Starting phenix.real_space_refine on Fri Sep 11 05:01:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6irt_9722/09_2026/6irt_9722_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6irt_9722/09_2026/6irt_9722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6irt_9722/09_2026/6irt_9722_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6irt_9722/09_2026/6irt_9722_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6irt_9722/09_2026/6irt_9722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6irt_9722/09_2026/6irt_9722.map" } resolution = 3.5 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= 0.006 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 P 2 5.49 5 S 27 5.16 5 C 4815 2.51 5 N 1173 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7348 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3650 Classifications: {'peptide': 469} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 446} Chain: "B" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3479 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 432} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 107 Unusual residues: {'3PH': 2, 'AUU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.64, per 1000 atoms: 0.22 Number of scatterers: 7348 At special positions: 0 Unit cell: (82.916, 84.007, 124.374, 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) S 27 16.00 P 2 15.00 O 1331 8.00 N 1173 7.00 C 4815 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 366 " " NAG E 1 " - " ASN A 382 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 477.9 milliseconds 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 3 sheets defined 58.4% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 168 through 175 removed outlier: 3.604A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 185 through 208 removed outlier: 3.616A pdb=" N PHE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 205 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.735A pdb=" N HIS A 221 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 222 " --> pdb=" O TRP A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.876A pdb=" N SER A 254 " --> pdb=" O ASP A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 removed outlier: 3.866A pdb=" N LYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 342 removed outlier: 4.203A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 354 Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.768A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 removed outlier: 3.665A pdb=" N LEU A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.787A pdb=" N GLN A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.522A pdb=" N GLN A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 457 " --> pdb=" O LEU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 497 removed outlier: 4.405A pdb=" N PHE A 497 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.595A pdb=" N ARG A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.784A pdb=" N HIS A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 removed outlier: 4.369A pdb=" N ALA B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE B 58 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 74 removed outlier: 4.759A pdb=" N THR B 71 " --> pdb=" O ILE B 68 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 81 through 110 removed outlier: 3.607A pdb=" N LEU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 93 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 removed outlier: 3.569A pdb=" N VAL B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 139 through 158 removed outlier: 3.581A pdb=" N SER B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 removed outlier: 4.333A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 182 " --> pdb=" O CYS B 178 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 199 removed outlier: 4.151A pdb=" N ARG B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 222 removed outlier: 3.544A pdb=" N LEU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 219 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 222 " --> pdb=" O GLN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 removed outlier: 4.399A pdb=" N GLU B 234 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 235 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 removed outlier: 3.633A pdb=" N SER B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 removed outlier: 3.727A pdb=" N VAL B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.079A pdb=" N ILE B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 300 removed outlier: 3.694A pdb=" N ALA B 277 