT: C 153 GLN cc_start: 0.8926 (pp30) cc_final: 0.8535 (pp30) REVERT: C 195 GLU cc_start: 0.8789 (pp20) cc_final: 0.8307 (pp20) REVERT: E 127 SER cc_start: 0.8939 (m) cc_final: 0.8611 (p) REVERT: E 203 PHE cc_start: 0.7874 (t80) cc_final: 0.7440 (t80) REVERT: E 276 MET cc_start: 0.8785 (mmt) cc_final: 0.8552 (mmt) REVERT: E 325 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8381 (mm) REVERT: E 409 ARG cc_start: 0.8272 (tpt90) cc_final: 0.8045 (mmm160) REVERT: F 131 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8859 (mtmm) REVERT: D 9 ASP cc_start: 0.8525 (p0) cc_final: 0.7937 (t70) REVERT: D 30 PHE cc_start: 0.8185 (t80) cc_final: 0.7633 (t80) REVERT: D 137 HIS cc_start: 0.8432 (p90) cc_final: 0.7786 (p90) REVERT: D 141 HIS cc_start: 0.8062 (m170) cc_final: 0.7845 (m170) REVERT: D 171 GLU cc_start: 0.8189 (tp30) cc_final: 0.7457 (tm-30) REVERT: D 212 MET cc_start: 0.7827 (tpp) cc_final: 0.7545 (tpp) outliers start: 36 outliers final: 26 residues processed: 242 average time/residue: 0.1001 time to fit residues: 33.7942 Evaluate side-chains 234 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 249 VAL 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 D residue 50 THR 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: 0.8980 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 110 optimal weight: 0.0030 chunk 20 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.0270 chunk 45 optimal weight: 0.1980 overall best weight: 0.3648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4050 r_free = 0.4050 target = 0.148172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.104329 restraints weight = 16398.251| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 3.20 r_work: 0.3305 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5347 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= 0.091 Angle : 0.567 12.586 13262 Z= 0.268 Chirality : 0.042 0.141 1553 Planarity : 0.003 0.036 1698 Dihedral : 5.154 55.839 1394 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.94 % Allowed : 21.82 % Favored : 75.24 % 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: -1.68 (0.23), residues: 1249 helix: -0.18 (0.26), residues: 458 sheet: -0.45 (0.44), residues: 139 loop : -2.00 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 139 TYR 0.008 0.001 TYR E 258 PHE 0.019 0.001 PHE D 68 TRP 0.016 0.001 TRP C 246 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9804) covalent geometry : angle 0.56692 (13262) hydrogen bonds : bond 0.02359 ( 249) hydrogen bonds : angle 4.19578 ( 714) Misc. bond : bond 0.00021 ( 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 247 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 GLN cc_start: 0.8878 (pp30) cc_final: 0.8514 (pp30) REVERT: C 195 GLU cc_start: 0.8699 (pp20) cc_final: 0.8267 (pp20) REVERT: C 231 LYS cc_start: 0.8731 (ptpp) cc_final: 0.8509 (mttt) REVERT: C 264 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8089 (mmmm) REVERT: C 375 ILE cc_start: 0.8884 (mt) cc_final: 0.8684 (tt) REVERT: E 123 GLU cc_start: 0.7757 (pt0) cc_final: 0.7521 (pp20) REVERT: E 127 SER cc_start: 0.8941 (m) cc_final: 0.8580 (p) REVERT: E 203 PHE cc_start: 0.7774 (t80) cc_final: 0.7400 (t80) REVERT: E 325 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8370 (mm) REVERT: E 332 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8919 (mm) REVERT: E 409 ARG cc_start: 0.8278 (tpt90) cc_final: 0.8048 (mmm160) REVERT: F 38 MET cc_start: 0.6727 (tmm) cc_final: 0.6518 (tmm) REVERT: F 131 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8959 (mtmm) REVERT: F 185 PHE cc_start: 0.8262 (m-80) cc_final: 0.7851 (m-80) REVERT: F 212 MET cc_start: 0.8085 (mmm) cc_final: 0.6971 (mmt) REVERT: D 4 ILE cc_start: 0.6267 (tp) cc_final: 0.6063 (tp) REVERT: D 9 ASP cc_start: 0.8465 (p0) cc_final: 0.7911 (t70) REVERT: D 30 PHE