Starting phenix.real_space_refine on Wed Aug 5 09:39:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xsm_67183/08_2026/9xsm_67183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xsm_67183/08_2026/9xsm_67183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xsm_67183/08_2026/9xsm_67183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xsm_67183/08_2026/9xsm_67183.map" model { file = "/net/cci-nas-00/data/ceres_data/9xsm_67183/08_2026/9xsm_67183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xsm_67183/08_2026/9xsm_67183.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 29 5.16 5 C 5758 2.51 5 N 1577 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8977 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 4425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4425 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 18, 'TRANS': 553} Chain: "D" Number of atoms: 4509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4509 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 27, 'TRANS': 554} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.18 Number of scatterers: 8977 At special positions: 0 Unit cell: (78.2, 94.35, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 29 16.00 O 1612 8.00 N 1577 7.00 C 5758 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 202.2 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2134 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 56.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 1 through 9 removed outlier: 3.614A pdb=" N LEU C 4 " --> pdb=" O MET C 1 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 5 " --> pdb=" O ARG C 2 " (cutoff:3.500A) Proline residue: C 6 - end of helix Processing helix chain 'C' and resid 10 through 14 Processing helix chain 'C' and resid 19 through 50 removed outlier: 4.237A pdb=" N ALA C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 32 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C 38 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 4.704A pdb=" N TYR C 55 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 63 removed outlier: 3.593A pdb=" N ALA C 63 " --> pdb=" O MET C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 60 through 63' Processing helix chain 'C' and resid 64 through 69 Processing helix chain 'C' and resid 77 through 104 removed outlier: 3.558A pdb=" N LEU C 82 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 95 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR C 98 " --> pdb=" O HIS C 94 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.791A pdb=" N VAL C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 147 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.119A pdb=" N VAL C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE C 153 " --> pdb=" O MET C 149 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 155 " --> pdb=" O VAL C 151 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.670A pdb=" N GLN C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU C 195 " --> pdb=" O ASN C 191 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 removed outlier: 3.564A pdb=" N LEU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR C 214 " --> pdb=" O GLN C 210 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 209 through 215' Processing helix chain 'C' and resid 220 through 237 removed outlier: 3.730A pdb=" N GLN C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN C 232 " --> pdb=" O ASN C 228 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 236 " --> pdb=" O GLN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 removed outlier: 3.621A pdb=" N LEU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 280 through 289 removed outlier: 3.864A pdb=" N CYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 301 through 318 removed outlier: 3.594A pdb=" N GLN C 306 " --> pdb=" O GLN C 302 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 307 " --> pdb=" O HIS C 303 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 385 removed outlier: 3.898A pdb=" N LEU C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN C 384 " --> pdb=" O SER C 380 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN C 385 " --> pdb=" O THR C 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 379 through 385' Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.740A pdb=" N LEU C 407 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 444 through 453 removed outlier: 