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.730A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 308 Processing helix chain 'B' and resid 310 through 320 removed outlier: 4.029A pdb=" N ASP B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 320 " --> pdb=" O GLY B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.550A pdb=" N VAL B 339 " --> pdb=" O CYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 344 through 355 removed outlier: 3.954A pdb=" N ARG B 348 " --> pdb=" O PHE B 344 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 355 " --> pdb=" O PHE B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 3.675A pdb=" N PHE B 379 " --> pdb=" O PRO B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 393 through 421 removed outlier: 3.509A pdb=" N PHE B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N PHE B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 412 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 419 " --> pdb=" O MET B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 453 removed outlier: 3.808A pdb=" N ALA B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 447 " --> pdb=" O CYS B 443 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 451 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP B 452 " --> pdb=" O ALA B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 removed outlier: 4.293A pdb=" N CYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE B 460 " --> pdb=" O VAL B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 476 Processing helix chain 'B' and resid 484 through 501 removed outlier: 3.950A pdb=" N PHE B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 400 through 401 removed outlier: 6.562A pdb=" N PHE A 346 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 305 " --> pdb=" O GLY A 345 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 226 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.700A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 556 " --> pdb=" O PHE A 564 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG A 626 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU A 596 " --> pdb=" O ARG A 626 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 852 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: 1.01 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2069 1.33 - 1.45: 1333 1.45 - 1.57: 4077 1.57 - 1.69: 3 1.69 - 1.81: 42 Bond restraints: 7524 Sorted by residual: bond pdb=" C06 AUU B 603 " pdb=" C08 AUU B 603 " ideal model delta sigma weight residual 1.531 1.707 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" C04 AUU B 603 " pdb=" C09 AUU B 603 " ideal model delta sigma weight residual 1.535 1.362 0.173 2.00e-02 2.50e+03 7.53e+01 bond pdb=" C04 AUU B 603 " pdb=" C08 AUU B 603 " ideal model delta sigma weight residual 1.533 1.699 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C06 AUU B 603 " pdb=" C07 AUU B 603 " ideal model delta sigma weight residual 1.534 1.370 0.164 2.00e-02 2.50e+03 6.71e+01 bond pdb=" C06 AUU B 603 " pdb=" C11 AUU B 603 " ideal model delta sigma weight residual 1.537 1.383 0.154 2.00e-02 2.50e+03 5.94e+01 ... (remaining 7519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9548 2.19 - 4.39: 554 4.39 - 6.58: 79 6.58 - 8.78: 35 8.78 - 10.97: 13 Bond angle restraints: 10229 Sorted by residual: angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 111.36 122.33 -10.97 1.09e+00 8.42e-01 1.01e+02 angle pdb=" C SER A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 128.89 -9.05 1.25e+00 6.40e-01 5.24e+01 angle pdb=" N LEU B 320 " pdb=" CA LEU B 320 " pdb=" C LEU B 320 " ideal model delta sigma weight residual 108.34 116.69 -8.35 1.31e+00 5.83e-01 4.07e+01 angle pdb=" C PHE B 161 " pdb=" N PRO B 162 " pdb=" CD PRO B 162 " ideal model delta sigma weight residual 120.60 109.75 10.85 2.20e+00 2.07e-01 2.43e+01 angle pdb=" CA LEU B 469 " pdb=" C LEU B 469 " pdb=" N PRO B 470 " ideal model delta sigma weight residual 120.81 116.58 4.23 8.60e-01 1.35e+00 2.42e+01 ... (remaining 10224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 4286 21.14 - 42.28: 208 42.28 - 63.42: 29 63.42 - 84.56: 11 84.56 - 105.70: 10 Dihedral angle restraints: 4544 sinusoidal: 1891 harmonic: 2653 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual -86.00 -157.02 71.02 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA VAL B 322 " pdb=" C VAL B 322 " pdb=" N MET B 323 " pdb=" CA MET B 323 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLN A 323 " pdb=" C GLN A 323 " pdb=" N VAL A 324 " pdb=" CA VAL A 324 " ideal model delta harmonic sigma weight residual 180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 