cc_start: 0.8181 (t80) cc_final: 0.7615 (t80) REVERT: D 137 HIS cc_start: 0.8404 (p90) cc_final: 0.7851 (p-80) REVERT: D 141 HIS cc_start: 0.8061 (m170) cc_final: 0.7830 (m170) REVERT: D 171 GLU cc_start: 0.8088 (tp30) cc_final: 0.7397 (tm-30) REVERT: D 212 MET cc_start: 0.7876 (tpp) cc_final: 0.7585 (tpp) outliers start: 30 outliers final: 23 residues processed: 236 average time/residue: 0.0982 time to fit residues: 32.5788 Evaluate side-chains 225 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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 169 MET 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 369 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 50 THR 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: 10.0000 chunk 34 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.0570 chunk 107 optimal weight: 10.0000 chunk 50 optimal weight: 0.0770 chunk 19 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 123 ASN F 195 GLN ** D 96 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 = 0.4034 r_free = 0.4034 target = 0.146970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.102909 restraints weight = 16256.229| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.18 r_work: 0.3281 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9806 Z= 0.097 Angle : 0.572 10.415 13262 Z= 0.274 Chirality : 0.042 0.137 1553 Planarity : 0.003 0.038 1698 Dihedral : 5.156 55.128 1394 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.52 % Allowed : 21.92 % 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: -1.45 (0.24), residues: 1249 helix: 0.17 (0.26), residues: 461 sheet: -0.45 (0.45), residues: 138 loop : -1.99 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 19 TYR 0.008 0.001 TYR E 258 PHE 0.018 0.001 PHE D 68 TRP 0.015 0.001 TRP C 246 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 9804) covalent geometry : angle 0.57241 (13262) hydrogen bonds : bond 0.02412 ( 249) hydrogen bonds : angle 4.08351 ( 714) Misc. bond : bond 0.00026 ( 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 245 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 123 ASP cc_start: 0.7885 (t70) cc_final: 0.7503 (t0) REVERT: C 153 GLN cc_start: 0.8896 (pp30) cc_final: 0.8548 (pp30) REVERT: C 195 GLU cc_start: 0.8727 (pp20) cc_final: 0.8372 (pp20) REVERT: C 375 ILE cc_start: 0.8884 (mt) cc_final: 0.8667 (tt) REVERT: E 69 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8246 (mt-10) REVERT: E 127 SER cc_start: 0.8934 (m) cc_final: 0.8565 (p) REVERT: E 203 PHE cc_start: 0.7889 (t80) cc_final: 0.7523 (t80) REVERT: E 243 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: E 325 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8341 (mm) REVERT: E 332 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8904 (mm) REVERT: E 409 ARG cc_start: 0.8287 (tpt90) cc_final: 0.8060 (mmm160) REVERT: F 11 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8209 (mm) REVERT: F 38 MET cc_start: 0.6812 (tmm) cc_final: 0.6280 (mtm) REVERT: F 131 LYS cc_start: 0.9286 (mtmm) cc_final: 0.9065 (mtmm) REVERT: F 185 PHE cc_start: 0.8200 (m-80) cc_final: 0.7823 (m-80) REVERT: D 9 ASP cc_start: 0.8451 (p0) cc_final: 0.7917 (t70) REVERT: D 30 PHE cc_start: 0.8065 (t80) cc_final: 0.7708 (t80) REVERT: D 137 HIS cc_start: 0.8433 (p90) cc_final: 0.7805 (p-80) REVERT: D 141 HIS cc_start: 0.8105 (m170) cc_final: 0.7846 (m170) REVERT: D 171 GLU cc_start: 0.8071 (tp30) cc_final: 0.7393 (tm-30) REVERT: D 212 MET cc_start: 0.7861 (tpp) cc_final: 0.7250 (tpp) outliers start: 36 outliers final: 22 residues processed: 234 average time/residue: 0.0985 time to fit residues: 32.4767 Evaluate side-chains 222 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 164 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 138 TRP Chi-restraints excluded: chain E residue 169 MET 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 369 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 182 ASP 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 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: 1.