3.637A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 removed outlier: 3.847A pdb=" N ILE C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 removed outlier: 4.490A pdb=" N SER C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 561 Processing helix chain 'C' and resid 564 through 569 Processing helix chain 'D' and resid 6 through 17 removed outlier: 3.752A pdb=" N THR D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 16 " --> pdb=" O TRP D 12 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER D 17 " --> pdb=" O LEU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.898A pdb=" N LEU D 24 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 33 removed outlier: 3.845A pdb=" N PHE D 32 " --> pdb=" O ARG D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 55 removed outlier: 4.231A pdb=" N MET D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 49 " --> pdb=" O MET D 45 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS D 51 " --> pdb=" O ARG D 47 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 63 through 83 removed outlier: 3.645A pdb=" N LEU D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL D 74 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 77 " --> pdb=" O PHE D 73 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TRP D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 108 removed outlier: 4.283A pdb=" N HIS D 93 " --> pdb=" O HIS D 89 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.885A pdb=" N TRP D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 117 No H-bonds generated for 'chain 'D' and resid 116 through 117' Processing helix chain 'D' and resid 118 through 122 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.895A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.623A pdb=" N LEU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 171 removed outlier: 4.023A pdb=" N ILE D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.892A pdb=" N MET D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.722A pdb=" N ASN D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 203 through 211 removed outlier: 3.581A pdb=" N ASP D 207 " --> pdb=" O GLY D 203 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG D 208 " --> pdb=" O HIS D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 247 removed outlier: 4.081A pdb=" N GLN D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 243 " --> pdb=" O THR D 239 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG D 244 " --> pdb=" O MET D 240 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 272 removed outlier: 4.416A pdb=" N ILE D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 301 removed outlier: 3.603A pdb=" N LEU D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.943A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.509A pdb=" N ARG D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.600A pdb=" N GLY D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 390 through 398 removed outlier: 3.598A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 411 Processing helix chain 'D' and resid 451 through 456 Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.783A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 500 " --> pdb=" O VAL D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 519 No H-bonds generated for 'chain 'D' and resid 517 through 519' Processing helix chain 'D' and resid 520 through 529 removed outlier: 3.829A pdb=" N GLU D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 533 removed outlier: 4.015A pdb=" N LEU D 533 " --> pdb=" O ALA D 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 530 through 533' Processing sheet with id=AA1, first strand: chain 'C' and resid 362 through 363 Processing sheet with id=AA2, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.573A pdb=" N ILE C 371 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ALA C 370 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET C 545 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 357 through 358 removed outlier: 3.601A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 379 through 380 removed outlier: 3.823A pdb=" N VAL D 380 " --> pdb=" O VAL D 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 507 through 509 removed outlier: 3.537A pdb=" N LEU D 509 " --> pdb=" O LEU D 538 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 801 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 3618 1.38 - 1.55: 5480 1.55 - 1.71: 2 1.71 - 