4541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 1194 0.277 - 0.553: 7 0.553 - 0.830: 0 0.830 - 1.106: 0 1.106 - 1.383: 2 Chirality restraints: 1203 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 507 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.78e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 382 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.22e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 366 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.88 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 1200 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 366 " 0.102 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" CG ASN A 366 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN A 366 " 0.153 2.00e-02 2.50e+03 pdb=" ND2 ASN A 366 " -0.471 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 382 " -0.123 2.00e-02 2.50e+03 2.00e-01 5.00e+02 pdb=" CG ASN A 382 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN A 382 " -0.058 2.00e-02 2.50e+03 pdb=" ND2 ASN A 382 " 0.353 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.231 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 507 " -0.072 2.00e-02 2.50e+03 8.36e-02 8.74e+01 pdb=" CG ASN A 507 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 507 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 507 " 0.139 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1762 2.77 - 3.30: 6596 3.30 - 3.84: 11683 3.84 - 4.37: 13661 4.37 - 4.90: 22977 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.241 3.040 nonbonded pdb=" OG SER A 599 " pdb=" OE2 GLU A 621 " model vdw 2.284 3.040 nonbonded pdb=" O ASP A 516 " pdb=" OG SER A 522 " model vdw 2.284 3.040 nonbonded pdb=" O THR A 460 " pdb=" NH1 ARG A 556 " model vdw 2.291 3.120 nonbonded pdb=" O GLY B 107 " pdb=" OG SER B 111 " model vdw 2.300 3.040 ... (remaining 56674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 7.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.012 0.176 7533 Z= 0.539 Angle : 1.297 17.404 10255 Z= 0.657 Chirality : 0.088 1.383 1203 Planarity : 0.008 0.063 1255 Dihedral : 14.093 105.703 2837 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.22 % Favored : 90.02 % Rotamer: Outliers : 3.01 % Allowed : 6.54 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -5.53 (0.19), residues: 922 helix: -4.19 (0.12), residues: 470 sheet: -1.95 (0.65), residues: 49 loop : -3.07 (0.26), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 227 TYR 0.036 0.004 TYR A 454 PHE 0.024 0.003 PHE A 552 TRP 0.031 0.004 TRP B 417 HIS 0.009 0.004 HIS A 620 Details of bonding type rmsd/Z covalent geometry : bond 0.01162 / 0.54 ( 7524) covalent geometry : angle 1.23365 / 0.64 (10229) SS BOND : bond 0.00530 / 0.28 ( 1) SS BOND : angle 1.23577 / 0.72 ( 2) hydrogen bonds : bond 0.31282 / 19.19 ( 297) hydrogen bonds : angle 10.07666 / 6.97 ( 852) link_BETA1-4 : bond 0.01414 / 0.68 ( 4) link_BETA1-4 : angle 3.79315 / 2.21 ( 12) link_NAG-ASN : bond 0.05936 / 2.65 ( 4) link_NAG-ASN : angle 11.21040 / 5.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7076 (mm-30) REVERT: B 146 TYR cc_start: 0.8685 (t80) cc_final: 0.8121 (t80) REVERT: B 195 ARG cc_start: 0.8020 (mtm110) cc_final: 0.7690 (ptt180) REVERT: B 218 GLN cc_start: 0.8445 (tp40) cc_final: 0.8213 (tp40) REVERT: B 315 PHE cc_start: 0.8297 (t80) cc_final: 0.8064 (t80) REVERT: B 419 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7342 (mmp-170) REVERT: B 440 ILE cc_start: 0.9232 (mt) cc_final: 0.9008 (mt) REVERT: B 466 LEU cc_start: 0.8515 (mp) cc_final: 0.8275 (tp) REVERT: B 478 TRP cc_start: 0.6616 (t-100) cc_final: 0.6280 (t-100) REVERT: B 501 GLN cc_start: 0.8096 (tt0) cc_final: 0.7827 (tm-30) outliers start: 23 outliers final: 5 residues processed: 234 average time/residue: 0.0895 time to fit residues: 27.6126 Evaluate side-chains 139 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 131 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 221 HIS A 232 GLN A 268 ASN A 388 GLN A 483 GLN A 561 ASN A 620 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095212 restraints weight = 13397.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098939 restraints weight = 6792.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101383 restraints weight = 4609.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102918 restraints weight = 3653.