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 88 optimal weight: 0.0370 chunk 20 optimal weight: 0.0670 chunk 60 optimal weight: 8.9990 chunk 110 optimal weight: 0.0060 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 141 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 = 0.4046 r_free = 0.4046 target = 0.147690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.103388 restraints weight = 16309.933| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.22 r_work: 0.3296 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5741 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= 0.092 Angle : 0.577 10.750 13262 Z= 0.275 Chirality : 0.042 0.146 1553 Planarity : 0.003 0.042 1698 Dihedral : 5.032 54.278 1394 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.23 % Allowed : 22.11 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.24), residues: 1249 helix: 0.40 (0.26), residues: 460 sheet: -0.32 (0.45), residues: 139 loop : -1.96 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 19 TYR 0.008 0.001 TYR E 258 PHE 0.016 0.001 PHE D 68 TRP 0.016 0.001 TRP C 246 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 9804) covalent geometry : angle 0.57713 (13262) hydrogen bonds : bond 0.02206 ( 249) hydrogen bonds : angle 3.97416 ( 714) Misc. bond : bond 0.00020 ( 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 239 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 136 ASP cc_start: 0.8988 (m-30) cc_final: 0.8730 (m-30) REVERT: C 153 GLN cc_start: 0.8875 (pp30) cc_final: 0.8521 (pp30) REVERT: C 195 GLU cc_start: 0.8690 (pp20) cc_final: 0.8353 (pp20) REVERT: C 291 MET cc_start: 0.8729 (mmp) cc_final: 0.8040 (mtt) REVERT: E 127 SER cc_start: 0.8966 (m) cc_final: 0.8594 (p) REVERT: E 203 PHE cc_start: 0.7866 (t80) cc_final: 0.7519 (t80) REVERT: E 325 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8546 (mt) REVERT: E 332 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8901 (mm) REVERT: E 409 ARG cc_start: 0.8290 (tpt90) cc_final: 0.8052 (mmm160) REVERT: F 38 MET cc_start: 0.6795 (tmm) cc_final: 0.6575 (mtm) REVERT: F 131 LYS cc_start: 0.9285 (mtmm) cc_final: 0.9052 (mtmm) REVERT: F 185 PHE cc_start: 0.8195 (m-80) cc_final: 0.7807 (m-80) REVERT: F 212 MET cc_start: 0.8200 (mmm) cc_final: 0.7057 (mmm) REVERT: D 9 ASP cc_start: 0.8432 (p0) cc_final: 0.7917 (t70) REVERT: D 30 PHE cc_start: 0.8029 (t80) cc_final: 0.7653 (t80) REVERT: D 123 ASN cc_start: 0.8957 (m-40) cc_final: 0.8657 (p0) REVERT: D 137 HIS cc_start: 0.8450 (p90) cc_final: 0.7808 (p-80) REVERT: D 141 HIS cc_start: 0.8150 (m170) cc_final: 0.7897 (m170) REVERT: D 171 GLU cc_start: 0.8048 (tp30) cc_final: 0.7355 (tm-30) REVERT: D 212 MET cc_start: 0.7773 (tpp) cc_final: 0.7197 (tpp) outliers start: 33 outliers final: 24 residues processed: 228 average time/residue: 0.0931 time to fit residues: 29.8617 Evaluate side-chains 221 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 306 THR Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 169 MET 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 369 ASP Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 182 ASP 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 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: 4.