1.87: 55 1.87 - 2.03: 4 Bond restraints: 9159 Sorted by residual: bond pdb=" C LEU C 92 " pdb=" N GLN C 93 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.40e-02 5.10e+03 1.88e+00 bond pdb=" CB TRP D 78 " pdb=" CG TRP D 78 " ideal model delta sigma weight residual 1.498 1.461 0.037 3.10e-02 1.04e+03 1.42e+00 bond pdb=" CG LEU C 559 " pdb=" CD2 LEU C 559 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" NB HEM D 601 " pdb="FE HEM D 601 " ideal model delta sigma weight residual 2.080 1.999 0.081 7.00e-02 2.04e+02 1.32e+00 bond pdb=" C TYR D 140 " pdb=" N LEU D 141 " ideal model delta sigma weight residual 1.337 1.319 0.018 1.61e-02 3.86e+03 1.30e+00 ... (remaining 9154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 12163 2.29 - 4.58: 265 4.58 - 6.87: 25 6.87 - 9.17: 4 9.17 - 11.46: 1 Bond angle restraints: 12458 Sorted by residual: angle pdb=" N SER C 32 " pdb=" CA SER C 32 " pdb=" C SER C 32 " ideal model delta sigma weight residual 113.43 107.90 5.53 1.26e+00 6.30e-01 1.93e+01 angle pdb=" N VAL D 443 " pdb=" CA VAL D 443 " pdb=" C VAL D 443 " ideal model delta sigma weight residual 111.91 108.26 3.65 8.90e-01 1.26e+00 1.68e+01 angle pdb=" N ILE C 26 " pdb=" CA ILE C 26 " pdb=" C ILE C 26 " ideal model delta sigma weight residual 111.58 107.47 4.11 1.06e+00 8.90e-01 1.50e+01 angle pdb=" N VAL D 572 " pdb=" CA VAL D 572 " pdb=" C VAL D 572 " ideal model delta sigma weight residual 111.88 107.83 4.05 1.06e+00 8.90e-01 1.46e+01 angle pdb=" N VAL C 137 " pdb=" CA VAL C 137 " pdb=" C VAL C 137 " ideal model delta sigma weight residual 113.71 110.42 3.29 9.50e-01 1.11e+00 1.20e+01 ... (remaining 12453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4792 17.75 - 35.50: 537 35.50 - 53.25: 100 53.25 - 71.00: 11 71.00 - 88.75: 7 Dihedral angle restraints: 5447 sinusoidal: 2137 harmonic: 3310 Sorted by residual: dihedral pdb=" CA GLU D 354 " pdb=" C GLU D 354 " pdb=" N LEU D 355 " pdb=" CA LEU D 355 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ARG D 22 " pdb=" C ARG D 22 " pdb=" N TRP D 23 " pdb=" CA TRP D 23 " ideal model delta harmonic sigma weight residual 180.00 154.18 25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ALA D 123 " pdb=" C ALA D 123 " pdb=" N THR D 124 " pdb=" CA THR D 124 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 688 0.030 - 0.059: 485 0.059 - 0.088: 192 0.088 - 0.118: 61 0.118 - 0.147: 15 Chirality restraints: 1441 Sorted by residual: chirality pdb=" CA PHE C 569 " pdb=" N PHE C 569 " pdb=" C PHE C 569 " pdb=" CB PHE C 569 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB VAL C 147 " pdb=" CA VAL C 147 " pdb=" CG1 VAL C 147 " pdb=" CG2 VAL C 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA SER C 107 " pdb=" N SER C 107 " pdb=" C SER C 107 " pdb=" CB SER C 107 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1438 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 64 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO D 65 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 65 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 65 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 493 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO C 494 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 494 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 494 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 468 " -0.024 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO D 469 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 469 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 469 " -0.020 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 150 2.66 - 3.22: 8652 3.22 - 3.78: 12537 3.78 - 4.34: 17044 4.34 - 4.90: 28804 Nonbonded interactions: 67187 Sorted by model distance: nonbonded pdb=" O ALA D 518 " pdb=" NH2 ARG D 523 " model vdw 2.094 3.120 nonbonded pdb=" NH2 ARG C 431 " pdb=" OD1 ASN C 465 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLN D 129 " pdb=" OG SER D 323 " model vdw 2.228 3.040 nonbonded pdb=" O GLY C 469 " pdb=" NE2 GLN C 474 " model vdw 2.248 3.120 nonbonded pdb=" O TRP D 550 " pdb=" NH1 ARG D 566 " model vdw 2.258 3.120 ... (remaining 67182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 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 : 0.008 0.408 9160 Z= 0.299 Angle : 0.821 11.458 12458 Z= 0.459 Chirality : 0.045 0.147 1441 Planarity : 0.004 0.047 1593 Dihedral : 14.993 88.751 3313 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.30 % Favored : 86.61 % Rotamer: Outliers : 0.11 % Allowed : 11.22 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.80 (0.19), residues: 1150 helix: -3.67 (0.15), residues: 603 sheet: -5.04 (0.52), residues: 49 loop : -3.85 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 523 TYR 0.009 0.001 TYR C 7 PHE 0.025 0.002 PHE C 569 TRP 0.016 0.001 TRP D 427 HIS 0.004 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.30 ( 9159) covalent geometry : angle 0.82064 / 0.46 (12458) hydrogen bonds : bond 0.20543 / 12.56 ( 287) hydrogen bonds : angle 6.23154 / 4.40 ( 801) Misc. bond : bond 0.40849 / 21.