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103909 restraints weight = 3171.744| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7533 Z= 0.173 Angle : 0.880 13.055 10255 Z= 0.418 Chirality : 0.051 0.674 1203 Planarity : 0.006 0.043 1255 Dihedral : 12.447 90.547 1256 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.03 % Favored : 91.76 % Rotamer: Outliers : 2.75 % Allowed : 13.61 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -4.01 (0.23), residues: 922 helix: -2.56 (0.17), residues: 489 sheet: -1.90 (0.62), residues: 60 loop : -2.76 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 355 TYR 0.014 0.002 TYR B 318 PHE 0.022 0.002 PHE B 95 TRP 0.020 0.002 TRP B 134 HIS 0.005 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 7524) covalent geometry : angle 0.84367 / 0.41 (10229) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 0.90123 / 0.53 ( 2) hydrogen bonds : bond 0.06286 / 3.89 ( 297) hydrogen bonds : angle 5.59889 / 3.86 ( 852) link_BETA1-4 : bond 0.00444 / 0.22 ( 4) link_BETA1-4 : angle 2.50084 / 1.40 ( 12) link_NAG-ASN : bond 0.00979 / 0.48 ( 4) link_NAG-ASN : angle 6.95318 / 3.97 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7823 (ttp) cc_final: 0.7555 (mmp) REVERT: A 279 LEU cc_start: 0.8072 (pp) cc_final: 0.7804 (pp) REVERT: A 313 TYR cc_start: 0.8648 (p90) cc_final: 0.8426 (p90) REVERT: B 120 MET cc_start: 0.9081 (tpp) cc_final: 0.8832 (tpp) REVERT: B 146 TYR cc_start: 0.8644 (t80) cc_final: 0.8097 (t80) REVERT: B 195 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7728 (ptt180) REVERT: B 218 GLN cc_start: 0.8707 (tp40) cc_final: 0.8434 (tp-100) REVERT: B 254 TYR cc_start: 0.8744 (m-80) cc_final: 0.8274 (m-80) REVERT: B 352 VAL cc_start: 0.9404 (t) cc_final: 0.9035 (t) REVERT: B 466 LEU cc_start: 0.8641 (mp) cc_final: 0.8324 (tp) REVERT: B 478 TRP cc_start: 0.6554 (t-100) cc_final: 0.6278 (t-100) REVERT: B 499 LEU cc_start: 0.9122 (tt) cc_final: 0.8878 (tt) outliers start: 21 outliers final: 10 residues processed: 187 average time/residue: 0.0661 time to fit residues: 17.4480 Evaluate side-chains 156 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.0470 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092501 restraints weight = 13726.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096083 restraints weight = 7234.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098430 restraints weight = 4997.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099766 restraints weight = 4006.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.100795 restraints weight = 3521.655| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7533 Z= 0.144 Angle : 0.777 11.198 10255 Z= 0.367 Chirality : 0.046 0.456 1203 Planarity : 0.005 0.039 1255 Dihedral : 10.462 80.388 1249 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.16 % Favored : 92.52 % Rotamer: Outliers : 3.66 % Allowed : 16.10 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.85 (0.25), residues: 922 helix: -1.39 (0.21), residues: 496 sheet: -1.11 (0.67), residues: 54 loop : -2.61 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 272 TYR 0.015 0.001 TYR B 119 PHE 0.021 0.001 PHE B 95 TRP 0.016 0.001 TRP B 405 HIS 0.005 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7524) covalent geometry : angle 0.74492 / 0.36 (10229) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.59892 / 0.34 ( 2) hydrogen bonds : bond 0.04949 / 3.08 ( 297) hydrogen bonds : angle 5.05001 / 3.47 ( 852) link_BETA1-4 : bond 0.00772 / 0.36 ( 4) link_BETA1-4 : angle 2.50935 / 1.41 ( 12) link_NAG-ASN : bond 0.00831 / 0.41 ( 4) link_NAG-ASN : angle 6.06778 / 3.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6362 (mt-10) REVERT: B 146 TYR cc_start: 0.8622 (t80) cc_final: 0.8088 (t80) REVERT: B 195 ARG cc_start: 0.7927 (mtm110) cc_final: 0.7613 (ptt180) REVERT: B 218 GLN cc_start: 0.8775 (tp40) cc_final: 0.8487 (tp-100) REVERT: B 248 TYR cc_start: 0.8477 (m-10) cc_final: 0.8256 (m-10) REVERT: B 254 TYR cc_start: 0.8739 (m-80) cc_final: 0.8296 (m-80) REVERT: B 293 ASN cc_start: 0.9136 (m-40) cc_final: 0.8860 (m110) REVERT: B 318 TYR cc_start: 0.6810 (t80) cc_final: 0.6593 (t80) REVERT: B 466 LEU cc_start: 0.8617 (mp) cc_final: 0.8307 (tp) REVERT: B 499 LEU cc_start: 0.9064 (tt) cc_final: 0.8861 (tt) outliers start: 28 outliers final: 15 residues processed: 173 average time/residue: 0.0599 time to fit residues: 15.1903 Evaluate side-chains 153 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 28 optimal weight: 0.0010 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.8766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 317 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.124188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096314 restraints weight = 13656.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.100236 restraints weight = 6852.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.102741 restraints weight = 4661.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104290 restraints weight = 3727.