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 364 GLN E 233 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.144151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099579 restraints weight = 16258.668| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.15 r_work: 0.3227 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.6080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9806 Z= 0.111 Angle : 0.594 11.179 13262 Z= 0.286 Chirality : 0.042 0.145 1553 Planarity : 0.003 0.046 1698 Dihedral : 5.413 57.629 1394 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.13 % Allowed : 22.80 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.13 (0.24), residues: 1249 helix: 0.51 (0.27), residues: 462 sheet: -0.12 (0.46), residues: 133 loop : -1.89 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 19 TYR 0.009 0.001 TYR E 258 PHE 0.015 0.001 PHE D 68 TRP 0.013 0.001 TRP C 246 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9804) covalent geometry : angle 0.59433 (13262) hydrogen bonds : bond 0.02606 ( 249) hydrogen bonds : angle 4.01406 ( 714) Misc. bond : bond 0.00039 ( 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 243 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8605 (ptpp) REVERT: C 195 GLU cc_start: 0.8688 (pp20) cc_final: 0.8437 (pp20) REVERT: C 291 MET cc_start: 0.8671 (mmp) cc_final: 0.8131 (mtt) REVERT: E 22 MET cc_start: 0.7742 (ppp) cc_final: 0.7122 (ptt) REVERT: E 127 SER cc_start: 0.8930 (m) cc_final: 0.8543 (p) REVERT: E 139 ARG cc_start: 0.8779 (mpp-170) cc_final: 0.8388 (mtm-85) REVERT: E 181 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7346 (mm110) REVERT: E 203 PHE cc_start: 0.8013 (t80) cc_final: 0.7713 (t80) REVERT: E 325 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8401 (mm) REVERT: E 409 ARG cc_start: 0.8307 (tpt90) cc_final: 0.8097 (mmm160) REVERT: F 11 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8079 (mm) REVERT: F 38 MET cc_start: 0.6968 (tmm) cc_final: 0.6720 (mtm) REVERT: F 48 LYS cc_start: 0.6904 (pttm) cc_final: 0.6614 (ptmm) REVERT: F 121 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8834 (tt0) REVERT: F 131 LYS cc_start: 0.9325 (mtmm) cc_final: 0.9117 (mtmm) REVERT: F 185 PHE cc_start: 0.8288 (m-80) cc_final: 0.7911 (m-80) REVERT: F 212 MET cc_start: 0.8173 (mmm) cc_final: 0.7122 (mmp) REVERT: D 30 PHE cc_start: 0.8072 (t80) cc_final: 0.7682 (t80) REVERT: D 94 GLN cc_start: 0.7809 (pt0) cc_final: 0.6640 (tt0) REVERT: D 123 ASN cc_start: 0.8906 (m-40) cc_final: 0.8640 (p0) REVERT: D 137 HIS cc_start: 0.8450 (p90) cc_final: 0.7955 (p-80) REVERT: D 141 HIS cc_start: 0.8252 (m170) cc_final: 0.7978 (m170) REVERT: D 171 GLU cc_start: 0.8064 (tp30) cc_final: 0.7326 (tm-30) REVERT: D 212 MET cc_start: 0.7818 (tpp) cc_final: 0.7278 (tpp) outliers start: 32 outliers final: 25 residues processed: 231 average time/residue: 0.1007 time to fit residues: 32.4582 Evaluate side-chains 229 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 328 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 169 MET 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 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 F residue 182 ASP 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 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: 8.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 85 optimal weight: 0.0030 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN F 123 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.145220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100946 restraints weight = 16237.667| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.22 r_work: 0.3251 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6166 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= 0.098 Angle : 0.594 11.352 13262 Z= 0.285 Chirality : 0.042 0.143 1553 Planarity : 0.003 0.041 1698 Dihedral : 5.171 56.180 1394 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.13 % Allowed : 23.68 % Favored : 73.19 % 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: -1.05 (0.24), residues: 1249 helix: 0.56 (0.26), residues: 473 sheet: -0.55 (0.42), residues: 152 loop : -1.76 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 