Starting phenix.real_space_refine on Mon Jul 28 03:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7arh_11882/07_2025/7arh_11882.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arh_11882/07_2025/7arh_11882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2025/7arh_11882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2025/7arh_11882.map" model { file = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2025/7arh_11882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arh_11882/07_2025/7arh_11882.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} 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: 5.74, per 1000 atoms: 0.59 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: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 2.46 Time building geometry restraints manager: 2.76 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.410 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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 : 2.92 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.000 TRP E 138 HIS 0.003 0.000 HIS D 137 PHE 0.010 0.001 PHE F 199 TYR 0.007 0.001 TYR C 199 ARG 0.006 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.36175 ( 249) hydrogen bonds : angle 11.14586 ( 714) covalent geometry : bond 0.00321 ( 9804) covalent geometry : angle 0.72398 (13262) 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 : 1.123 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: 0.7471 (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: 0.7515 (tpp80) REVERT: D 30 PHE cc_start: 0.7834 (t80) cc_final: 0.7491 (t80) REVERT: D 94 GLN cc_start: 0.7184 (pt0) cc_final: 0.6909 (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: 0.2566 time to fit residues: 122.5056 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 : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 317 GLN C 339 GLN E 174 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN D 10 ASN D 137 HIS D 141 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 = 0.4008 r_free = 0.4008 target = 0.144950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.100489 restraints weight = 16428.801| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 3.17 r_work: 0.3244 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9806 Z= 0.209 Angle : 0.701 8.712 13262 Z= 0.355 Chirality : 0.045 0.149 1553 Planarity : 0.005 0.048 1698 Dihedral : 6.027 63.348 1394 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.52 % Allowed : 17.61 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.19), residues: 1249 helix: -3.34 (0.16), residues: 446 sheet: -1.49 (0.42), residues: 155 loop : -2.65 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 246 HIS 0.007 0.001 HIS D 141 PHE 0.022 0.002 PHE E 132 TYR 0.012 0.002 TYR E 273 ARG 0.010 0.001 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 249) hydrogen bonds : angle 5.56713 ( 714) covalent geometry : bond 0.00473 ( 9804) covalent geometry : angle 0.70054 (13262) Misc. bond : bond 0.00024 ( 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 290 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 254 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.6206 (mtt) cc_final: 0.5486 (mtt) REVERT: C 54 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8383 (mm-30) REVERT: C 141 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8569 (mtmm) REVERT: C 153 GLN cc_start: 0.8958 (pp30) cc_final: 0.8513 (pp30) REVERT: C 312 MET cc_start: 0.8792 (ttt) cc_final: 0.8568 (ttp) REVERT: E 127 SER cc_start: 0.8933 (m) cc_final: 0.8603 (p) REVERT: E 325 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8637 (mm) REVERT: F 131 LYS cc_start: 0.9141 (mtmm) cc_final: 0.8829 (mtmm) REVERT: F 219 ARG cc_start: 0.7369 (mmm160) cc_final: 0.7026 (ttm110) REVERT: D 4 ILE cc_start: 0.6340 (tp) cc_final: 0.6127 (tp) REVERT: D 13 LYS cc_start: 0.7921 (tptm) cc_final: 0.7659 (tptp) REVERT: D 30 PHE cc_start: 0.8215 (t80) cc_final: 0.7965 (t80) REVERT: D 137 HIS cc_start: 0.8545 (p-80) cc_final: 0.8069 (p90) REVERT: D 141 HIS cc_start: 0.7988 (m-70) cc_final: 0.7703 (m170) REVERT: D 142 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7560 (tpp80) REVERT: D 171 GLU cc_start: 0.8251 (tp30) cc_final: 0.7592 (tm-30) REVERT: D 179 ARG cc_start: 0.8480 (tpt90) cc_final: 0.8192 (tpt90) REVERT: D 212 MET cc_start: 0.8071 (mmt) cc_final: 0.7516 (tpp) outliers start: 36 outliers final: 22 residues processed: 283 average time/residue: 0.2234 time to fit residues: 85.5109 Evaluate side-chains 233 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 126 THR 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 328 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU 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 F residue 32 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 0.0000 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 301 GLN ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 180 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.140734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095941 restraints weight = 16502.206| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.14 r_work: 0.3171 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9806 Z= 0.171 Angle : 0.640 9.788 13262 Z= 0.318 Chirality : 0.044 0.139 1553 Planarity : 0.004 0.034 1698 Dihedral : 5.911 62.012 1394 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.60 % Allowed : 18.20 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.21), residues: 1249 helix: -1.93 (0.22), residues: 456 sheet: -0.55 (0.48), residues: 114 loop : -2.33 (0.21), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.006 0.001 HIS F 97 PHE 0.019 0.002 PHE D 68 TYR 0.014 0.001 TYR E 258 ARG 0.010 0.001 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.04096 ( 249) hydrogen bonds : angle 4.96605 ( 714) covalent geometry : bond 0.00400 ( 9804) covalent geometry : angle 0.64022 (13262) Misc. bond : bond 0.00059 ( 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 279 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8234 (mm-30) REVERT: C 123 ASP cc_start: 0.7952 (t70) cc_final: 0.7485 (t70) REVERT: C 153 GLN cc_start: 0.9117 (pp30) cc_final: 0.8915 (pp30) REVERT: C 195 GLU cc_start: 0.8798 (pp20) cc_final: 0.8583 (pp20) REVERT: C 239 LYS cc_start: 0.8567 (tppt) cc_final: 0.8237 (tptp) REVERT: E 127 SER cc_start: 0.8965 (m) cc_final: 0.8692 (p) REVERT: E 141 PHE cc_start: 0.7640 (m-80) cc_final: 0.7332 (m-80) REVERT: E 161 LYS cc_start: 0.8525 (mmmm) cc_final: 0.8141 (ptpp) REVERT: E 325 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8518 (mm) REVERT: E 364 ASP cc_start: 0.9034 (t0) cc_final: 0.8818 (t0) REVERT: F 129 MET cc_start: 0.8616 (mmm) cc_final: 0.8321 (mmt) REVERT: F 131 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8925 (mtmm) REVERT: F 212 MET cc_start: 0.7874 (mmm) cc_final: 0.7103 (mmt) REVERT: D 30 PHE cc_start: 0.8292 (t80) cc_final: 0.7936 (t80) REVERT: D 137 HIS cc_start: 0.8459 (p-80) cc_final: 0.7772 (p-80) REVERT: D 141 HIS cc_start: 0.8297 (m-70) cc_final: 0.8070 (m170) REVERT: D 142 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7750 (tpp80) REVERT: D 212 MET cc_start: 0.8127 (mmt) cc_final: 0.7922 (tpp) outliers start: 47 outliers final: 28 residues processed: 265 average time/residue: 0.2313 time to fit residues: 83.9408 Evaluate side-chains 248 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain D residue 50 THR 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 32 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 49 optimal weight: 0.0000 chunk 55 optimal weight: 3.9990 chunk 56 optimal weight: 0.0870 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 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 = 0.3953 r_free = 0.3953 target = 0.140531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096242 restraints weight = 16300.882| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.11 r_work: 0.3174 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9806 Z= 0.130 Angle : 0.578 9.062 13262 Z= 0.286 Chirality : 0.043 0.142 1553 Planarity : 0.003 0.026 1698 Dihedral : 5.687 59.453 1394 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.60 % Allowed : 20.55 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.22), residues: 1249 helix: -1.23 (0.24), residues: 470 sheet: -0.61 (0.48), residues: 114 loop : -2.08 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 138 HIS 0.005 0.001 HIS D 96 PHE 0.017 0.001 PHE D 68 TYR 0.010 0.001 