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105147 restraints weight = 3255.432| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7533 Z= 0.142 Angle : 0.747 10.636 10255 Z= 0.350 Chirality : 0.046 0.425 1203 Planarity : 0.004 0.040 1255 Dihedral : 9.401 70.496 1246 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.48 % Favored : 92.30 % Rotamer: Outliers : 3.53 % Allowed : 16.75 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.26 (0.26), residues: 922 helix: -0.84 (0.22), residues: 499 sheet: -0.91 (0.66), residues: 55 loop : -2.47 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 272 TYR 0.016 0.001 TYR A 405 PHE 0.023 0.001 PHE B 95 TRP 0.016 0.001 TRP B 405 HIS 0.009 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7524) covalent geometry : angle 0.71875 / 0.34 (10229) SS BOND : bond 0.00128 / 0.07 ( 1) SS BOND : angle 0.53854 / 0.30 ( 2) hydrogen bonds : bond 0.04382 / 2.75 ( 297) hydrogen bonds : angle 4.77324 / 3.26 ( 852) link_BETA1-4 : bond 0.00638 / 0.30 ( 4) link_BETA1-4 : angle 2.52371 / 1.41 ( 12) link_NAG-ASN : bond 0.00612 / 0.30 ( 4) link_NAG-ASN : angle 5.44803 / 3.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6768 (mmp) cc_final: 0.6345 (mmp) REVERT: A 534 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6352 (mt-10) REVERT: A 555 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8882 (pt) REVERT: B 146 TYR cc_start: 0.8679 (t80) cc_final: 0.8205 (t80) REVERT: B 195 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7637 (ptt180) REVERT: B 254 TYR cc_start: 0.8774 (m-80) cc_final: 0.8279 (m-80) REVERT: B 318 TYR cc_start: 0.6955 (t80) cc_final: 0.6682 (t80) REVERT: B 466 LEU cc_start: 0.8589 (mp) cc_final: 0.8275 (tp) outliers start: 27 outliers final: 16 residues processed: 158 average time/residue: 0.0584 time to fit residues: 13.5821 Evaluate side-chains 152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.0870 chunk 42 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 GLN B 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.096355 restraints weight = 13467.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.100176 restraints weight = 6714.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.102685 restraints weight = 4583.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104246 restraints weight = 3657.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105091 restraints weight = 3187.291| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7533 Z= 0.140 Angle : 0.727 9.471 10255 Z= 0.340 Chirality : 0.045 0.416 1203 Planarity : 0.004 0.039 1255 Dihedral : 8.714 59.968 1244 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.59 % Favored : 92.19 % Rotamer: Outliers : 3.66 % Allowed : 16.75 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.26), residues: 922 helix: -0.43 (0.23), residues: 497 sheet: -0.65 (0.67), residues: 55 loop : -2.43 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.017 0.001 TYR A 405 PHE 0.024 0.001 PHE B 95 TRP 0.019 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7524) covalent geometry : angle 0.70165 / 0.33 (10229) SS BOND : bond 0.00163 / 0.09 ( 1) SS BOND : angle 0.37943 / 0.22 ( 2) hydrogen bonds : bond 0.04012 / 2.51 ( 297) hydrogen bonds : angle 4.61116 / 3.15 ( 852) link_BETA1-4 : bond 0.00716 / 0.34 ( 4) link_BETA1-4 : angle 2.51120 / 1.40 ( 12) link_NAG-ASN : bond 0.00521 / 0.26 ( 4) link_NAG-ASN : angle 5.00722 / 2.80 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6890 (mmp) cc_final: 0.6602 (mmp) REVERT: B 146 TYR cc_start: 0.8654 (t80) cc_final: 0.8193 (t80) REVERT: B 195 ARG cc_start: 0.7909 (mtm110) cc_final: 0.7639 (ptt180) REVERT: B 254 TYR cc_start: 0.8807 (m-80) cc_final: 0.8286 (m-80) REVERT: B 438 PHE cc_start: 0.8061 (t80) cc_final: 0.7790 (t80) REVERT: B 466 LEU cc_start: 0.8642 (mp) cc_final: 0.8308 (tp) REVERT: B 501 GLN cc_start: 0.8475 (tm-30) cc_final: 0.7793 (tm-30) outliers start: 28 outliers final: 18 residues processed: 159 average time/residue: 0.0523 time to fit residues: 12.5042 Evaluate side-chains 154 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 0.4980 chunk 38 optimal weight: 0.0170 chunk 78 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097859 restraints weight = 13425.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101679 restraints weight = 6683.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104222 restraints weight = 4543.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105808 restraints weight = 3606.