Starting phenix.real_space_refine on Sat Jul 4 04:00:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nf8_12298/07_2026/7nf8_12298.cif" } resolution = 2.83 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= 0.003 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 2 5.49 5 S 98 5.16 5 C 11508 2.51 5 N 2834 2.21 5 O 3190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17634 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 3506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3506 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 25, 'TRANS': 429} Chain: "A" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5090 Classifications: {'peptide': 623} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 596} 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 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 chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 109 Unusual residues: {' CA': 1, 'LBN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: F, E, G, H Time building chain proxies: 7.08, per 1000 atoms: 0.40 Number of scatterers: 17634 At special positions: 0 Unit cell: (135.123, 119.743, 139.517, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 98 16.00 P 2 15.00 O 3190 8.00 N 2834 7.00 C 11508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS A 114 " distance=2.08 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.04 Simple disulfide: pdb=" SG CYS A 673 " - pdb=" SG CYS A 685 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS F 114 " distance=2.08 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS F 273 " distance=2.03 Simple disulfide: pdb=" SG CYS F 571 " - pdb=" SG CYS F 666 " distance=2.04 Simple disulfide: pdb=" SG CYS F 673 " - pdb=" SG CYS F 685 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 703 " - " ASN A 513 " " NAG A 704 " - " ASN A 246 " " NAG A 705 " - " ASN A 228 " " NAG A 706 " - " ASN A 523 " " NAG C 1 " - " ASN A 332 " " NAG D 1 " - " ASN A 261 " " NAG F 703 " - " ASN F 513 " " NAG F 704 " - " ASN F 246 " " NAG F 705 " - " ASN F 228 " " NAG F 706 " - " ASN F 523 " " NAG G 1 " - " ASN F 332 " " NAG H 1 " - " ASN F 261 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 738.6 milliseconds 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4036 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 18 sheets defined 55.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'B' and resid 31 through 44 removed outlier: 4.439A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 41 " --> pdb=" O CYS B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 60 removed outlier: 4.184A pdb=" N SER B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 90 removed outlier: 3.658A pdb=" N ILE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 86 " --> pdb=" O CYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 3.556A pdb=" N LEU B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 4.196A pdb=" N ALA B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 137 removed outlier: 3.709A pdb=" N SER B 133 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 147 through 169 removed outlier: 3.507A pdb=" N ILE B 151 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.951A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 201 removed outlier: 3.529A pdb=" N ALA B 182 " --> pdb=" O ASN B 178 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 3.585A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.920A pdb=" N ILE B 241 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 243 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 258 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 259 through 276 removed outlier: 3.587A pdb=" N MET B 270 " --> pdb=" O CYS B 266 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 284 removed outlier: 4.199A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 removed outlier: 3.647A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 323 removed outlier: 3.501A pdb=" N ALA B 310 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 323 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 4.183A pdb=" N LEU B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.502A pdb=" N MET B 360 " --> pdb=" O MET B 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 364 " --> pdb=" O MET B 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 367 " --> pdb=" O ILE B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 399 removed outlier: 3.605A pdb=" N ASN B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 390 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 432 removed outlier: 3.774A pdb=" N ILE B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 434 through 455 removed outlier: 4.013A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 439 " --> pdb=" O TRP B 435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 444 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 478 removed outlier: 3.782A pdb=" N GLN B 463 " --> pdb=" O PHE B 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Proline residue: B 468 - end of helix removed outlier: 3.829A pdb=" N MET B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 removed outlier: 3.742A pdb=" N LEU A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 111 removed outlier: 3.648A pdb=" N GLU A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 4.115A pdb=" N GLY A 121 " --> pdb=" O TRP A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.974A pdb=" N PHE A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 148 removed outlier: 3.579A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 153 Processing helix chain 'A' and resid 185 through 188 Processing helix chain 'A' and resid 189 through 203 removed outlier: 3.599A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.608A pdb=" N ASN A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.761A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 removed outlier: 3.889A pdb=" N GLN A 293 " --> pdb=" O ASN A 289 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.752A pdb=" N ILE A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 removed outlier: 3.522A pdb=" N VAL A 395 " --> pdb=" O GLU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.522A pdb=" N LYS A 415 " --> pdb=" O TYR A 412 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 416 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 416' Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.664A pdb=" N VAL A 427 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 461 through 472 removed outlier: 3.550A pdb=" N VAL A 469 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 471 " --> pdb=" O MET A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 519 removed outlier: 3.504A pdb=" N ALA A 517 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.529A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.858A pdb=" N ILE A 589 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A 590 " --> pdb=" O ASP A 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 590' Processing helix chain 'A' and resid 606 through 611 removed outlier: 4.175A pdb=" N MET A 610 " --> pdb=" O ASN A 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 4.439A pdb=" N ILE E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 41 " --> pdb=" O CYS E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.184A pdb=" N SER E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 90 removed outlier: 3.658A pdb=" N ILE E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP E 69 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 77 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E 86 " --> pdb=" O CYS E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 104 removed outlier: 3.556A pdb=" N LEU E 100 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA E 103 " --> pdb=" O TYR E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 119 removed outlier: 4.196A pdb=" N ALA E 109 " --> pdb=" O GLY E 105 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 137 removed outlier: 3.709A pdb=" N SER E 133 " --> pdb=" O CYS E 129 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 147 through 169 removed outlier: 3.507A pdb=" N ILE E 151 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 155 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.951A pdb=" N VAL E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 201 removed outlier: 3.529A pdb=" N ALA E 182 " --> pdb=" O ASN E 178 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET E 185 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 231 removed outlier: 3.585A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 231 " --> pdb=" O ASN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 244 removed outlier: 3.920A pdb=" N