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: C 170 MET cc_start: 0.8807 (mtp) cc_final: 0.8577 (mtp) REVERT: D 41 GLN cc_start: 0.8598 (pp30) cc_final: 0.8328 (pp30) REVERT: D 144 MET cc_start: 0.8466 (tmm) cc_final: 0.7999 (tmm) REVERT: D 185 MET cc_start: 0.7304 (tmm) cc_final: 0.7075 (tmm) REVERT: D 325 LYS cc_start: 0.9143 (tttp) cc_final: 0.8901 (tttm) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1512 time to fit residues: 16.1239 Evaluate side-chains 65 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN C 302 GLN C 306 GLN C 491 HIS C 556 HIS D 191 ASN D 194 ASN D 280 HIS D 456 GLN ** D 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.094460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075894 restraints weight = 21605.567| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.26 r_work: 0.2935 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 9160 Z= 0.115 Angle : 0.634 9.082 12458 Z= 0.311 Chirality : 0.039 0.149 1441 Planarity : 0.004 0.060 1593 Dihedral : 6.243 82.943 1265 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.83 % Allowed : 13.16 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.22), residues: 1150 helix: -2.57 (0.18), residues: 616 sheet: -5.15 (0.44), residues: 55 loop : -2.90 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 192 TYR 0.009 0.001 TYR D 567 PHE 0.017 0.001 PHE C 569 TRP 0.007 0.001 TRP D 421 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 ( 9159) covalent geometry : angle 0.63410 / 0.31 (12458) hydrogen bonds : bond 0.04301 / 2.77 ( 287) hydrogen bonds : angle 4.38326 / 3.14 ( 801) Misc. bond : bond 0.12947 / 6.81 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: C 160 PHE cc_start: 0.8362 (t80) cc_final: 0.7845 (t80) REVERT: C 164 PHE cc_start: 0.8705 (m-80) cc_final: 0.8250 (m-80) REVERT: C 170 MET cc_start: 0.8945 (mtp) cc_final: 0.8668 (mtp) REVERT: D 66 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7613 (t80) REVERT: D 144 MET cc_start: 0.9156 (tmm) cc_final: 0.8899 (tmm) REVERT: D 175 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8505 (tt) REVERT: D 185 MET cc_start: 0.7195 (tmm) cc_final: 0.6931 (tmm) REVERT: D 521 GLU cc_start: 0.8310 (tp30) cc_final: 0.7799 (mm-30) REVERT: D 523 ARG cc_start: 0.7354 (mpp-170) cc_final: 0.6643 (mpp-170) outliers start: 17 outliers final: 7 residues processed: 97 average time/residue: 0.1110 time to fit residues: 14.1518 Evaluate side-chains 79 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 544 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 GLN D 191 ASN D 194 ASN D 557 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075426 restraints weight = 21515.147| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.22 r_work: 0.2924 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 9160 Z= 0.136 Angle : 0.610 8.802 12458 Z= 0.297 Chirality : 0.039 0.137 1441 Planarity : 0.004 0.051 1593 Dihedral : 6.033 83.202 1265 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.56 % Allowed : 14.89 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.72 (0.23), residues: 1150 helix: -2.02 (0.20), residues: 615 sheet: -4.58 (0.54), residues: 48 loop : -2.72 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 85 TYR 0.007 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.009 0.001 TRP C 41 HIS 0.003 0.000 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9159) covalent geometry : angle 0.60977 / 0.30 (12458) hydrogen bonds : bond 0.04101 / 2.65 ( 287) hydrogen bonds : angle 4.23784 / 3.03 ( 801) Misc. bond : bond 0.08192 / 4.31 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: C 160 PHE cc_start: 0.8416 (t80) cc_final: 0.7913 (t80) REVERT: C 164 PHE cc_start: 0.8720 (m-80) cc_final: 0.8249 (m-80) REVERT: C 170 MET cc_start: 0.8910 (mtp) cc_final: 0.8652 (mtp) REVERT: C 490 