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106702 restraints weight = 3131.480| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7533 Z= 0.123 Angle : 0.714 9.400 10255 Z= 0.334 Chirality : 0.045 0.414 1203 Planarity : 0.004 0.040 1255 Dihedral : 8.214 58.894 1244 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.48 % Favored : 92.30 % Rotamer: Outliers : 2.88 % Allowed : 18.98 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.27), residues: 922 helix: -0.14 (0.23), residues: 501 sheet: -0.37 (0.69), residues: 55 loop : -2.40 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.017 0.001 TYR A 405 PHE 0.024 0.001 PHE B 95 TRP 0.019 0.001 TRP B 405 HIS 0.002 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7524) covalent geometry : angle 0.69041 / 0.33 (10229) SS BOND : bond 0.00146 / 0.08 ( 1) SS BOND : angle 0.29731 / 0.17 ( 2) hydrogen bonds : bond 0.03676 / 2.31 ( 297) hydrogen bonds : angle 4.50718 / 3.09 ( 852) link_BETA1-4 : bond 0.00729 / 0.35 ( 4) link_BETA1-4 : angle 2.48424 / 1.38 ( 12) link_NAG-ASN : bond 0.00528 / 0.26 ( 4) link_NAG-ASN : angle 4.84586 / 2.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6870 (mmp) cc_final: 0.6518 (mmp) REVERT: A 249 LEU cc_start: 0.9265 (mt) cc_final: 0.8923 (mt) REVERT: A 554 TYR cc_start: 0.9298 (p90) cc_final: 0.9090 (p90) REVERT: B 120 MET cc_start: 0.9064 (tpp) cc_final: 0.8683 (tpp) REVERT: B 146 TYR cc_start: 0.8657 (t80) cc_final: 0.8211 (t80) REVERT: B 195 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7618 (ptt180) REVERT: B 254 TYR cc_start: 0.8788 (m-80) cc_final: 0.8289 (m-80) REVERT: B 265 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 297 PHE cc_start: 0.7957 (m-80) cc_final: 0.7609 (m-80) REVERT: B 438 PHE cc_start: 0.8109 (t80) cc_final: 0.7723 (t80) REVERT: B 453 LYS cc_start: 0.8449 (tppt) cc_final: 0.7962 (mmtt) REVERT: B 466 LEU cc_start: 0.8700 (mp) cc_final: 0.8397 (tp) REVERT: B 501 GLN cc_start: 0.8479 (tm-30) cc_final: 0.7791 (tm-30) outliers start: 22 outliers final: 17 residues processed: 154 average time/residue: 0.0572 time to fit residues: 12.8495 Evaluate side-chains 159 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 77 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 0.0050 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.125238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097644 restraints weight = 13467.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101612 restraints weight = 6695.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104151 restraints weight = 4548.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105701 restraints weight = 3632.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106516 restraints weight = 3170.409| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7533 Z= 0.126 Angle : 0.715 9.191 10255 Z= 0.333 Chirality : 0.045 0.408 1203 Planarity : 0.004 0.038 1255 Dihedral : 7.855 58.569 1244 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.16 % Favored : 92.52 % Rotamer: Outliers : 3.14 % Allowed : 19.37 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.27), residues: 922 helix: 0.01 (0.23), residues: 500 sheet: -0.26 (0.68), residues: 62 loop : -2.38 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.015 0.001 TYR A 405 PHE 0.024 0.001 PHE B 95 TRP 0.022 0.001 TRP B 405 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 7524) covalent geometry : angle 0.69244 / 0.33 (10229) SS BOND : bond 0.00130 / 0.07 ( 1) SS BOND : angle 0.34875 / 0.21 ( 2) hydrogen bonds : bond 0.03573 / 2.26 ( 297) hydrogen bonds : angle 4.42212 / 3.04 ( 852) link_BETA1-4 : bond 0.00721 / 0.34 ( 4) link_BETA1-4 : angle 2.45882 / 1.36 ( 12) link_NAG-ASN : bond 0.00474 / 0.24 ( 4) link_NAG-ASN : angle 4.75592 / 2.63 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6871 (mmp) cc_final: 0.6596 (mmp) REVERT: A 249 LEU cc_start: 0.9257 (mt) cc_final: 0.8925 (mt) REVERT: B 146 TYR cc_start: 0.8670 (t80) cc_final: 0.8256 (t80) REVERT: B 195 ARG cc_start: 0.7930 (mtm110) cc_final: 0.7631 (ptt180) REVERT: B 206 LEU cc_start: 0.9035 (tt) cc_final: 0.8829 (pp) REVERT: B 254 TYR cc_start: 0.8799 (m-80) cc_final: 0.8281 (m-80) REVERT: B 265 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7123 (tm-30) REVERT: B 297 PHE cc_start: 0.7870 (m-80) cc_final: 0.7468 (m-80) REVERT: B 438 PHE cc_start: 0.8093 (t80) cc_final: 0.7791 (t80) REVERT: B 453 LYS cc_start: 0.8403 (tppt) cc_final: 0.7902 (mmtt) REVERT: B 466 LEU cc_start: 0.8687 (mp) cc_final: 0.8400 (tp) REVERT: B 501 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7955 (tm-30) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.0574 time to fit residues: 12.7267 Evaluate side-chains 146 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 467 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 57 optimal weight: 0.0980 chunk 37 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097684 restraints weight = 13457.