ILE E 241 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU E 243 " --> pdb=" O TYR E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 Proline residue: E 253 - end of helix Processing helix chain 'E' and resid 259 through 276 removed outlier: 3.587A pdb=" N MET E 270 " --> pdb=" O CYS E 266 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 275 " --> pdb=" O ASN E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 4.199A pdb=" N LEU E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.647A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 323 removed outlier: 3.501A pdb=" N ALA E 310 " --> pdb=" O PRO E 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 334 removed outlier: 4.183A pdb=" N LEU E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL E 328 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE E 329 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL E 330 " --> pdb=" O ARG E 326 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU E 334 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 351 through 367 removed outlier: 3.502A pdb=" N MET E 360 " --> pdb=" O MET E 356 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA E 362 " --> pdb=" O HIS E 358 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 364 " --> pdb=" O MET E 360 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 367 " --> pdb=" O ILE E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 399 removed outlier: 3.605A pdb=" N ASN E 376 " --> pdb=" O ASN E 372 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 377 " --> pdb=" O SER E 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA E 381 " --> pdb=" O TYR E 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP E 383 " --> pdb=" O SER E 379 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 390 " --> pdb=" O TYR E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 432 removed outlier: 3.774A pdb=" N ILE E 415 " --> pdb=" O ILE E 411 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 423 " --> pdb=" O LEU E 419 " (cutoff:3.500A) Proline residue: E 428 - end of helix Processing helix chain 'E' and resid 434 through 455 removed outlier: 4.013A pdb=" N LEU E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR E 439 " --> pdb=" O TRP E 435 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET E 444 " --> pdb=" O CYS E 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE E 452 " --> pdb=" O LEU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 478 removed outlier: 3.782A pdb=" N GLN E 463 " --> pdb=" O PHE E 459 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Proline residue: E 468 - end of helix removed outlier: 3.829A pdb=" N MET E 471 " --> pdb=" O LYS E 467 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS E 472 " --> pdb=" O PRO E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 77 removed outlier: 3.742A pdb=" N LEU F 73 " --> pdb=" O PRO F 69 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.648A pdb=" N GLU F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE F 105 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 4.115A pdb=" N GLY F 121 " --> pdb=" O TRP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 131 removed outlier: 3.974A pdb=" N PHE F 131 " --> pdb=" O PRO F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 148 removed outlier: 3.579A pdb=" N LYS F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 153 Processing helix chain 'F' and resid 185 through 188 Processing helix chain 'F' and resid 189 through 203 removed outlier: 3.599A pdb=" N LYS F 203 " --> pdb=" O ALA F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 228 removed outlier: 3.608A pdb=" N ASN F 228 " --> pdb=" O GLN F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 236 removed outlier: 3.761A pdb=" N THR F 234 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP F 235 " --> pdb=" O LYS F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 306 removed outlier: 3.889A pdb=" N GLN F 293 " --> pdb=" O ASN F 289 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS F 306 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 356 through 368 removed outlier: 3.752A pdb=" N ILE F 360 " --> pdb=" O GLY F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 398 removed outlier: 3.522A pdb=" N VAL F 395 " --> pdb=" O GLU F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 416 removed outlier: 3.522A pdb=" N LYS F 415 " --> pdb=" O TYR F 412 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 416 " --> pdb=" O LEU F 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 412 through 416' Processing helix chain 'F' and resid 420 through 435 removed outlier: 3.664A pdb=" N VAL F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN F 434 " --> pdb=" O SER F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 458 through 460 No H-bonds generated for 'chain 'F' and resid 458 through 460' Processing helix chain 'F' and resid 461 through 472 removed outlier: 3.550A pdb=" N VAL F 469 " --> pdb=" O MET F 465 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 471 " --> pdb=" O MET F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 514 through 519 removed outlier: 3.504A pdb=" N ALA F 517 " --> pdb=" O SER F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 542 Processing helix chain 'F' and resid 547 through 561 removed outlier: 3.529A pdb=" N LEU F 557 " --> pdb=" O GLN F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 590 removed outlier: 3.858A pdb=" N ILE F 589 " --> pdb=" O LEU F 586 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN F 590 " --> pdb=" O ASP F 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 586 through 590' Processing helix chain 'F' and resid 606 through 611 removed outlier: 4.175A pdb=" N MET F 610 " --> pdb=" O ASN F 606 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'B' and resid 344 through 345 Processing sheet with id=2, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.762A pdb=" N MET A 381 " --> pdb=" O PHE A 407 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE A 409 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR A 383 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 310 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 166 through 170 removed outlier: 7.138A pdb=" N LYS A 167 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA A 176 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.776A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 244 through 245 Processing sheet with id=6, first strand: chain 'A' and resid 329 through 330 removed outlier: 4.135A pdb=" N ALA A 329 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 632 through 634 removed outlier: 3.622A pdb=" N ARG A 619 " --> pdb=" O GLU A 649 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE A 647 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER A 623 " --> pdb=" O GLY A 645 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 645 " --> pdb=" O SER A 623 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 603 through 605 Processing sheet with id=9, first strand: chain 'A' and resid 673 through 675 Processing sheet with id=10, first strand: chain 'E' and resid 344 through 345 Processing sheet with id=11, first strand: chain 'F' and resid 407 through 409 removed outlier: 6.762A pdb=" N MET F 381 " --> pdb=" O PHE F 407 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N PHE F 409 " --> pdb=" O MET F 381 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR F 383 " --> pdb=" O PHE F 409 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY F 310 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 166 through 170 removed outlier: 7.138A pdb=" N LYS F 167 " --> pdb=" O GLU F 178 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA F 176 " --> pdb=" O SER F 169 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'F' and resid 239 through 240 removed outlier: 3.776A pdb=" N GLN F 272 " --> pdb=" O ASP F 267 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'F' and resid 244 through 245 Processing sheet with id=15, first strand: chain 'F' and resid 329 through 330 removed outlier: 4.135A pdb=" N ALA F 329 " --> pdb=" O HIS F 347 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'F' and resid 632 through 634 removed outlier: 3.622A pdb=" N ARG F 619 " --> pdb=" O GLU F 649 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE F 647 " --> pdb=" O ARG F 621 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER F 623 " --> pdb=" O GLY F 645 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY F 645 " --> pdb=" O SER F 623 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'F' and resid 603 through 605 Processing sheet with id=18, first strand: chain 'F' and resid 673 through 675 742 hydrogen bonds defined for protein. 