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8616 (mm) REVERT: D 66 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7469 (t80) REVERT: D 144 MET cc_start: 0.9178 (tmm) cc_final: 0.8777 (tmm) REVERT: D 175 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8457 (tt) REVERT: D 185 MET cc_start: 0.7262 (tmm) cc_final: 0.7009 (tmm) REVERT: D 237 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8339 (mp10) REVERT: D 353 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: D 523 ARG cc_start: 0.7264 (mpp-170) cc_final: 0.6722 (mpp-170) REVERT: D 553 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8741 (mt) outliers start: 33 outliers final: 18 residues processed: 99 average time/residue: 0.1029 time to fit residues: 13.8085 Evaluate side-chains 92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075533 restraints weight = 22064.513| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.37 r_work: 0.2920 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9160 Z= 0.138 Angle : 0.595 8.610 12458 Z= 0.290 Chirality : 0.039 0.131 1441 Planarity : 0.004 0.044 1593 Dihedral : 5.918 82.763 1265 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.67 % Allowed : 16.83 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.24), residues: 1150 helix: -1.70 (0.21), residues: 619 sheet: -4.35 (0.66), residues: 41 loop : -2.60 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 85 TYR 0.007 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.007 0.001 TRP D 427 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9159) covalent geometry : angle 0.59451 / 0.29 (12458) hydrogen bonds : bond 0.03993 / 2.60 ( 287) hydrogen bonds : angle 4.15023 / 2.97 ( 801) Misc. bond : bond 0.06519 / 3.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 160 PHE cc_start: 0.8411 (t80) cc_final: 0.7902 (t80) REVERT: C 164 PHE cc_start: 0.8747 (m-80) cc_final: 0.8277 (m-80) REVERT: C 170 MET cc_start: 0.8935 (mtp) cc_final: 0.8684 (mtp) REVERT: C 490 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8621 (mm) REVERT: D 66 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.7484 (t80) REVERT: D 89 HIS cc_start: 0.8659 (m-70) cc_final: 0.8350 (m-70) REVERT: D 144 MET cc_start: 0.9171 (tmm) cc_final: 0.8789 (tmm) REVERT: D 167 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8661 (mt) REVERT: D 185 MET cc_start: 0.7288 (tmm) cc_final: 0.7030 (tmm) REVERT: D 237 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: D 353 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6931 (pm20) outliers start: 34 outliers final: 23 residues processed: 102 average time/residue: 0.1065 time to fit residues: 14.5641 Evaluate side-chains 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 69 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 369 LEU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 87 optimal weight: 0.0070 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.0470 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.096648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.077898 restraints weight = 21553.293| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.24 r_work: 0.2974 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 9160 Z= 0.092 Angle : 0.563 7.586 12458 Z= 0.271 Chirality : 0.038 0.127 1441 Planarity : 0.004 0.037 1593 Dihedral : 5.590 81.320 1265 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.78 % Allowed : 17.15 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.24), residues: 1150 helix: -1.29 (0.21), residues: 623 sheet: -3.95 (0.74), residues: 40 loop : -2.54 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 85 TYR 0.005 0.000 TYR C 78 PHE 0.016 0.001 PHE C 569 TRP 0.007 0.001 TRP C 41 HIS 0.003 0.000 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.09 ( 9159) covalent geometry : angle 0.56341 / 0.27 (12458) hydrogen bonds : bond 0.03113 / 2.02 ( 287) hydrogen bonds : angle 3.86779 / 2.78 ( 801) Misc. bond : bond 0.07819 / 4.