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 0.006 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9804) covalent geometry : angle 0.59427 (13262) hydrogen bonds : bond 0.02309 ( 249) hydrogen bonds : angle 3.97343 ( 714) Misc. bond : bond 0.00025 ( 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 249 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 141 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8481 (ptpp) REVERT: C 195 GLU cc_start: 0.8689 (pp20) cc_final: 0.8460 (pp20) REVERT: C 291 MET cc_start: 0.8600 (mmp) cc_final: 0.8107 (mtt) REVERT: E 22 MET cc_start: 0.7718 (ppp) cc_final: 0.7277 (ptt) REVERT: E 25 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8031 (tt) REVERT: E 127 SER cc_start: 0.8933 (m) cc_final: 0.8581 (p) REVERT: E 139 ARG cc_start: 0.8803 (mpp-170) cc_final: 0.8319 (mtm-85) REVERT: E 181 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7670 (mm-40) REVERT: E 203 PHE cc_start: 0.8071 (t80) cc_final: 0.7786 (t80) REVERT: E 325 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8512 (mt) REVERT: F 11 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8056 (mm) REVERT: F 121 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8840 (tt0) REVERT: F 131 LYS cc_start: 0.9313 (mtmm) cc_final: 0.8974 (mtmm) REVERT: F 185 PHE cc_start: 0.8229 (m-80) cc_final: 0.7930 (m-80) REVERT: F 212 MET cc_start: 0.8227 (mmm) cc_final: 0.7187 (mmp) REVERT: D 9 ASP cc_start: 0.8528 (p0) cc_final: 0.7816 (t0) REVERT: D 30 PHE cc_start: 0.8105 (t80) cc_final: 0.7784 (t80) REVERT: D 38 MET cc_start: 0.6777 (mtp) cc_final: 0.6020 (mtt) REVERT: D 94 GLN cc_start: 0.7772 (pt0) cc_final: 0.6626 (tt0) REVERT: D 123 ASN cc_start: 0.8959 (m-40) cc_final: 0.8653 (p0) REVERT: D 137 HIS cc_start: 0.8491 (p90) cc_final: 0.8041 (p-80) REVERT: D 141 HIS cc_start: 0.8260 (m170) cc_final: 0.7963 (m170) REVERT: D 171 GLU cc_start: 0.8059 (tp30) cc_final: 0.7344 (tm-30) REVERT: D 212 MET cc_start: 0.7790 (tpp) cc_final: 0.7217 (tpp) outliers start: 32 outliers final: 24 residues processed: 238 average time/residue: 0.0968 time to fit residues: 32.4378 Evaluate side-chains 226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 292 GLU 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 138 TRP Chi-restraints excluded: chain E residue 169 MET 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 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 59 ASP Chi-restraints excluded: chain F residue 182 ASP 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 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: 0.0970 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN E 146 GLN E 213 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.142176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097218 restraints weight = 16244.804| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.21 r_work: 0.3189 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.6429 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= 0.129 Angle : 0.642 11.447 13262 Z= 0.311 Chirality : 0.044 0.148 1553 Planarity : 0.003 0.042 1698 Dihedral : 5.540 57.053 1394 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.33 % Allowed : 24.17 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.24), residues: 1249 helix: 0.50 (0.26), residues: 477 sheet: -0.50 (0.41), residues: 157 loop : -1.75 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 15 TYR 0.010 0.001 TYR D 15 PHE 0.014 0.001 PHE D 68 TRP 0.014 0.001 TRP C 246 HIS 0.007 0.001 HIS F 97 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9804) covalent geometry : angle 0.64177 (13262) hydrogen bonds : bond 0.02801 ( 249) hydrogen bonds : angle 4.10170 ( 714) Misc. bond : bond 0.00046 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.40 seconds wall clock time: 42 minutes 39.26 seconds (2559.26 seconds total)