2070 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: 3.07 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3078 1.32 - 1.45: 4886 1.45 - 1.57: 9980 1.57 - 1.70: 4 1.70 - 1.82: 162 Bond restraints: 18110 Sorted by residual: bond pdb=" C9 LBN A 701 " pdb=" O2 LBN A 701 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" C9 LBN F 701 " pdb=" O2 LBN F 701 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.33e+00 bond pdb=" O2 LBN A 701 " pdb=" P1 LBN A 701 " ideal model delta sigma weight residual 1.650 1.605 0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" O2 LBN F 701 " pdb=" P1 LBN F 701 " ideal model delta sigma weight residual 1.650 1.605 0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 LBN F 701 " pdb=" O1 LBN F 701 " ideal model delta sigma weight residual 1.410 1.453 -0.043 2.00e-02 2.50e+03 4.71e+00 ... (remaining 18105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 24022 1.94 - 3.89: 528 3.89 - 5.83: 68 5.83 - 7.78: 18 7.78 - 9.72: 8 Bond angle restraints: 24644 Sorted by residual: angle pdb=" C GLU E 96 " pdb=" N TYR E 97 " pdb=" CA TYR E 97 " ideal model delta sigma weight residual 120.09 125.58 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" C GLU B 96 " pdb=" N TYR B 97 " pdb=" CA TYR B 97 " ideal model delta sigma weight residual 120.09 125.58 -5.49 1.25e+00 6.40e-01 1.93e+01 angle pdb=" C PHE A 173 " pdb=" N ARG A 174 " pdb=" CA ARG A 174 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" C PHE F 173 " pdb=" N ARG F 174 " pdb=" CA ARG F 174 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" CA TYR F 65 " pdb=" CB TYR F 65 " pdb=" CG TYR F 65 " ideal model delta sigma weight residual 113.90 120.26 -6.36 1.80e+00 3.09e-01 1.25e+01 ... (remaining 24639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.27: 9672 26.27 - 52.54: 702 52.54 - 78.81: 84 78.81 - 105.08: 14 105.08 - 131.34: 6 Dihedral angle restraints: 10478 sinusoidal: 4188 harmonic: 6290 Sorted by residual: dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N HIS A 175 " pdb=" CA HIS A 175 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.35e+01 dihedral pdb=" CA ARG F 174 " pdb=" C ARG F 174 " pdb=" N HIS F 175 " pdb=" CA HIS F 175 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.35e+01 dihedral pdb=" CA GLN F 79 " pdb=" C GLN F 79 " pdb=" N ALA F 80 " pdb=" CA ALA F 80 " ideal model delta harmonic sigma weight residual -180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 10475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2630 0.087 - 0.174: 162 0.174 - 0.261: 2 0.261 - 0.348: 4 0.348 - 0.434: 2 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.50e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.50e+01 chirality pdb=" C1 NAG A 704 " pdb=" ND2 ASN A 246 " pdb=" C2 NAG A 704 " pdb=" O5 NAG A 704 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2797 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 523 " 0.233 2.00e-02 2.50e+03 3.33e-01 1.38e+03 pdb=" CG ASN A 523 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN A 523 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN A 523 " -0.558 2.00e-02 2.50e+03 pdb=" C1 NAG A 706 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 523 " 0.233 2.00e-02 2.50e+03 3.33e-01 1.38e+03 pdb=" CG ASN F 523 " -0.117 2.00e-02 2.50e+03 pdb=" OD1 ASN F 523 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN F 523 " -0.558 2.00e-02 2.50e+03 pdb=" C1 NAG F 706 " 0.416 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 513 " -0.080 2.00e-02 2.50e+03 2.30e-01 6.59e+02 pdb=" CG ASN F 513 " -0.062 2.00e-02 2.50e+03 pdb=" OD1 ASN F 513 " 0.228 2.00e-02 2.50e+03 pdb=" ND2 ASN F 513 " -0.357 2.00e-02 2.50e+03 pdb=" C1 NAG F 703 " 0.271 2.00e-02 2.50e+03 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 195 2.61 - 3.18: 15181 3.18 - 3.75: 26329 3.75 - 4.33: 39501 4.33 - 4.90: 63604 Nonbonded interactions: 144810 Sorted by model distance: nonbonded pdb=" CE2 TYR B 175 " pdb=" CE2 TYR E 175 " model vdw 2.034 3.640 nonbonded pdb=" O GLY B 47 " pdb=" OG SER B 51 " model vdw 2.114 3.040 nonbonded pdb=" O GLY E 47 " pdb=" OG SER E 51 " model vdw 2.114 3.040 nonbonded pdb=" OG SER B 345 " pdb=" O ARG B 348 " model vdw 2.140 3.040 nonbonded pdb=" OG SER E 345 " pdb=" O ARG E 348 " model vdw 2.140 3.040 ... (remaining 144805 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.800 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 : 0.006 0.139 18134 Z= 0.285 Angle : 0.806 16.143 24708 Z= 0.429 Chirality : 0.047 0.434 2800 Planarity : 0.005 0.043 3040 Dihedral : 17.573 131.344 6418 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer: Outliers : 8.17 % Allowed : 22.27 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.81 (0.13), residues: 2148 helix: -4.11 (0.09), residues: 974 sheet: -2.26 (0.31), residues: 176 loop : -2.22 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 574 TYR 0.018 0.002 TYR F 65 PHE 0.023 0.002 PHE F 407 TRP 0.017 0.001 TRP B 383 HIS 0.008 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.27 (18110) covalent geometry : angle 0.74709 / 0.42 (24644) SS BOND : bond 0.02548 / 1.57 ( 8) SS BOND : angle 1.43062 / 0.74 ( 16) hydrogen bonds : bond 0.30241 / 19.56 ( 742) hydrogen bonds : angle 10.10272 / 6.97 ( 2070) link_BETA1-4 : bond 0.03842 / 1.96 ( 4) link_BETA1-4 : angle 8.31775 / 4.62 ( 12) link_NAG-ASN : bond 0.06076 / 4.44 ( 12) link_NAG-ASN : angle 6.31466 / 3.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 358 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 SER cc_start: 0.8303 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 124 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7001 (p) REVERT: B 128 ILE cc_start: 0.7688 (mt) cc_final: 0.7318 (mm) REVERT: B 142 SER cc_start: 0.7266 (OUTLIER) cc_final: 0.7030 (t) REVERT: B 151 ILE cc_start: 0.7943 (pt) cc_final: 0.7656 (pp) REVERT: B 171 ARG cc_start: 0.4861 (ptm160) cc_final: 0.4443 (mtp180) REVERT: B 172 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4789 (mt) REVERT: B 207 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.3561 (p90) REVERT: B 209 ASN cc_start: 0.6310 (t0) cc_final: 0.5623 (t0) REVERT: B 221 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6924 (mt) REVERT: B 258 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6773 (pp) REVERT: B 261 PRO cc_start: 0.8048 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: B 268 ILE cc_start: 0.8396 (pt) cc_final: 0.8185 (pp) REVERT: B 282 GLU cc_start: 0.7494 (tt0) cc_final: 0.7281 (tp30) REVERT: B 304 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7137 (pp) REVERT: B 308 PHE cc_start: 0.6409 (m-10) cc_final: 0.6126 (m-10) REVERT: B 338 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6244 (tt) REVERT: B 356 MET cc_start: 0.6523 (mmm) cc_final: 0.5969 (mmm) REVERT: B 393 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6411 (tt) REVERT: B 403 LEU cc_start: 0.6298 (OUTLIER) cc_final: 0.5809 (pt) REVERT: B 454 PHE cc_start: 0.6507 (OUTLIER) cc_final: 0.5888 (t80) REVERT: B 473 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 113 LYS cc_start: 0.7929 (mttm) cc_final: 0.7299 (tttm) REVERT: A 250 ILE cc_start: 0.8574 (pp) cc_final: 0.8282 (mm) REVERT: A 426 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7286 (pp20) REVERT: A 433 GLU cc_start: 0.7498 (pt0) cc_final: 0.7272 (pt0) REVERT: A 500 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8656 (m) REVERT: A 589 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8000 (mp) REVERT: E 113 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.7868 (p) REVERT: E 124 SER cc_start: 0.7733 (OUTLIER) cc_final: 0.7006 (p) REVERT: E 128 ILE cc_start: 0.7686 (mt) cc_final: 0.7317 (mm) REVERT: E 142 SER cc_start: 0.7267 (OUTLIER) cc_final: 0.7027 (t) REVERT: E 151 ILE cc_start: 0.7946 (pt) cc_final: 0.7657 (pp) REVERT: E 171 ARG cc_start: 0.4861 (ptm160) cc_final: 0.4628 (mtt-85) REVERT: E 172 LEU cc_start: 0.5147 (OUTLIER) cc_final: 0.4789 (mt) REVERT: E 207 PHE cc_start: 0.5388 (OUTLIER) cc_final: 0.3559 (p90) REVERT: E 209 ASN cc_start: 0.6312 (t0) cc_final: 0.5622 (t0) REVERT: E 221 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6928 (mt) REVERT: E 258 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6775 (pp) REVERT: E 261 PRO cc_start: 0.8049 (Cg_exo) cc_final: 0.7826 (Cg_endo) REVERT: E 268 ILE cc_start: 0.8396 (pt) cc_final: 0.8186 (pp) REVERT: E 282 GLU cc_start: 0.7492 (tt0) cc_final: 0.7280 (tp30) REVERT: E 304 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7139 (pp) REVERT: E 308 PHE cc_start: 0.6412 (m-10) cc_final: 0.6128 (m-10) REVERT: E 338 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6240 (tt) REVERT: E 356 MET cc_start: 0.6526 (mmm) cc_final: 