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101666 restraints weight = 6783.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104227 restraints weight = 4641.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105757 restraints weight = 3723.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106478 restraints weight = 3259.655| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7533 Z= 0.126 Angle : 0.732 10.684 10255 Z= 0.341 Chirality : 0.046 0.407 1203 Planarity : 0.004 0.039 1255 Dihedral : 7.618 58.658 1244 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.05 % Favored : 92.62 % Rotamer: Outliers : 2.88 % Allowed : 20.68 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.27), residues: 922 helix: 0.10 (0.23), residues: 501 sheet: -0.32 (0.66), residues: 62 loop : -2.38 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.015 0.001 TYR A 405 PHE 0.028 0.001 PHE A 346 TRP 0.022 0.001 TRP B 405 HIS 0.001 0.001 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7524) covalent geometry : angle 0.71050 / 0.34 (10229) SS BOND : bond 0.00127 / 0.07 ( 1) SS BOND : angle 0.32825 / 0.19 ( 2) hydrogen bonds : bond 0.03474 / 2.19 ( 297) hydrogen bonds : angle 4.37880 / 3.00 ( 852) link_BETA1-4 : bond 0.00762 / 0.36 ( 4) link_BETA1-4 : angle 2.42801 / 1.35 ( 12) link_NAG-ASN : bond 0.00472 / 0.24 ( 4) link_NAG-ASN : angle 4.70021 / 2.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6853 (mmp) cc_final: 0.6586 (mmp) REVERT: A 249 LEU cc_start: 0.9243 (mt) cc_final: 0.8915 (mt) REVERT: A 554 TYR cc_start: 0.9319 (p90) cc_final: 0.9100 (p90) REVERT: B 146 TYR cc_start: 0.8659 (t80) cc_final: 0.8280 (t80) REVERT: B 195 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7590 (ptt180) REVERT: B 254 TYR cc_start: 0.8806 (m-80) cc_final: 0.8281 (m-80) REVERT: B 265 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7110 (tm-30) REVERT: B 365 MET cc_start: 0.8768 (mmm) cc_final: 0.8339 (mtp) REVERT: B 438 PHE cc_start: 0.8062 (t80) cc_final: 0.7807 (t80) REVERT: B 453 LYS cc_start: 0.8439 (tppt) cc_final: 0.7923 (mmtt) REVERT: B 466 LEU cc_start: 0.8765 (mp) cc_final: 0.8502 (tp) REVERT: B 501 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8082 (tm-30) outliers start: 22 outliers final: 17 residues processed: 150 average time/residue: 0.0542 time to fit residues: 11.9938 Evaluate side-chains 151 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 427 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 47 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097826 restraints weight = 13279.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.101679 restraints weight = 6708.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104198 restraints weight = 4619.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.105761 restraints weight = 3694.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106556 restraints weight = 3220.625| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7533 Z= 0.133 Angle : 0.733 9.141 10255 Z= 0.343 Chirality : 0.046 0.403 1203 Planarity : 0.004 0.040 1255 Dihedral : 7.385 58.438 1244 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.83 % Favored : 92.84 % Rotamer: Outliers : 2.62 % Allowed : 20.94 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.27), residues: 922 helix: 0.15 (0.23), residues: 502 sheet: -0.26 (0.66), residues: 62 loop : -2.32 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.014 0.001 TYR A 405 PHE 0.024 0.001 PHE B 95 TRP 0.023 0.001 TRP B 405 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7524) covalent geometry : angle 0.71164 / 0.34 (10229) SS BOND : bond 0.00113 / 0.06 ( 1) SS BOND : angle 0.41738 / 0.25 ( 2) hydrogen bonds : bond 0.03452 / 2.17 ( 297) hydrogen bonds : angle 4.35141 / 2.99 ( 852) link_BETA1-4 : bond 0.00716 / 0.34 ( 4) link_BETA1-4 : angle 2.40103 / 1.34 ( 12) link_NAG-ASN : bond 0.00407 / 0.20 ( 4) link_NAG-ASN : angle 4.64551 / 2.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6663 (mmp) cc_final: 0.6383 (mmp) REVERT: A 249 LEU cc_start: 0.9235 (mt) cc_final: 0.8908 (mt) REVERT: B 146 TYR cc_start: 0.8684 (t80) cc_final: 0.8324 (t80) REVERT: B 195 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7571 (ptt180) REVERT: B 254 TYR cc_start: 0.8832 (m-80) cc_final: 0.8282 (m-80) REVERT: B 265 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 365 MET cc_start: 0.8830 (mmm) cc_final: 0.8447 (mtp) REVERT: B 438 PHE cc_start: 0.8070 (t80) cc_final: 0.7845 (t80) REVERT: B 453 LYS cc_start: 0.8460 (tppt) cc_final: 0.7955 (mmtt) REVERT: B 466 LEU cc_start: 0.8739 (mp) cc_final: 0.8477 (tp) REVERT: B 501 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8098 (tm-30) outliers start: 20 outliers final: 17 residues processed: 146 average time/residue: 0.0622 time to fit residues: 13.5028 Evaluate side-chains 150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 24 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 0.2980 chunk 46 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.3980 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099463 restraints weight = 13319.