TYR E 258 ARG 0.007 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03052 ( 249) hydrogen bonds : angle 4.52404 ( 714) covalent geometry : bond 0.00305 ( 9804) covalent geometry : angle 0.57834 (13262) Misc. bond : bond 0.00050 ( 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 265 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 153 GLN cc_start: 0.9130 (pp30) cc_final: 0.8634 (pp30) REVERT: C 195 GLU cc_start: 0.8770 (pp20) cc_final: 0.8547 (pp20) REVERT: E 67 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7593 (mm-30) REVERT: E 127 SER cc_start: 0.8930 (m) cc_final: 0.8615 (p) REVERT: E 325 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8446 (mm) REVERT: F 11 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8473 (mm) REVERT: F 38 MET cc_start: 0.6637 (tmm) cc_final: 0.6240 (tmm) REVERT: F 129 MET cc_start: 0.8723 (mmm) cc_final: 0.8406 (mmt) REVERT: F 212 MET cc_start: 0.8098 (mmm) cc_final: 0.7094 (mmp) REVERT: D 30 PHE cc_start: 0.8091 (t80) cc_final: 0.7737 (t80) REVERT: D 137 HIS cc_start: 0.8529 (p-80) cc_final: 0.7916 (p-80) REVERT: D 141 HIS cc_start: 0.8375 (m-70) cc_final: 0.8108 (m170) REVERT: D 142 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7572 (tpp80) REVERT: D 171 GLU cc_start: 0.8229 (tp30) cc_final: 0.7619 (tm-30) REVERT: D 212 MET cc_start: 0.8204 (mmt) cc_final: 0.7766 (tpp) outliers start: 47 outliers final: 32 residues processed: 249 average time/residue: 0.2660 time to fit residues: 90.2529 Evaluate side-chains 231 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL 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 164 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 VAL 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 257 THR Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 102 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098182 restraints weight = 16276.436| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.15 r_work: 0.3207 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9806 Z= 0.099 Angle : 0.565 9.587 13262 Z= 0.274 Chirality : 0.042 0.140 1553 Planarity : 0.003 0.028 1698 Dihedral : 5.356 55.521 1394 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.01 % Allowed : 22.11 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1249 helix: -0.55 (0.25), residues: 456 sheet: -0.51 (0.49), residues: 114 loop : -1.98 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.005 0.001 HIS D 96 PHE 0.018 0.001 PHE D 68 TYR 0.010 0.001 TYR E 258 ARG 0.005 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.02614 ( 249) hydrogen bonds : angle 4.29385 ( 714) covalent geometry : bond 0.00232 ( 9804) covalent geometry : angle 0.56467 (13262) 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 264 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.8922 (ttp) cc_final: 0.8709 (ttp) REVERT: C 54 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8379 (mm-30) REVERT: C 148 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8257 (tp30) REVERT: C 153 GLN cc_start: 0.9043 (pp30) cc_final: 0.8804 (pt0) REVERT: C 161 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: C 195 GLU cc_start: 0.8713 (pp20) cc_final: 0.8504 (pp20) REVERT: C 239 LYS cc_start: 0.8529 (tppt) cc_final: 0.8167 (tptp) REVERT: E 67 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7603 (mm-30) REVERT: E 127 SER cc_start: 0.8946 (m) cc_final: 0.8486 (p) REVERT: E 325 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8342 (mm) REVERT: F 11 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8411 (mm) REVERT: F 38 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6235 (tmm) REVERT: F 129 MET cc_start: 0.8603 (mmm) cc_final: 0.8315 (mmt) REVERT: F 212 MET cc_start: 0.8167 (mmm) cc_final: 0.7162 (mmp) REVERT: F 220 ASP cc_start: 0.7174 (t70) cc_final: 0.6105 (m-30) REVERT: D 30 PHE cc_start: 0.8126 (t80) cc_final: 0.7800 (t80) REVERT: D 137 HIS cc_start: 0.8496 (p-80) cc_final: 0.7807 (p-80) REVERT: D 141 HIS cc_start: 0.8405 (m-70) cc_final: 0.8109 (m170) REVERT: D 142 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7864 (tpp80) REVERT: D 171 GLU cc_start: 0.8065 (tp30) cc_final: 0.7571 (tm-30) REVERT: D 212 MET cc_start: 0.8197 (mmt) cc_final: 0.7772 (tpp) outliers start: 41 outliers