0.5973 (mmm) REVERT: E 393 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6413 (tt) REVERT: E 403 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5812 (pt) REVERT: E 454 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5890 (t80) REVERT: E 473 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8051 (mt) REVERT: F 113 LYS cc_start: 0.7926 (mttm) cc_final: 0.7296 (tttm) REVERT: F 250 ILE cc_start: 0.8574 (pp) cc_final: 0.8282 (mm) REVERT: F 426 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: F 433 GLU cc_start: 0.7496 (pt0) cc_final: 0.7271 (pt0) REVERT: F 500 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8656 (m) REVERT: F 589 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7999 (mp) outliers start: 154 outliers final: 24 residues processed: 478 average time/residue: 0.5038 time to fit residues: 275.6400 Evaluate side-chains 282 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 226 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 321 CYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 393 LEU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 431 SER Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 65 CYS Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 321 CYS Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 431 SER Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 500 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 589 ILE Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0470 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 148 GLN B 203 ASN B 237 GLN B 251 ASN B 372 ASN B 456 HIS A 79 GLN A 146 GLN A 156 ASN A 181 GLN A 201 HIS A 220 HIS A 224 GLN A 282 GLN A 293 GLN A 301 GLN A 335 GLN A 345 GLN A 366 GLN A 370 GLN A 403 GLN A 442 ASN A 466 ASN A 510 GLN A 544 GLN A 577 ASN A 606 ASN E 148 GLN E 203 ASN E 237 GLN E 251 ASN E 372 ASN E 456 HIS F 79 GLN F 146 GLN F 156 ASN F 181 GLN F 201 HIS F 220 HIS F 224 GLN F 282 GLN F 293 GLN F 301 GLN F 335 GLN F 345 GLN F 366 GLN F 370 GLN F 403 GLN F 442 ASN F 466 ASN F 510 GLN F 544 GLN F 577 ASN F 606 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.184003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.105436 restraints weight = 21067.989| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.48 r_work: 0.3009 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18134 Z= 0.169 Angle : 0.768 9.735 24708 Z= 0.380 Chirality : 0.048 0.328 2800 Planarity : 0.006 0.045 3040 Dihedral : 9.456 116.754 2532 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 6.68 % Allowed : 23.97 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.65 (0.16), residues: 2148 helix: -1.79 (0.14), residues: 1012 sheet: -1.91 (0.31), residues: 180 loop : -1.52 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 671 TYR 0.014 0.002 TYR A 65 PHE 0.014 0.002 PHE A 407 TRP 0.014 0.001 TRP E 383 HIS 0.008 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (18110) covalent geometry : angle 0.74602 / 0.37 (24644) SS BOND : bond 0.01083 / 0.60 ( 8) SS BOND : angle 1.30397 / 0.68 ( 16) hydrogen bonds : bond 0.05316 / 3.50 ( 742) hydrogen bonds : angle 5.04506 / 3.51 ( 2070) link_BETA1-4 : bond 0.01134 / 0.58 ( 4) link_BETA1-4 : angle 3.93628 / 2.11 ( 12) link_NAG-ASN : bond 0.00716 / 0.41 ( 12) link_NAG-ASN : angle 4.22523 / 2.79 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 254 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 MET cc_start: 0.6578 (ttm) cc_final: 0.6117 (ttp) REVERT: B 111 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7111 (mp) REVERT: B 128 ILE cc_start: 0.7649 (mt) cc_final: 0.7414 (mm) REVERT: B 205 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6129 (mtp-110) REVERT: B 209 ASN cc_start: 0.6197 (t0) cc_final: 0.5807 (t0) REVERT: B 212 GLU cc_start: 0.6787 (pm20) cc_final: 0.6572 (pm20) REVERT: B 220 SER cc_start: 0.7186 (OUTLIER) cc_final: 0.6947 (p) REVERT: B 233 ASP cc_start: 0.7070 (t70) cc_final: 0.6768 (t70) REVERT: B 258 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6479 (pp) REVERT: B 356 MET cc_start: 0.6572 (mmm) cc_final: 0.5987 (mmt) REVERT: B 390 ILE cc_start: 0.7082 (mm) cc_final: 0.6750 (mm) REVERT: B 454 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5822 (t80) REVERT: B 471 MET cc_start: 0.8095 (ppp) cc_final: 0.7290 (pmt) REVERT: B 473 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8080 (mp) REVERT: A 113 LYS cc_start: 0.8088 (mttm) cc_final: 0.7136 (tttm) REVERT: A 250 ILE cc_start: 0.8614 (pp) cc_final: 0.8371 (mm) REVERT: A 363 SER cc_start: 0.8773 (t) cc_final: 0.8559 (m) REVERT: A 374 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: A 423 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8219 (m) REVERT: A 426 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7876 (pp20) REVERT: A 500 THR cc_start: 0.9146 (p) cc_final: 0.8863 (m) REVERT: A 617 ARG cc_start: 0.8040 (ttt90) cc_final: 0.7624 (ttm-80) REVERT: E 71 MET cc_start: 0.6586 (ttm) cc_final: 0.6123 (ttp) REVERT: E 111 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7119 (mp) REVERT: E 128 ILE cc_start: 0.7646 (mt) cc_final: 0.7412 (mm) REVERT: E 205 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.6067 (mtp-110) REVERT: E 209 ASN cc_start: 0.6197 (t0) cc_final: 0.5804 (t0) REVERT: E 212 GLU cc_start: 0.6782 (pm20) cc_final: 0.6566 (pm20) REVERT: E 220 SER cc_start: 0.7188 (OUTLIER) cc_final: 0.6948 (p) REVERT: E 233 ASP cc_start: 0.7079 (t70) cc_final: 0.6776 (t70) REVERT: E 258 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6482 (pp) REVERT: E 356 MET cc_start: 0.6593 (mmm) cc_final: 0.6012 (mmt) REVERT: E 390 ILE cc_start: 0.7084 (mm) cc_final: 0.6750 (mm) REVERT: E 454 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5823 (t80) REVERT: E 471 MET cc_start: 0.8097 (ppp) cc_final: 0.7278 (pmt) REVERT: E 473 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8077 (mp) REVERT: F 113 LYS cc_start: 0.8095 (mttm) cc_final: 0.7142 (tttm) REVERT: F 250 ILE cc_start: 0.8613 (pp) cc_final: 0.8372 (mm) REVERT: F 363 SER cc_start: 0.8781 (t) cc_final: 0.8566 (m) REVERT: F 374 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: F 423 SER cc_start: 0.8912 (OUTLIER) cc_final: 0.8222 (m) REVERT: F 426 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7893 (pp20) REVERT: F 500 THR cc_start: 0.9151 (p) cc_final: 0.8867 (m) REVERT: F 617 ARG cc_start: 0.8041 (ttt90) cc_final: 0.7628 (ttm-80) outliers start: 126 outliers final: 22 residues processed: 350 average time/residue: 0.4926 time to fit residues: 198.5097 Evaluate side-chains 260 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 220 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 587 ASP Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 587 ASP Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 86 optimal weight: 0.5980 chunk 29 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 192 optimal weight: 0.0170 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN B 474 GLN A 403 GLN A 577 ASN A 654 ASN E 237 GLN E 474 GLN ** F 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN F 577 ASN F 654 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.182961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.103406 restraints weight = 21109.962| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.35 r_work: 0.2994 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18134 Z= 0.143 Angle : 0.716 16.308 24708 Z= 0.343 Chirality : 0.045 0.331 2800 Planarity : 0.005 0.042 3040 Dihedral : 8.177 102.714 2474 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 5.09 % Allowed : 25.34 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.56 (0.17), residues: 2148 helix: -0.60 (0.16), residues: 1010 sheet: -1.41 (0.33), residues: 160 loop : -1.33 (0.18), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 326 TYR 0.013 0.001 TYR A 65 PHE 0.013 0.001 PHE A 407 TRP 0.014 0.001 TRP E 383 HIS 0.005 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (18110) covalent geometry : angle 0.67981 / 0.34 (24644) SS BOND : bond 0.00840 / 0.51 ( 8) SS BOND : angle 1.16745 / 0.61 ( 16) hydrogen bonds : bond 0.04472 / 2.96 ( 742) hydrogen bonds : angle 4.56219 / 3.18 ( 2070) link_BETA1-4 : bond 0.01809 / 0.93 ( 4) link_BETA1-4 : angle 3.67491 / 1.98 ( 12) link_NAG-ASN : bond 0.00849 / 0.46 ( 12) link_NAG-ASN : angle 5.53922 / 3.28 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 244 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.6244 (ppp) REVERT: B 128 ILE cc_start: 0.7777 (mt) cc_final: 0.7533 (mm) REVERT: B 134 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: B 171 ARG cc_start: 0.5033 (ptm160) cc_final: 0.4588 (mtt-85) REVERT: B 209 ASN cc_start: 0.6370 (t0) cc_final: 0.6087 (t0) REVERT: B 233 ASP cc_start: 0.7206 (t70) cc_final: 0.6836 (t70) REVERT: B 250 ARG cc_start: 0.6409 (mmm-85) cc_final: 0.4929 (tmm-80) REVERT: B 333 ARG cc_start: 0.6461 (mmp80) cc_final: 0.6025 (mmp-170) REVERT: B 337 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6242 (ppp) REVERT: B 348 ARG cc_start: 0.3804 (OUTLIER) cc_final: 0.3350 (mpp-170) REVERT: B 356 MET cc_start: 0.6588 (mmm) cc_final: 0.6018 (mmm) REVERT: B 390 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6645 (mm) REVERT: B 454 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5790 (t80) REVERT: B 473 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 113 LYS cc_start: 0.8049 (mttm) cc_final: 0.7528 (tppt) REVERT: A 437 GLU cc_start: 0.7759 (tp30) cc_final: 0.7556 (mm-30) REVERT: A 486 MET cc_start: 0.9285 (mtp) cc_final: 0.9041 (mtm) REVERT: A 500 THR cc_start: 0.9165 (p) cc_final: 0.8887 (m) REVERT: A 524 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7025 (p-80) REVERT: A 609 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: A 617 ARG cc_start: 0.8039 (ttt90) cc_final: 0.7709 (ttm-80) REVERT: A 671 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7933 (ptp90) REVERT: E 89 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6249 (ppp) REVERT: E 128 ILE cc_start: 0.7754 (mt) cc_final: 0.7511 (mm) REVERT: E 134 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: E 171 ARG cc_start: 0.5041 (ptm160) cc_final: 0.4684 (mtt180) REVERT: E 209 ASN cc_start: 0.6367 (t0) cc_final: 0.6083 (t0) REVERT: E 233 ASP cc_start: 0.7208 (t70) cc_final: 0.6838 (t70) REVERT: E 250 ARG cc_start: 0.6408 (mmm-85) cc_final: 0.4925 (tmm-80) REVERT: E 333 ARG cc_start: 0.6461 (mmp80) cc_final: 0.6027 (mmp-170) REVERT: E 337 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6223 (ppp) REVERT: E 348 ARG cc_start: 0.3795 (OUTLIER) cc_final: 0.3344 (mpp-170) REVERT: E 356 MET cc_start: 0.6588 (mmm) cc_final: 0.6018 (mmm) REVERT: E 390 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6647 (mm) REVERT: E 454 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5791 (t80) REVERT: E 473 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8211 (mp) REVERT: F 113 LYS cc_start: 0.8054 (mttm) cc_final: 0.7533 (tppt) REVERT: F 437 GLU cc_start: 0.7759 (tp30) cc_final: 0.7555 (mm-30) REVERT: F 486 MET cc_start: 0.9283 (mtp) cc_final: 0.9042 (mtm) REVERT: F 500 THR cc_start: 0.9169 (p) cc_final: 0.8888 (m) REVERT: F 524 HIS cc_start: 0.7735 (OUTLIER) cc_final: 0.7019 (p-80) REVERT: F 609 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7925 (pt0) REVERT: F 617 ARG cc_start: 0.8039 (ttt90) cc_final: 0.7708 (ttm-80) REVERT: F 671 ARG cc_start: 0.8200 (ptm160) cc_final: 0.7929 (ptp90) outliers start: 96 outliers final: 34 residues processed: 308 average time/residue: 0.6547 time to fit residues: 224.9032 Evaluate side-chains 274 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 ARG Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 609 GLU Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 186 optimal weight: 0.5980 chunk 113 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN B 474 GLN E 237 GLN E 474 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.103331 restraints weight = 21058.691| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.65 r_work: 0.2939 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18134 Z= 0.155 Angle : 0.692 14.961 24708 Z= 0.335 Chirality : 0.045 0.330 2800 Planarity : 0.005 0.067 3040 Dihedral : 7.422 85.410 2464 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 5.94 % Allowed : 24.71 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.10 (0.18), residues: 2148 helix: -0.13 (0.17), residues: 1012 sheet: -1.19 (0.34), residues: 160 loop : -1.21 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 405 TYR 0.018 0.001 TYR E 97 PHE 0.017 0.001 PHE A 407 TRP 0.014 0.001 TRP E 383 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (18110) covalent geometry : angle 0.66073 / 0.33 (24644) SS BOND : bond 0.00295 / 0.15 ( 8) SS BOND : angle 1.47228 / 0.81 ( 16) hydrogen bonds : bond 0.04131 / 2.73 ( 742) hydrogen bonds : angle 4.36707 / 3.04 ( 2070) link_BETA1-4 : bond 0.01602 / 0.82 ( 4) link_BETA1-4 : angle 3.54480 / 1.90 ( 12) link_NAG-ASN : bond 0.00970 / 0.53 ( 12) link_NAG-ASN : angle 4.94693 / 3.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 220 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: B 171 ARG cc_start: 0.5073 (ptm160) cc_final: 0.4594 (mtt-85) REVERT: B 207 PHE cc_start: 0.5418 (OUTLIER) cc_final: 0.3792 (p90) REVERT: B 209 ASN cc_start: 0.6434 (t0) cc_final: 0.6126 (t0) REVERT: B 233 ASP cc_start: 0.6983 (t70) cc_final: 0.6673 (t70) REVERT: B 250 ARG cc_start: 0.6457 (mmm-85) cc_final: 0.4966 (tmm-80) REVERT: B 282 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6752 (pt0) REVERT: B 333 ARG cc_start: 0.6560 (mmp80) cc_final: 0.6145 (mmp-170) REVERT: B 337 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.6087 (ppp) REVERT: B 343 TYR cc_start: 0.5992 (m-10) cc_final: 0.5602 (m-80) REVERT: B 356 MET cc_start: 0.6457 (mmm) cc_final: 0.5916 (mmm) REVERT: B 454 PHE cc_start: 0.6515 (OUTLIER) cc_final: 0.6102 (t80) REVERT: B 474 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: A 68 MET cc_start: 0.5317 (mtm) cc_final: 0.4273 (mtm) REVERT: A 113 LYS cc_start: 0.8185 (mttm) cc_final: 0.7712 (mttm) REVERT: A 243 ASN cc_start: 0.8089 (t0) cc_final: 0.7797 (t0) REVERT: A 423 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8262 (m) REVERT: A 426 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7861 (pp20) REVERT: A 486 MET cc_start: 0.9288 (mtp) cc_final: 0.8883 (mtm) REVERT: A 500 THR cc_start: 0.9152 (p) cc_final: 0.8901 (m) REVERT: A 524 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7042 (p-80) REVERT: A 617 ARG cc_start: 0.8005 (ttt90) cc_final: 0.7683 (ttm-80) REVERT: A 639 THR cc_start: 0.7916 (t) cc_final: 0.7709 (m) REVERT: A 671 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7909 (ptp90) REVERT: E 134 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: E 171 ARG cc_start: 0.5079 (ptm160) cc_final: 0.4740 (ttt-90) REVERT: E 207 PHE cc_start: 0.5415 (OUTLIER) cc_final: 0.3795 (p90) REVERT: E 209 ASN cc_start: 0.6431 (t0) cc_final: 0.6124 (t0) REVERT: E 233 ASP cc_start: 0.7006 (t70) cc_final: 0.6695 (t70) REVERT: E 250 ARG cc_start: 0.6458 (mmm-85) cc_final: 0.4966 (tmm-80) REVERT: E 282 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6758 (pt0) REVERT: E 333 ARG cc_start: 0.6563 (mmp80) cc_final: 0.6150 (mmp-170) REVERT: E 337 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.6071 (ppp) REVERT: E 343 TYR cc_start: 0.5985 (m-10) cc_final: 0.5598 (m-80) REVERT: E 356 MET cc_start: 0.6462 (mmm) cc_final: 0.5914 (mmm) REVERT: E 454 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.6106 (t80) REVERT: E 474 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6256 (tt0) REVERT: F 68 MET cc_start: 0.5311 (mtm) cc_final: 0.4281 (mtm) REVERT: F 113 LYS cc_start: 0.8188 (mttm) cc_final: 0.7711 (mttm) REVERT: F 243 ASN cc_start: 0.8091 (t0) cc_final: 0.7800 (t0) REVERT: F 374 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: F 423 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8265 (m) REVERT: F 426 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7864 (pp20) REVERT: F 437 GLU cc_start: 0.7804 (tp30) cc_final: 0.7603 (mm-30) REVERT: F 486 MET cc_start: 0.9285 (mtp) cc_final: 0.8884 (mtm) REVERT: F 500 THR cc_start: 0.9156 (p) cc_final: 0.8904 (m) REVERT: F 524 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7027 (p-80) REVERT: F 617 ARG cc_start: 0.8002 (ttt90) cc_final: 0.7678 (ttm-80) REVERT: F 639 THR cc_start: 0.7921 (t) cc_final: 0.7715 (m) REVERT: F 671 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7898 (ptp90) outliers start: 112 outliers final: 43 residues processed: 294 average time/residue: 0.6664 time to fit residues: 217.8343 Evaluate side-chains 280 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 216 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 426 GLU Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 671 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 7 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 0.0270 chunk 71 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN A 670 ASN E 237 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.181885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106444 restraints weight = 20812.936| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.71 r_work: 0.2950 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18134 Z= 0.136 Angle : 0.662 12.741 24708 Z= 0.322 Chirality : 0.044 0.333 2800 Planarity : 0.004 0.037 3040 Dihedral : 7.097 77.397 2460 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 