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103496 restraints weight = 6664.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106057 restraints weight = 4537.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107660 restraints weight = 3619.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108554 restraints weight = 3152.928| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7533 Z= 0.122 Angle : 0.733 9.274 10255 Z= 0.341 Chirality : 0.045 0.411 1203 Planarity : 0.004 0.041 1255 Dihedral : 7.105 59.283 1244 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.83 % Favored : 92.84 % Rotamer: Outliers : 2.36 % Allowed : 21.73 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.27), residues: 922 helix: 0.17 (0.24), residues: 497 sheet: -0.68 (0.61), residues: 69 loop : -2.34 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.014 0.001 TYR A 405 PHE 0.023 0.001 PHE B 95 TRP 0.022 0.001 TRP B 405 HIS 0.002 0.001 HIS A 543 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7524) covalent geometry : angle 0.71220 / 0.34 (10229) SS BOND : bond 0.00108 / 0.06 ( 1) SS BOND : angle 0.16644 / 0.09 ( 2) hydrogen bonds : bond 0.03270 / 2.07 ( 297) hydrogen bonds : angle 4.28587 / 2.96 ( 852) link_BETA1-4 : bond 0.00704 / 0.33 ( 4) link_BETA1-4 : angle 2.34229 / 1.31 ( 12) link_NAG-ASN : bond 0.00445 / 0.22 ( 4) link_NAG-ASN : angle 4.66668 / 2.57 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1844 Ramachandran restraints generated. 922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.6799 (mmp) cc_final: 0.6513 (mmp) REVERT: A 554 TYR cc_start: 0.9243 (p90) cc_final: 0.8944 (p90) REVERT: B 105 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8589 (tp30) REVERT: B 146 TYR cc_start: 0.8678 (t80) cc_final: 0.8294 (t80) REVERT: B 195 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7548 (ptt180) REVERT: B 254 TYR cc_start: 0.8805 (m-80) cc_final: 0.8295 (m-80) REVERT: B 265 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 365 MET cc_start: 0.8835 (mmm) cc_final: 0.8394 (mtp) REVERT: B 453 LYS cc_start: 0.8454 (tppt) cc_final: 0.7955 (mmtt) REVERT: B 466 LEU cc_start: 0.8692 (mp) cc_final: 0.8461 (tp) REVERT: B 501 GLN cc_start: 0.8429 (tt0) cc_final: 0.8055 (tm-30) outliers start: 18 outliers final: 16 residues processed: 158 average time/residue: 0.0631 time to fit residues: 14.5487 Evaluate side-chains 150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 4 optimal weight: 0.0370 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098397 restraints weight = 13385.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102434 restraints weight = 6645.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.105003 restraints weight = 4509.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106595 restraints weight = 3601.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107564 restraints weight = 3139.834| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7533 Z= 0.131 Angle : 0.755 9.371 10255 Z= 0.352 Chirality : 0.045 0.405 1203 Planarity : 0.004 0.038 1255 Dihedral : 6.997 58.883 1244 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.83 % Favored : 92.84 % Rotamer: Outliers : 2.36 % Allowed : 22.25 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.27), residues: 922 helix: 0.17 (0.23), residues: 497 sheet: -0.42 (0.64), residues: 63 loop : -2.30 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 349 TYR 0.012 0.001 TYR B 472 PHE 0.044 0.002 PHE B 438 TRP 0.022 0.001 TRP B 405 HIS 0.002 0.001 HIS B 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7524) covalent geometry : angle 0.73524 / 0.35 (10229) SS BOND : bond 0.00107 / 0.06 ( 1) SS BOND : angle 0.35159 / 0.21 ( 2) hydrogen bonds : bond 0.03335 / 2.11 ( 297) hydrogen bonds : angle 4.28137 / 2.94 ( 852) link_BETA1-4 : bond 0.00698 / 0.33 ( 4) link_BETA1-4 : angle 2.31937 / 1.30 ( 12) link_NAG-ASN : bond 0.00414 / 0.21 ( 4) link_NAG-ASN : angle 4.60201 / 2.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.18 seconds wall clock time: 22 minutes 20.89 seconds (1340.89 seconds total)