final: 29 residues processed: 249 average time/residue: 0.2594 time to fit residues: 90.8000 Evaluate side-chains 232 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL 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 161 GLN Chi-restraints excluded: chain C residue 164 VAL 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 C residue 328 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 129 LEU 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 F residue 11 LEU Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 116 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 114 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.141631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096749 restraints weight = 16447.282| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.20 r_work: 0.3181 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.6028 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= 0.108 Angle : 0.578 11.856 13262 Z= 0.280 Chirality : 0.043 0.178 1553 Planarity : 0.003 0.027 1698 Dihedral : 5.416 56.900 1394 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.79 % Allowed : 20.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.24), residues: 1249 helix: -0.16 (0.26), residues: 470 sheet: -0.78 (0.44), residues: 144 loop : -1.88 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 138 HIS 0.006 0.001 HIS F 96 PHE 0.018 0.001 PHE D 68 TYR 0.009 0.001 TYR E 258 ARG 0.004 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 249) hydrogen bonds : angle 4.20950 ( 714) covalent geometry : bond 0.00254 ( 9804) covalent geometry : angle 0.57811 (13262) Misc. bond : bond 0.00038 ( 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 257 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.8952 (ttp) cc_final: 0.8722 (ttp) REVERT: C 54 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8343 (mm-30) REVERT: C 153 GLN cc_start: 0.9088 (pp30) cc_final: 0.8834 (pt0) REVERT: C 161 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: C 199 TYR cc_start: 0.8876 (p90) cc_final: 0.8645 (p90) REVERT: E 127 SER cc_start: 0.8985 (m) cc_final: 0.8611 (p) REVERT: E 203 PHE cc_start: 0.7945 (t80) cc_final: 0.7576 (t80) REVERT: E 325 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8324 (mm) REVERT: F 11 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8363 (mm) REVERT: F 38 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.6136 (tmm) REVERT: F 88 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7751 (mmmt) REVERT: F 129 MET cc_start: 0.8634 (mmm) cc_final: 0.8327 (mmt) REVERT: F 185 PHE cc_start: 0.8403 (m-80) cc_final: 0.7945 (m-80) REVERT: F 212 MET cc_start: 0.8237 (mmm) cc_final: 0.7143 (mmp) REVERT: F 220 ASP cc_start: 0.7265 (t70) cc_final: 0.5993 (m-30) REVERT: D 30 PHE cc_start: 0.8081 (t80) cc_final: 0.7733 (t80) REVERT: D 137 HIS cc_start: 0.8550 (p-80) cc_final: 0.7985 (p-80) REVERT: D 141 HIS cc_start: 0.8517 (m-70) cc_final: 0.8199 (m170) REVERT: D 142 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7865 (tpp80) REVERT: D 171 GLU cc_start: 0.8016 (tp30) cc_final: 0.7479 (tm-30) REVERT: D 212 MET cc_start: 0.8212 (mmt) cc_final: 0.7772 (tpp) outliers start: 49 outliers final: 35 residues processed: 238 average time/residue: 0.2952 time to fit residues: 98.5587 Evaluate side-chains 235 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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 161 GLN 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 C residue 344 MET Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 208 LEU 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 F residue 11 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 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 = 0.3939 r_free = 0.3939 target = 0.139606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.094678 restraints weight = 16443.467| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.17 r_work: 0.3144 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9806 Z= 0.124 Angle : 0.587 10.394 13262 Z= 0.286 Chirality : 0.043 0.205 1553 Planarity : 0.003 0.026 1698 Dihedral : 5.607 56.912 1394 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.60 % Allowed : 21.43 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.24), residues: 