5.51 % Allowed : 25.08 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.88 (0.18), residues: 2148 helix: 0.12 (0.17), residues: 982 sheet: -1.07 (0.35), residues: 160 loop : -1.15 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 405 TYR 0.018 0.001 TYR A 65 PHE 0.017 0.001 PHE E 249 TRP 0.014 0.001 TRP E 383 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (18110) covalent geometry : angle 0.63595 / 0.32 (24644) SS BOND : bond 0.00216 / 0.10 ( 8) SS BOND : angle 0.78253 / 0.36 ( 16) hydrogen bonds : bond 0.03892 / 2.58 ( 742) hydrogen bonds : angle 4.28923 / 2.99 ( 2070) link_BETA1-4 : bond 0.01524 / 0.78 ( 4) link_BETA1-4 : angle 3.44041 / 1.85 ( 12) link_NAG-ASN : bond 0.00864 / 0.46 ( 12) link_NAG-ASN : angle 4.47803 / 2.76 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 223 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: B 171 ARG cc_start: 0.4981 (ptm160) cc_final: 0.4493 (mtt-85) REVERT: B 207 PHE cc_start: 0.5461 (OUTLIER) cc_final: 0.3751 (p90) REVERT: B 209 ASN cc_start: 0.6440 (t0) cc_final: 0.6132 (t0) REVERT: B 233 ASP cc_start: 0.7033 (t70) cc_final: 0.6711 (t70) REVERT: B 250 ARG cc_start: 0.6555 (mmm-85) cc_final: 0.4948 (tmm-80) REVERT: B 282 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6794 (tm-30) REVERT: B 333 ARG cc_start: 0.6576 (mmp80) cc_final: 0.6179 (mmp-170) REVERT: B 337 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.6121 (ppp) REVERT: B 356 MET cc_start: 0.6442 (mmm) cc_final: 0.5906 (mmm) REVERT: B 454 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6095 (t80) REVERT: B 473 LEU cc_start: 0.8490 (mt) cc_final: 0.8125 (mp) REVERT: A 113 LYS cc_start: 0.8165 (mttm) cc_final: 0.7701 (mttm) REVERT: A 243 ASN cc_start: 0.8096 (t0) cc_final: 0.7808 (t0) REVERT: A 374 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: A 486 MET cc_start: 0.9304 (mtp) cc_final: 0.8912 (mtm) REVERT: A 500 THR cc_start: 0.9159 (p) cc_final: 0.8931 (m) REVERT: A 521 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: A 524 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7048 (p-80) REVERT: A 617 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7685 (ttm-80) REVERT: A 671 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7956 (ptp90) REVERT: E 134 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: E 171 ARG cc_start: 0.4982 (ptm160) cc_final: 0.4636 (ttt-90) REVERT: E 207 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.3757 (p90) REVERT: E 209 ASN cc_start: 0.6433 (t0) cc_final: 0.6125 (t0) REVERT: E 233 ASP cc_start: 0.7050 (t70) cc_final: 0.6727 (t70) REVERT: E 250 ARG cc_start: 0.6560 (mmm-85) cc_final: 0.4953 (tmm-80) REVERT: E 282 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6805 (tm-30) REVERT: E 333 ARG cc_start: 0.6581 (mmp80) cc_final: 0.6182 (mmp-170) REVERT: E 337 MET cc_start: 0.6315 (OUTLIER) cc_final: 0.6112 (ppp) REVERT: E 356 MET cc_start: 0.6444 (mmm) cc_final: 0.5905 (mmm) REVERT: E 454 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.6097 (t80) REVERT: E 473 LEU cc_start: 0.8490 (mt) cc_final: 0.8125 (mp) REVERT: F 113 LYS cc_start: 0.8170 (mttm) cc_final: 0.7710 (mttm) REVERT: F 243 ASN cc_start: 0.8100 (t0) cc_final: 0.7815 (t0) REVERT: F 374 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: F 486 MET cc_start: 0.9303 (mtp) cc_final: 0.8913 (mtm) REVERT: F 500 THR cc_start: 0.9158 (p) cc_final: 0.8930 (m) REVERT: F 521 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: F 524 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7041 (p-80) REVERT: F 617 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7683 (ttm-80) REVERT: F 671 ARG cc_start: 0.8200 (ptm160) cc_final: 0.7942 (ptp90) outliers start: 104 outliers final: 54 residues processed: 294 average time/residue: 0.6554 time to fit residues: 215.0087 Evaluate side-chains 283 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 213 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 454 PHE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 153 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.0470 chunk 47 optimal weight: 0.6980 chunk 196 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN B 358 HIS B 474 GLN A 670 ASN E 237 GLN E 358 HIS E 474 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.182528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102338 restraints weight = 20768.297| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.25 r_work: 0.2985 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18134 Z= 0.118 Angle : 0.643 11.550 24708 Z= 0.313 Chirality : 0.043 0.332 2800 Planarity : 0.004 0.040 3040 Dihedral : 6.849 71.146 2460 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 5.09 % Allowed : 25.87 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.66 (0.18), residues: 2148 helix: 0.34 (0.17), residues: 980 sheet: -1.05 (0.35), residues: 160 loop : -1.06 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 326 TYR 0.017 0.001 TYR A 65 PHE 0.012 0.001 PHE A 407 TRP 0.014 0.001 TRP E 383 HIS 0.007 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (18110) covalent geometry : angle 0.61903 / 0.31 (24644) SS BOND : bond 0.00183 / 0.09 ( 8) SS BOND : angle 0.71602 / 0.32 ( 16) hydrogen bonds : bond 0.03607 / 2.39 ( 742) hydrogen bonds : angle 4.21845 / 2.93 ( 2070) link_BETA1-4 : bond 0.01503 / 0.77 ( 4) link_BETA1-4 : angle 3.39818 / 1.83 ( 12) link_NAG-ASN : bond 0.00844 / 0.45 ( 12) link_NAG-ASN : angle 4.17232 / 2.62 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 229 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: B 171 ARG cc_start: 0.4926 (ptm160) cc_final: 0.4529 (ttt-90) REVERT: B 175 TYR cc_start: 0.3738 (OUTLIER) cc_final: 0.3227 (t80) REVERT: B 209 ASN cc_start: 0.6329 (t0) cc_final: 0.6027 (t0) REVERT: B 233 ASP cc_start: 0.7008 (t70) cc_final: 0.6698 (t70) REVERT: B 250 ARG cc_start: 0.6515 (mmm-85) cc_final: 0.4924 (tmm-80) REVERT: B 282 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: B 333 ARG cc_start: 0.6542 (mmp80) cc_final: 0.6174 (mmp-170) REVERT: B 356 MET cc_start: 0.6355 (mmm) cc_final: 0.5858 (mmm) REVERT: B 475 MET cc_start: 0.8011 (mtm) cc_final: 0.7772 (ptt) REVERT: A 68 MET cc_start: 0.5427 (mtm) cc_final: 0.4593 (mpt) REVERT: A 113 LYS cc_start: 0.8172 (mttm) cc_final: 0.7564 (tppt) REVERT: A 243 ASN cc_start: 0.8042 (t0) cc_final: 0.7737 (t0) REVERT: A 374 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7277 (pt0) REVERT: A 486 MET cc_start: 0.9283 (mtp) cc_final: 0.8880 (mtm) REVERT: A 500 THR cc_start: 0.9136 (p) cc_final: 0.8923 (m) REVERT: A 521 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6744 (tp30) REVERT: A 617 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7615 (ttm-80) REVERT: A 658 ARG cc_start: 0.7472 (mmp80) cc_final: 0.7238 (mmp-170) REVERT: E 134 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: E 171 ARG cc_start: 0.4937 (ptm160) cc_final: 0.4535 (ttt-90) REVERT: E 175 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.3222 (t80) REVERT: E 209 ASN cc_start: 0.6326 (t0) cc_final: 0.6023 (t0) REVERT: E 233 ASP cc_start: 0.7017 (t70) cc_final: 0.6707 (t70) REVERT: E 250 ARG cc_start: 0.6523 (mmm-85) cc_final: 0.4927 (tmm-80) REVERT: E 282 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: E 333 ARG cc_start: 0.6538 (mmp80) cc_final: 0.6171 (mmp-170) REVERT: E 356 MET cc_start: 0.6356 (mmm) cc_final: 0.5854 (mmm) REVERT: E 475 MET cc_start: 0.8021 (mtm) cc_final: 0.7761 (ptt) REVERT: F 68 MET cc_start: 0.5439 (mtm) cc_final: 0.4602 (mpt) REVERT: F 113 LYS cc_start: 0.8174 (mttm) cc_final: 0.7567 (tppt) REVERT: F 243 ASN cc_start: 0.8053 (t0) cc_final: 0.7745 (t0) REVERT: F 374 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: F 486 MET cc_start: 0.9280 (mtp) cc_final: 0.8879 (mtm) REVERT: F 500 THR cc_start: 0.9139 (p) cc_final: 0.8925 (m) REVERT: F 521 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6757 (tp30) REVERT: F 617 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7611 (ttm-80) REVERT: F 658 ARG cc_start: 0.7483 (mmp80) cc_final: 0.7247 (mmp-170) REVERT: F 671 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7920 (ptp90) outliers start: 96 outliers final: 50 residues processed: 289 average time/residue: 0.7081 time to fit residues: 226.4971 Evaluate side-chains 275 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 GLU Chi-restraints excluded: chain B residue 175 TYR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 363 ILE Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 418 LYS Chi-restraints excluded: chain F residue 521 GLU Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 140 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN A 314 ASN A 403 GLN A 516 ASN A 670 ASN E 237 GLN F 314 ASN F 403 GLN F 516 