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TRP cc_start: 0.8122 (m100) cc_final: 0.7616 (m-10) REVERT: C 160 PHE cc_start: 0.8412 (t80) cc_final: 0.7919 (t80) REVERT: C 164 PHE cc_start: 0.8727 (m-80) cc_final: 0.8291 (m-80) REVERT: C 170 MET cc_start: 0.8876 (mtp) cc_final: 0.8623 (mtp) REVERT: C 451 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8262 (mtt90) REVERT: C 490 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8511 (mm) REVERT: D 33 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.9104 (p) REVERT: D 66 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7330 (t80) REVERT: D 144 MET cc_start: 0.9109 (tmm) cc_final: 0.8743 (tmm) REVERT: D 167 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8715 (mt) REVERT: D 185 MET cc_start: 0.7280 (tmm) cc_final: 0.7037 (tmm) REVERT: D 237 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: D 353 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: D 553 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8674 (mp) outliers start: 35 outliers final: 18 residues processed: 106 average time/residue: 0.1170 time to fit residues: 16.4416 Evaluate side-chains 92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075964 restraints weight = 21619.910| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.25 r_work: 0.2934 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9160 Z= 0.142 Angle : 0.589 7.920 12458 Z= 0.284 Chirality : 0.039 0.131 1441 Planarity : 0.004 0.048 1593 Dihedral : 5.648 81.886 1265 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.99 % Allowed : 18.34 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.25), residues: 1150 helix: -1.18 (0.22), residues: 620 sheet: -3.85 (0.76), residues: 40 loop : -2.52 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 85 TYR 0.007 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.007 0.001 TRP D 427 HIS 0.003 0.001 HIS D 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 ( 9159) covalent geometry : angle 0.58935 / 0.28 (12458) hydrogen bonds : bond 0.03760 / 2.43 ( 287) hydrogen bonds : angle 3.96625 / 2.85 ( 801) Misc. bond : bond 0.05777 / 3.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TRP cc_start: 0.8145 (m100) cc_final: 0.7788 (m-10) REVERT: C 160 PHE cc_start: 0.8439 (t80) cc_final: 0.7925 (t80) REVERT: C 164 PHE cc_start: 0.8746 (m-80) cc_final: 0.8280 (m-80) REVERT: C 170 MET cc_start: 0.8934 (mtp) cc_final: 0.8707 (mtp) REVERT: C 451 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8266 (mtt90) REVERT: C 490 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8636 (mm) REVERT: D 33 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.9115 (p) REVERT: D 66 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7389 (t80) REVERT: D 144 MET cc_start: 0.9127 (tmm) cc_final: 0.8753 (tmm) REVERT: D 167 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8668 (mt) REVERT: D 185 MET cc_start: 0.7310 (tmm) cc_final: 0.7062 (tmm) REVERT: D 237 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: D 353 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: D 553 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8585 (mp) outliers start: 37 outliers final: 23 residues processed: 98 average time/residue: 0.0857 time to fit residues: 11.5652 Evaluate side-chains 92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 93 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.0270 chunk 40 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076103 restraints weight = 21662.438| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.27 r_work: 0.2937 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9160 Z= 0.126 Angle : 0.586 8.321 12458 Z= 0.281 Chirality : 0.039 0.128 1441 Planarity : 0.004 0.047 1593 Dihedral : 5.598 81.452 1265 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.88 % Allowed : 18.55 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.25), residues: 1150 helix: -1.00 (0.22), residues: 617 sheet: -3.80 (0.77), residues: 40 loop : -2.43 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 85 TYR 0.006 0.001 TYR C 7 PHE 0.017 0.001 PHE C 569 TRP 0.007 0.001 TRP D 427 HIS 0.003 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 9159) covalent geometry : angle 0.58584 / 0.28 (12458) hydrogen bonds : bond 0.03617 / 2.35 ( 287) hydrogen bonds : angle 3.95349 / 2.85 ( 801) Misc. bond : bond 0.05686 / 2.99 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TRP cc_start: 0.8147 (m100) cc_final: 0.7771 (m-10) REVERT: C 160 PHE cc_start: 0.8448 (t80) cc_final: 0.7937 (t80) REVERT: C 164 PHE cc_start: 0.8729 (m-80) cc_final: 0.8276 (m-80) REVERT: C 170 MET cc_start: 0.8907 (mtp) cc_final: 0.8685 (mtp) REVERT: C 451 ARG cc_start: 0.8710 (ttm110) cc_final: 0.8275 (mtt90) REVERT: D 11 ARG cc_start: 0.8596 (mtm110) cc_final: 0.8179 (ttp80) REVERT: D 33 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9102 (p) REVERT: D 66 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.7514 (t80) REVERT: D 144 MET cc_start: 0.9101 (tmm) cc_final: 0.8739 (tmm) REVERT: D 167 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8657 (mt) REVERT: D 185 MET cc_start: 0.7268 (tmm) cc_final: 0.7033 (tmm) REVERT: D 237 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7988 (mp10) REVERT: D 353 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: D 553 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8609 (mp) outliers start: 36 outliers final: 23 residues processed: 97 average time/residue: 0.1060 time to fit residues: 13.8616 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.094493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.075929 restraints weight = 21538.493| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.25 r_work: 0.2928 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9160 Z= 0.137 Angle : 0.589 7.776 12458 Z= 0.284 Chirality : 0.039 0.128 1441 Planarity : 0.004 0.059 1593 Dihedral : 5.612 81.588 1265 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.88 % Allowed : 18.88 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.25), residues: 1150 helix: -0.91 (0.22), residues: 614 sheet: -3.80 (0.77), residues: 40 loop : -2.36 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 85 TYR 0.006 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.007 0.001 TRP D 427 HIS 0.002 0.001 HIS C 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 9159) covalent geometry : angle 0.58867 / 0.28 (12458) hydrogen bonds : bond 0.03763 / 2.45 ( 287) hydrogen bonds : angle 3.98319 / 2.88 ( 801) Misc. bond : bond 0.05264 / 2.77 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TRP cc_start: 0.8162 (m100) cc_final: 0.7772 (m-10) REVERT: C 160 PHE cc_start: 0.8468 (t80) cc_final: 0.7964 (t80) REVERT: C 164 PHE cc_start: 0.8721 (m-80) cc_final: 0.8271 (m-80) REVERT: C 170 MET cc_start: 0.8909 (mtp) cc_final: 0.8674 (mtp) REVERT: C 451 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8253 (mtt90) REVERT: D 11 ARG cc_start: 0.8595 (mtm110) cc_final: 0.8304 (ttp80) REVERT: D 33 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9110 (p) REVERT: D 66 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7525 (t80) REVERT: D 144 MET cc_start: 0.9098 (tmm) cc_final: 0.8732 (tmm) REVERT: D 167 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8668 (mt) REVERT: D 185 MET cc_start: 0.7277 (tmm) cc_final: 0.7038 (tmm) REVERT: D 237 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8027 (mp10) REVERT: D 353 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: D 553 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8610 (mp) outliers start: 36 outliers final: 27 residues processed: 97 average time/residue: 0.1011 time to fit residues: 13.3140 Evaluate side-chains 95 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 88 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 194 ASN D 424 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.094348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.075735 restraints weight = 21647.150| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.24 r_work: 0.2931 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 9160 Z= 0.143 Angle : 0.591 7.844 12458 Z= 0.286 Chirality : 0.040 0.128 1441 Planarity : 0.004 0.060 1593 Dihedral : 5.626 81.592 1265 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.99 % Allowed : 18.77 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.25), residues: 1150 helix: -0.86 (0.22), residues: 613 sheet: -3.76 (0.77), residues: 40 loop : -2.29 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 85 TYR 0.006 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.008 0.001 TRP D 427 HIS 0.002 0.001 HIS D 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.14 ( 9159) covalent geometry : angle 0.59115 / 0.29 (12458) hydrogen bonds : bond 0.03824 / 2.49 ( 287) hydrogen bonds : angle 4.00400 / 2.89 ( 801) Misc. bond : bond 0.04369 / 2.