1249 helix: 0.04 (0.26), residues: 480 sheet: -0.79 (0.43), residues: 144 loop : -1.89 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.010 0.001 HIS F 96 PHE 0.016 0.001 PHE D 68 TYR 0.009 0.001 TYR E 258 ARG 0.003 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.02796 ( 249) hydrogen bonds : angle 4.16555 ( 714) covalent geometry : bond 0.00294 ( 9804) covalent geometry : angle 0.58691 (13262) Misc. bond : bond 0.00048 ( 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 254 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 MET cc_start: 0.8939 (ttp) cc_final: 0.8672 (ttp) REVERT: C 54 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8383 (mm-30) REVERT: C 153 GLN cc_start: 0.9130 (pp30) cc_final: 0.8824 (tm-30) REVERT: C 161 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: C 239 LYS cc_start: 0.8503 (tppt) cc_final: 0.8074 (tptp) REVERT: E 127 SER cc_start: 0.8985 (m) cc_final: 0.8611 (p) REVERT: E 203 PHE cc_start: 0.7983 (t80) cc_final: 0.7627 (t80) REVERT: E 325 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8417 (mm) REVERT: F 38 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6226 (tmm) REVERT: F 129 MET cc_start: 0.8670 (mmm) cc_final: 0.8354 (mmt) REVERT: F 185 PHE cc_start: 0.8415 (m-80) cc_final: 0.8007 (m-80) REVERT: F 212 MET cc_start: 0.8078 (mmm) cc_final: 0.7209 (mmp) REVERT: D 30 PHE cc_start: 0.8089 (t80) cc_final: 0.7770 (t80) REVERT: D 123 ASN cc_start: 0.8987 (m-40) cc_final: 0.8724 (p0) REVERT: D 137 HIS cc_start: 0.8530 (p-80) cc_final: 0.7977 (p-80) REVERT: D 141 HIS cc_start: 0.8567 (m-70) cc_final: 0.8230 (m170) REVERT: D 142 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7872 (tpp80) REVERT: D 212 MET cc_start: 0.8189 (mmt) cc_final: 0.7685 (tpp) outliers start: 47 outliers final: 37 residues processed: 236 average time/residue: 0.2175 time to fit residues: 71.1055 Evaluate side-chains 235 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 161 GLN 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 C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 0.0170 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 101 optimal weight: 8.9990 overall best weight: 1.2624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 GLN E 181 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.138659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093713 restraints weight = 16519.048| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 3.18 r_work: 0.3127 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9806 Z= 0.133 Angle : 0.607 10.809 13262 Z= 0.297 Chirality : 0.043 0.157 1553 Planarity : 0.003 0.025 1698 Dihedral : 5.683 55.789 1394 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.89 % Allowed : 21.72 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.24), residues: 1249 helix: 0.08 (0.25), residues: 498 sheet: -0.76 (0.45), residues: 132 loop : -1.87 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 246 HIS 0.010 0.001 HIS F 96 PHE 0.043 0.002 PHE F 95 TYR 0.008 0.001 TYR E 258 ARG 0.004 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 249) hydrogen bonds : angle 4.20993 ( 714) covalent geometry : bond 0.00316 ( 9804) covalent geometry : angle 0.60711 (13262) Misc. bond : bond 0.00053 ( 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 249 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8362 (mm-30) REVERT: C 153 GLN cc_start: 0.9139 (pp30) cc_final: 0.8820 (tm-30) REVERT: C 161 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: E 127 SER cc_start: 0.9001 (m) cc_final: 0.8622 (p) REVERT: E 181 GLN cc_start: 0.7831 (mm110) cc_final: 0.7509 (pm20) REVERT: E 203 PHE cc_start: 0.7971 (t80) cc_final: 0.7623 (t80) REVERT: E 315 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8889 (mm) REVERT: E 325 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8460 (mm) REVERT: F 38 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6445 (tmm) REVERT: F 73 MET cc_start: 0.8439 (ptp) cc_final: 0.7929 (mtp) REVERT: F 129 MET cc_start: 0.8643 (mmm) cc_final: 0.8330 (mmt) REVERT: F 185 PHE cc_start: 0.8422 (m-80) cc_final: 0.8010 (m-80) REVERT: F 212 MET cc_start: 0.8028 (mmm) cc_final: 0.7248 (mmp) REVERT: F 220 ASP cc_start: 0.7519 (t70) cc_final: 0.5839 (m-30) REVERT: D 30 PHE cc_start: 0.8185 (t80) cc_final: 0.7887 (t80) REVERT: D 123 ASN cc_start: 0.9009 (m-40) cc_final: 0.8764 (p0) REVERT: D 137 HIS cc_start: 0.8503 (p-80) cc_final: 0.7975 (p-80) REVERT: D 141 HIS cc_start: 0.8617 (m-70) cc_final: 0.8239 (m170) REVERT: D 171 GLU cc_start: 0.8169 (tp30) cc_final: 0.7685 (tm-30) REVERT: D 212 MET cc_start: 0.8155 (mmt) cc_final: 0.7650 (tpp) outliers start: 50 outliers final: 39 residues processed: 233 average time/residue: 0.2309 time to fit residues: 77.2848 Evaluate side-chains 234 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 103 LEU Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL 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 208 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 182 ASP Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.140085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095569 restraints weight = 16373.813| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.16 r_work: 0.3158 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.6596 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= 0.110 Angle : 0.600 11.039 13262 Z= 0.293 Chirality : 0.043 0.171 1553 Planarity : 0.003 0.027 1698 Dihedral : 5.429 54.491 1394 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.31 % Allowed : 22.31 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.24), residues: 1249 helix: 0.25 (0.25), residues: 498 sheet: -0.77 (0.45), residues: 132 loop : -1.80 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.009 0.001 HIS F 96 PHE 0.014 0.001 PHE D 68 TYR 0.007 0.001 TYR E 258 ARG 0.004 0.000 ARG D 179 Details of bonding type rmsd hydrogen bonds : bond 0.02558 ( 249) hydrogen bonds : angle 4.11965 ( 714) covalent geometry : bond 0.00260 ( 9804) covalent geometry : angle 0.60042 (13262) Misc. bond : bond 0.00031 ( 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 254 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8293 (mm-30) REVERT: C 153 GLN cc_start: 0.9118 (pp30) cc_final: 0.8828 (tm-30) REVERT: C 161 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: C 386 ARG cc_start: 0.8752 (mmm160) cc_final: 0.8548 (mmm-85) REVERT: E 127 SER cc_start: 0.8951 (m) cc_final: 0.8513 (p) REVERT: E 181 GLN cc_start: 0.7840 (mm110) cc_final: 0.7622 (mm-40) REVERT: E 325 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8372 (mm) REVERT: F 7 GLN cc_start: 0.8338 (tp40) cc_final: 0.8132 (tp40) REVERT: F 38 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6537 (tmm) REVERT: F 73 MET cc_start: 0.8411 (ptp) cc_final: 0.7825 (mtp) REVERT: F 129 MET cc_start: 0.8592 (mmm) cc_final: 0.8300 (mmt) REVERT: F 185 PHE cc_start: 0.8337 (m-80) cc_final: 0.7921 (m-80) REVERT: F 212 MET cc_start: 0.8004 (mmm) cc_final: 0.7245 (mmp) REVERT: D 9 ASP cc_start: 0.8453 (p0) cc_final: 0.7666 (t0) REVERT: D 30 PHE cc_start: 0.8220 (t80) cc_final: 0.7874 (t80) REVERT: D 37 MET cc_start: 0.5131 (mmt) cc_final: 0.4854 (mmt) REVERT: D 123 ASN cc_start: 0.9017 (m-40) cc_final: 0.8765 (p0) REVERT: D 137 HIS cc_start: 0.8512 (p-80) cc_final: 0.8010 (p-80) REVERT: D 141 HIS cc_start: 0.8621 (m-70) cc_final: 0.8232 (m170) REVERT: D 170 ASP cc_start: 0.8161 (t0) cc_final: 0.7946 (t0) REVERT: D 171 GLU cc_start: 0.8170 (tp30) cc_final: 0.7700 (tm-30) REVERT: D 212 MET cc_start: 0.8096 (mmt) cc_final: 0.7661 (tpp) outliers start: 44 outliers final: 35 residues processed: 239 average time/residue: 0.2182 time to fit residues: 72.6751 Evaluate side-chains 231 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL 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 208 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 38 MET 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 F residue 200 LEU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.0470 chunk 59 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.139895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095704 restraints weight = 16534.872| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.15 r_work: 0.3157 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.6682 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= 0.114 Angle : 0.618 11.615 13262 Z= 0.300 Chirality : 0.043 0.269 1553 Planarity : 0.003 