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.180591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.100100 restraints weight = 20855.471| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.13 r_work: 0.2959 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18134 Z= 0.191 Angle : 0.692 10.587 24708 Z= 0.337 Chirality : 0.046 0.336 2800 Planarity : 0.005 0.040 3040 Dihedral : 6.895 67.747 2456 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 5.62 % Allowed : 26.03 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.68 (0.18), residues: 2148 helix: 0.36 (0.17), residues: 976 sheet: -1.01 (0.36), residues: 160 loop : -1.11 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 326 TYR 0.017 0.002 TYR A 65 PHE 0.024 0.002 PHE B 249 TRP 0.013 0.001 TRP B 383 HIS 0.006 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (18110) covalent geometry : angle 0.66959 / 0.33 (24644) SS BOND : bond 0.00395 / 0.17 ( 8) SS BOND : angle 1.69030 / 1.02 ( 16) hydrogen bonds : bond 0.04224 / 2.81 ( 742) hydrogen bonds : angle 4.29130 / 2.99 ( 2070) link_BETA1-4 : bond 0.01629 / 0.83 ( 4) link_BETA1-4 : angle 3.56014 / 1.91 ( 12) link_NAG-ASN : bond 0.00770 / 0.41 ( 12) link_NAG-ASN : angle 3.98825 / 2.53 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 215 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6741 (mmp) cc_final: 0.6514 (mmm) REVERT: B 171 ARG cc_start: 0.4964 (ptm160) cc_final: 0.4473 (ttt-90) REVERT: B 207 PHE cc_start: 0.5858 (OUTLIER) cc_final: 0.4340 (p90) REVERT: B 209 ASN cc_start: 0.6406 (t0) cc_final: 0.6088 (t0) REVERT: B 233 ASP cc_start: 0.6990 (t70) cc_final: 0.6690 (t70) REVERT: B 250 ARG cc_start: 0.6487 (mmm-85) cc_final: 0.4989 (tmm-80) REVERT: B 282 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6889 (tm-30) REVERT: B 333 ARG cc_start: 0.6491 (mmp80) cc_final: 0.6104 (mmp-170) REVERT: B 356 MET cc_start: 0.6331 (mmm) cc_final: 0.5911 (mmm) REVERT: B 361 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6675 (mm) REVERT: B 415 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7054 (tp) REVERT: B 475 MET cc_start: 0.7935 (mtm) cc_final: 0.7640 (ptt) REVERT: A 68 MET cc_start: 0.5840 (mtm) cc_final: 0.5026 (mtm) REVERT: A 113 LYS cc_start: 0.8217 (mttm) cc_final: 0.7758 (mttm) REVERT: A 243 ASN cc_start: 0.7898 (t0) cc_final: 0.7691 (t0) REVERT: A 374 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7400 (pt0) REVERT: A 486 MET cc_start: 0.9288 (mtp) cc_final: 0.8897 (mtm) REVERT: A 617 ARG cc_start: 0.7962 (ttt90) cc_final: 0.7688 (ttm-80) REVERT: A 658 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7485 (mmp-170) REVERT: A 671 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.8005 (ptp90) REVERT: E 59 MET cc_start: 0.6743 (mmp) cc_final: 0.6516 (mmm) REVERT: E 171 ARG cc_start: 0.4962 (ptm160) cc_final: 0.4469 (ttt-90) REVERT: E 207 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.4340 (p90) REVERT: E 209 ASN cc_start: 0.6400 (t0) cc_final: 0.6081 (t0) REVERT: E 233 ASP cc_start: 0.6998 (t70) cc_final: 0.6698 (t70) REVERT: E 250 ARG cc_start: 0.6489 (mmm-85) cc_final: 0.4991 (tmm-80) REVERT: E 282 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6892 (tm-30) REVERT: E 333 ARG cc_start: 0.6428 (mmp80) cc_final: 0.6039 (mmp-170) REVERT: E 356 MET cc_start: 0.6331 (mmm) cc_final: 0.5907 (mmm) REVERT: E 361 ILE cc_start: 0.6983 (OUTLIER) cc_final: 0.6677 (mm) REVERT: E 415 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7050 (tp) REVERT: E 475 MET cc_start: 0.7935 (mtm) cc_final: 0.7639 (ptt) REVERT: F 68 MET cc_start: 0.5839 (mtm) cc_final: 0.5025 (mtm) REVERT: F 113 LYS cc_start: 0.8223 (mttm) cc_final: 0.7764 (mttm) REVERT: F 243 ASN cc_start: 0.7899 (t0) cc_final: 0.7692 (t0) REVERT: F 374 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: F 486 MET cc_start: 0.9291 (mtp) cc_final: 0.8902 (mtm) REVERT: F 500 THR cc_start: 0.9157 (p) cc_final: 0.8956 (m) REVERT: F 617 ARG cc_start: 0.7960 (ttt90) cc_final: 0.7687 (ttm-80) REVERT: F 658 ARG cc_start: 0.7727 (mmp80) cc_final: 0.7493 (mmp-170) REVERT: F 671 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7989 (ptp90) outliers start: 106 outliers final: 53 residues processed: 287 average time/residue: 0.6845 time to fit residues: 218.3670 Evaluate side-chains 274 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 539 ASP Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 665 ARG Chi-restraints excluded: chain F residue 671 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 130 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN A 403 GLN A 670 ASN E 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.181229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110729 restraints weight = 20741.716| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.96 r_work: 0.2926 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18134 Z= 0.149 Angle : 0.669 9.608 24708 Z= 0.326 Chirality : 0.045 0.336 2800 Planarity : 0.004 0.039 3040 Dihedral : 6.812 64.804 2456 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 3.61 % Allowed : 27.73 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.59 (0.18), residues: 2148 helix: 0.47 (0.17), residues: 968 sheet: -0.98 (0.36), residues: 160 loop : -1.10 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 326 TYR 0.018 0.001 TYR A 65 PHE 0.016 0.001 PHE F 407 TRP 0.013 0.001 TRP B 383 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (18110) covalent geometry : angle 0.64860 / 0.32 (24644) SS BOND : bond 0.00288 / 0.13 ( 8) SS BOND : angle 1.32193 / 0.77 ( 16) hydrogen bonds : bond 0.03838 / 2.54 ( 742) hydrogen bonds : angle 4.23195 / 2.94 ( 2070) link_BETA1-4 : bond 0.01552 / 0.80 ( 4) link_BETA1-4 : angle 3.42290 / 1.84 ( 12) link_NAG-ASN : bond 0.00748 / 0.40 ( 12) link_NAG-ASN : angle 3.77607 / 2.43 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 213 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6755 (mmp) cc_final: 0.6544 (mmm) REVERT: B 207 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.4368 (p90) REVERT: B 209 ASN cc_start: 0.6422 (t0) cc_final: 0.6110 (t0) REVERT: B 233 ASP cc_start: 0.7065 (t70) cc_final: 0.6779 (t70) REVERT: B 250 ARG cc_start: 0.6380 (mmm-85) cc_final: 0.5108 (tmm-80) REVERT: B 282 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: B 333 ARG cc_start: 0.6578 (mmp80) cc_final: 0.6162 (mmp-170) REVERT: B 356 MET cc_start: 0.6520 (mmm) cc_final: 0.6106 (mmm) REVERT: B 365 TYR cc_start: 0.7771 (m-80) cc_final: 0.7445 (m-80) REVERT: B 396 MET cc_start: 0.6171 (ptp) cc_final: 0.5879 (ptm) REVERT: B 397 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6825 (mmm-85) REVERT: B 415 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7038 (tp) REVERT: B 475 MET cc_start: 0.7904 (mtm) cc_final: 0.7552 (ptt) REVERT: A 113 LYS cc_start: 0.8171 (mttm) cc_final: 0.7660 (mttm) REVERT: A 374 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7387 (pt0) REVERT: A 486 MET cc_start: 0.9300 (mtp) cc_final: 0.8908 (mtm) REVERT: A 524 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7193 (p-80) REVERT: A 617 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7698 (ttm-80) REVERT: A 658 ARG cc_start: 0.7769 (mmp80) cc_final: 0.7532 (mmp-170) REVERT: A 671 ARG cc_start: 0.8266 (ptm160) cc_final: 0.8013 (ptp90) REVERT: E 59 MET cc_start: 0.6764 (mmp) cc_final: 0.6552 (mmm) REVERT: E 207 PHE cc_start: 0.5946 (OUTLIER) cc_final: 0.4370 (p90) REVERT: E 209 ASN cc_start: 0.6417 (t0) cc_final: 0.6104 (t0) REVERT: E 233 ASP cc_start: 0.7073 (t70) cc_final: 0.6787 (t70) REVERT: E 250 ARG cc_start: 0.6381 (mmm-85) cc_final: 0.5113 (tmm-80) REVERT: E 282 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6549 (tm-30) REVERT: E 333 ARG cc_start: 0.6583 (mmp80) cc_final: 0.6164 (mmp-170) REVERT: E 356 MET cc_start: 0.6516 (mmm) cc_final: 0.6098 (mmm) REVERT: E 365 TYR cc_start: 0.7763 (m-80) cc_final: 0.7440 (m-80) REVERT: E 396 MET cc_start: 0.6169 (ptp) cc_final: 0.5879 (ptm) REVERT: E 397 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.6826 (mmm-85) REVERT: E 415 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.7039 (tp) REVERT: E 475 MET cc_start: 0.7900 (mtm) cc_final: 0.7552 (ptt) REVERT: F 113 LYS cc_start: 0.8177 (mttm) cc_final: 0.7666 (mttm) REVERT: F 374 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7394 (pt0) REVERT: F 486 MET cc_start: 0.9302 (mtp) cc_final: 0.8909 (mtm) REVERT: F 500 THR cc_start: 0.9152 (p) cc_final: 0.8946 (m) REVERT: F 524 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7185 (p-80) REVERT: F 617 ARG cc_start: 0.7928 (ttt90) cc_final: 0.7698 (ttm-80) REVERT: F 658 ARG cc_start: 0.7775 (mmp80) cc_final: 0.7537 (mmp-170) REVERT: F 671 ARG cc_start: 0.8254 (ptm160) cc_final: 0.8002 (ptp90) outliers