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TRP cc_start: 0.8177 (m100) cc_final: 0.7813 (m-10) REVERT: C 126 ASP cc_start: 0.8511 (m-30) cc_final: 0.8001 (m-30) REVERT: C 160 PHE cc_start: 0.8488 (t80) cc_final: 0.7990 (t80) REVERT: C 164 PHE cc_start: 0.8731 (m-80) cc_final: 0.8294 (m-80) REVERT: C 170 MET cc_start: 0.8912 (mtp) cc_final: 0.8679 (mtp) REVERT: C 451 ARG cc_start: 0.8688 (ttm110) cc_final: 0.8247 (mtt90) REVERT: D 11 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8327 (ttp80) REVERT: D 33 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9099 (p) REVERT: D 66 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7563 (t80) REVERT: D 144 MET cc_start: 0.9065 (tmm) cc_final: 0.8705 (tmm) REVERT: D 167 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8662 (mt) REVERT: D 185 MET cc_start: 0.7258 (tmm) cc_final: 0.7030 (tmm) REVERT: D 237 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: D 353 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: D 553 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8612 (mp) outliers start: 37 outliers final: 28 residues processed: 98 average time/residue: 0.0860 time to fit residues: 11.5850 Evaluate side-chains 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 114 optimal weight: 0.0070 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.075805 restraints weight = 21507.380| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.23 r_work: 0.2935 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 9160 Z= 0.166 Angle : 0.892 59.199 12458 Z= 0.504 Chirality : 0.041 0.424 1441 Planarity : 0.004 0.071 1593 Dihedral : 5.671 81.584 1265 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.78 % Allowed : 18.77 % Favored : 77.45 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.25), residues: 1150 helix: -0.84 (0.22), residues: 613 sheet: -3.75 (0.77), residues: 40 loop : -2.29 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 85 TYR 0.005 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.008 0.001 TRP D 427 HIS 0.002 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 9159) covalent geometry : angle 0.89220 / 0.50 (12458) hydrogen bonds : bond 0.03807 / 2.48 ( 287) hydrogen bonds : angle 4.00352 / 2.89 ( 801) Misc. bond : bond 0.04337 / 2.28 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 63 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TRP cc_start: 0.8166 (m100) cc_final: 0.7787 (m-10) REVERT: C 126 ASP cc_start: 0.8502 (m-30) cc_final: 0.7989 (m-30) REVERT: C 160 PHE cc_start: 0.8476 (t80) cc_final: 0.7976 (t80) REVERT: C 164 PHE cc_start: 0.8719 (m-80) cc_final: 0.8280 (m-80) REVERT: C 170 MET cc_start: 0.8912 (mtp) cc_final: 0.8680 (mtp) REVERT: C 451 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8242 (mtt90) REVERT: D 33 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9098 (p) REVERT: D 66 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7565 (t80) REVERT: D 144 MET cc_start: 0.9064 (tmm) cc_final: 0.8702 (tmm) REVERT: D 167 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8665 (mt) REVERT: D 185 MET cc_start: 0.7250 (tmm) cc_final: 0.7021 (tmm) REVERT: D 237 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7991 (mp10) REVERT: D 353 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: D 553 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8605 (mp) outliers start: 35 outliers final: 28 residues processed: 92 average time/residue: 0.1072 time to fit residues: 13.3432 Evaluate side-chains 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 304 LEU Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 427 TRP Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 500 LEU Chi-restraints excluded: chain D residue 523 ARG Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 539 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 553 ILE Chi-restraints excluded: chain D residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077337 restraints weight = 21612.510| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.18 r_work: 0.2935 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 9160 Z= 0.213 Angle : 1.131 59.190 12458 Z= 0.671 Chirality : 0.041 0.391 1441 Planarity : 0.005 0.056 1593 Dihedral : 5.675 81.576 1265 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.88 % Allowed : 18.77 % Favored : 77.35 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.25), residues: 1150 helix: -0.84 (0.22), residues: 613 sheet: -3.75 (0.77), residues: 40 loop : -2.29 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 85 TYR 0.004 0.001 TYR C 7 PHE 0.018 0.001 PHE C 569 TRP 0.008 0.001 TRP D 427 HIS 0.002 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 ( 9159) covalent geometry : angle 1.13142 / 0.67 (12458) hydrogen bonds : bond 0.03767 / 2.45 ( 287) hydrogen bonds : angle 4.00065 / 2.89 ( 801) Misc. bond : bond 0.04308 / 2.27 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1647.88 seconds wall clock time: 28 minutes 55.54 seconds (1735.54 seconds total)