0.032 1698 Dihedral : 5.459 54.554 1394 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.01 % Allowed : 22.90 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1249 helix: 0.43 (0.26), residues: 488 sheet: -0.84 (0.45), residues: 134 loop : -1.81 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 246 HIS 0.007 0.001 HIS F 96 PHE 0.053 0.002 PHE F 95 TYR 0.007 0.001 TYR E 258 ARG 0.007 0.000 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.02568 ( 249) hydrogen bonds : angle 4.05341 ( 714) covalent geometry : bond 0.00270 ( 9804) covalent geometry : angle 0.61763 (13262) Misc. bond : bond 0.00034 ( 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 243 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 54 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8283 (mm-30) REVERT: C 153 GLN cc_start: 0.9125 (pp30) cc_final: 0.8834 (tm-30) REVERT: C 161 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: E 127 SER cc_start: 0.9009 (m) cc_final: 0.8565 (p) REVERT: E 181 GLN cc_start: 0.7795 (mm110) cc_final: 0.7567 (mm-40) REVERT: E 203 PHE cc_start: 0.7965 (t80) cc_final: 0.7746 (t80) REVERT: E 325 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8375 (mm) REVERT: F 38 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6626 (tmm) REVERT: F 73 MET cc_start: 0.8401 (ptp) cc_final: 0.7763 (mtp) REVERT: F 129 MET cc_start: 0.8607 (mmm) cc_final: 0.8324 (mmt) REVERT: F 185 PHE cc_start: 0.8306 (m-80) cc_final: 0.7884 (m-80) REVERT: F 212 MET cc_start: 0.8077 (mmm) cc_final: 0.7239 (mmp) REVERT: D 9 ASP cc_start: 0.8463 (p0) cc_final: 0.7718 (t0) REVERT: D 30 PHE cc_start: 0.8210 (t80) cc_final: 0.7868 (t80) REVERT: D 94 GLN cc_start: 0.7869 (pt0) cc_final: 0.6633 (tt0) REVERT: D 123 ASN cc_start: 0.9004 (m-40) cc_final: 0.8769 (p0) REVERT: D 137 HIS cc_start: 0.8516 (p-80) cc_final: 0.8036 (p-80) REVERT: D 141 HIS cc_start: 0.8623 (m-70) cc_final: 0.8240 (m170) REVERT: D 170 ASP cc_start: 0.8319 (t0) cc_final: 0.8068 (t0) REVERT: D 171 GLU cc_start: 0.8149 (tp30) cc_final: 0.7645 (tm-30) REVERT: D 212 MET cc_start: 0.8109 (mmt) cc_final: 0.7782 (tpp) outliers start: 41 outliers final: 38 residues processed: 229 average time/residue: 0.2047 time to fit residues: 66.0733 Evaluate side-chains 241 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 161 GLN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain E residue 9 ILE Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 115 VAL 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 201 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 365 ILE Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 38 MET 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 F residue 200 LEU Chi-restraints excluded: chain D residue 8 CYS Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 199 PHE Chi-restraints excluded: chain V residue 1 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.0030 chunk 70 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 17 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.0170 chunk 97 optimal weight: 0.0060 chunk 41 optimal weight: 0.5980 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.142358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098479 restraints weight = 16386.609| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.15 r_work: 0.3208 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9806 Z= 0.103 Angle : 0.639 11.503 13262 Z= 0.305 Chirality : 0.043 0.291 1553 Planarity : 0.003 0.031 1698 Dihedral : 5.173 55.031 1394 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.03 % Allowed : 24.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.24), residues: 1249 helix: 0.77 (0.26), residues: 460 sheet: -0.85 (0.42), residues: 154 loop : -1.65 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 246 HIS 0.004 0.001 HIS D 96 PHE 0.023 0.001 PHE D 68 TYR 0.006 0.001 TYR E 258 ARG 0.008 0.000 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.02188 ( 249) hydrogen bonds : angle 3.98347 ( 714) covalent geometry : bond 0.00238 ( 9804) covalent geometry : angle 0.63855 (13262) Misc. bond : bond 0.00024 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5522.89 seconds wall clock time: 98 minutes 3.66 seconds (5883.66 seconds total)