start: 68 outliers final: 45 residues processed: 262 average time/residue: 0.7055 time to fit residues: 205.0287 Evaluate side-chains 268 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 237 GLN B 474 GLN A 403 GLN A 670 ASN E 237 GLN E 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.180975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109031 restraints weight = 20921.045| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.92 r_work: 0.2934 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18134 Z= 0.164 Angle : 0.674 9.106 24708 Z= 0.329 Chirality : 0.045 0.339 2800 Planarity : 0.004 0.044 3040 Dihedral : 6.814 61.680 2456 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.10 % Favored : 95.81 % Rotamer: Outliers : 3.66 % Allowed : 27.89 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.58 (0.18), residues: 2148 helix: 0.48 (0.17), residues: 980 sheet: -1.02 (0.36), residues: 160 loop : -1.10 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 671 TYR 0.017 0.001 TYR A 65 PHE 0.019 0.002 PHE A 407 TRP 0.013 0.001 TRP B 383 HIS 0.006 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (18110) covalent geometry : angle 0.65501 / 0.32 (24644) SS BOND : bond 0.00321 / 0.14 ( 8) SS BOND : angle 1.28306 / 0.73 ( 16) hydrogen bonds : bond 0.03997 / 2.66 ( 742) hydrogen bonds : angle 4.24823 / 2.95 ( 2070) link_BETA1-4 : bond 0.01558 / 0.80 ( 4) link_BETA1-4 : angle 3.46551 / 1.86 ( 12) link_NAG-ASN : bond 0.00697 / 0.37 ( 12) link_NAG-ASN : angle 3.63833 / 2.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6689 (mmp) cc_final: 0.6394 (mmm) REVERT: B 207 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.4371 (p90) REVERT: B 209 ASN cc_start: 0.6425 (t0) cc_final: 0.6045 (t0) REVERT: B 221 ILE cc_start: 0.7095 (mm) cc_final: 0.6808 (mt) REVERT: B 233 ASP cc_start: 0.7051 (t70) cc_final: 0.6773 (t70) REVERT: B 250 ARG cc_start: 0.6003 (mmm-85) cc_final: 0.5128 (tmm-80) REVERT: B 282 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6374 (pt0) REVERT: B 333 ARG cc_start: 0.6486 (mmp80) cc_final: 0.6118 (mmp-170) REVERT: B 356 MET cc_start: 0.6526 (mmm) cc_final: 0.6117 (mmm) REVERT: B 365 TYR cc_start: 0.7736 (m-80) cc_final: 0.7458 (m-80) REVERT: B 397 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.6966 (mmm-85) REVERT: B 415 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.7004 (tp) REVERT: B 475 MET cc_start: 0.7876 (mtm) cc_final: 0.7208 (tpt) REVERT: A 68 MET cc_start: 0.5376 (mtm) cc_final: 0.4748 (mpt) REVERT: A 113 LYS cc_start: 0.8186 (mttm) cc_final: 0.7662 (mttm) REVERT: A 374 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7428 (pt0) REVERT: A 486 MET cc_start: 0.9292 (mtp) cc_final: 0.8903 (mtm) REVERT: A 524 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7190 (p-80) REVERT: E 59 MET cc_start: 0.6699 (mmp) cc_final: 0.6405 (mmm) REVERT: E 207 PHE cc_start: 0.5985 (OUTLIER) cc_final: 0.4374 (p90) REVERT: E 209 ASN cc_start: 0.6427 (t0) cc_final: 0.6044 (t0) REVERT: E 221 ILE cc_start: 0.7104 (mm) cc_final: 0.6815 (mt) REVERT: E 233 ASP cc_start: 0.7047 (t70) cc_final: 0.6769 (t70) REVERT: E 250 ARG cc_start: 0.6003 (mmm-85) cc_final: 0.5131 (tmm-80) REVERT: E 282 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6379 (pt0) REVERT: E 333 ARG cc_start: 0.6489 (mmp80) cc_final: 0.6117 (mmp-170) REVERT: E 356 MET cc_start: 0.6533 (mmm) cc_final: 0.6119 (mmm) REVERT: E 365 TYR cc_start: 0.7728 (m-80) cc_final: 0.7445 (m-80) REVERT: E 397 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.6969 (mmm-85) REVERT: E 415 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7005 (tp) REVERT: E 475 MET cc_start: 0.7869 (mtm) cc_final: 0.7205 (tpt) REVERT: F 68 MET cc_start: 0.5391 (mtm) cc_final: 0.4757 (mpt) REVERT: F 113 LYS cc_start: 0.8181 (mttm) cc_final: 0.7654 (mttm) REVERT: F 374 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7449 (pt0) REVERT: F 486 MET cc_start: 0.9291 (mtp) cc_final: 0.8900 (mtm) REVERT: F 524 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7186 (p-80) REVERT: F 671 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7997 (ptp90) outliers start: 69 outliers final: 47 residues processed: 263 average time/residue: 0.6816 time to fit residues: 199.4177 Evaluate side-chains 264 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 206 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 670 ASN Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 207 PHE Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 282 GLU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 111 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 374 GLU Chi-restraints excluded: chain F residue 417 ASP Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 535 THR Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 631 ARG Chi-restraints excluded: chain F residue 671 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 178 optimal weight: 0.0980 chunk 177 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 154 optimal weight: 0.0070 chunk 150 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 161 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN A 403 GLN A 670 ASN E 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.180025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.104648 restraints weight = 20796.130| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.57 r_work: 0.2924 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18134 Z= 0.118 Angle : 0.644 9.073 24708 Z= 0.313 Chirality : 0.043 0.332 2800 Planarity : 0.004 0.039 3040 Dihedral : 6.580 52.364 2456 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 2.81 % Allowed : 29.22 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.38 (0.18), residues: 2148 helix: 0.74 (0.17), residues: 968 sheet: -1.02 (0.36), residues: 160 loop : -1.06 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 671 TYR 0.018 0.001 TYR A 65 PHE 0.013 0.001 PHE F 570 TRP 0.014 0.001 TRP E 383 HIS 0.008 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (18110) covalent geometry : angle 0.62687 / 0.31 (24644) SS BOND : bond 0.00410 / 0.18 ( 8) SS BOND : angle 1.25326 / 0.74 ( 16) hydrogen bonds : bond 0.03434 / 2.27 ( 742) hydrogen bonds : angle 4.14640 / 2.88 ( 2070) link_BETA1-4 : bond 0.01507 / 0.77 ( 4) link_BETA1-4 : angle 3.31947 / 1.79 ( 12) link_NAG-ASN : bond 0.00704 / 0.37 ( 12) link_NAG-ASN : angle 3.40028 / 2.26 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4296 Ramachandran restraints generated. 2148 Oldfield, 0 Emsley, 2148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 220 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6627 (mmp) cc_final: 0.6350 (mmm) REVERT: B 77 THR cc_start: 0.5606 (m) cc_final: 0.5279 (p) REVERT: B 205 ARG cc_start: 0.6944 (mtp-110) cc_final: 0.6580 (mtp-110) REVERT: B 209 ASN cc_start: 0.6484 (t0) cc_final: 0.6098 (t0) REVERT: B 221 ILE cc_start: 0.6976 (mm) cc_final: 0.6703 (mt) REVERT: B 233 ASP cc_start: 0.6832 (t70) cc_final: 0.6552 (t70) REVERT: B 241 ILE cc_start: 0.6929 (mt) cc_final: 0.6722 (tp) REVERT: B 250 ARG cc_start: 0.5835 (mmm-85) cc_final: 0.4989 (tmm-80) REVERT: B 282 GLU cc_start: 0.6638 (tt0) cc_final: 0.6329 (pt0) REVERT: B 326 ARG cc_start: 0.6630 (mmt90) cc_final: 0.6280 (mpt180) REVERT: B 333 ARG cc_start: 0.6440 (mmp80) cc_final: 0.6072 (mmp-170) REVERT: B 356 MET cc_start: 0.6374 (mmm) cc_final: 0.5990 (mmm) REVERT: B 365 TYR cc_start: 0.7475 (m-80) cc_final: 0.7175 (m-80) REVERT: B 397 ARG cc_start: 0.7362 (mmm-85) cc_final: 0.7071 (mmm-85) REVERT: B 415 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6973 (tp) REVERT: B 475 MET cc_start: 0.7910 (mtm) cc_final: 0.7481 (ptt) REVERT: A 113 LYS cc_start: 0.8105 (mttm) cc_final: 0.7449 (tppt) REVERT: A 486 MET cc_start: 0.9192 (mtp) cc_final: 0.8779 (mtm) REVERT: A 524 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7119 (p-80) REVERT: E 59 MET cc_start: 0.6622 (mmp) cc_final: 0.6345 (mmm) REVERT: E 77 THR cc_start: 0.5605 (m) cc_final: 0.5279 (p) REVERT: E 104 PHE cc_start: 0.6433 (t80) cc_final: 0.6225 (t80) REVERT: E 205 ARG cc_start: 0.6943 (mtp-110) cc_final: 0.6579 (mtp-110) REVERT: E 209 ASN cc_start: 0.6487 (t0) cc_final: 0.6100 (t0) REVERT: E 221 ILE cc_start: 0.6976 (mm) cc_final: 0.6703 (mt) REVERT: E 233 ASP cc_start: 0.6832 (t70) cc_final: 0.6550 (t70) REVERT: E 241 ILE cc_start: 0.6928 (mt) cc_final: 0.6719 (tp) REVERT: E 250 ARG cc_start: 0.5838 (mmm-85) cc_final: 0.4991 (tmm-80) REVERT: E 282 GLU cc_start: 0.6636 (tt0) cc_final: 0.6327 (pt0) REVERT: E 326 ARG cc_start: 0.6626 (mmt90) cc_final: 0.6282 (mpt180) REVERT: E 333 ARG cc_start: 0.6439 (mmp80) cc_final: 0.6070 (mmp-170) REVERT: E 356 MET cc_start: 0.6367 (mmm) cc_final: 0.5982 (mmm) REVERT: E 365 TYR cc_start: 0.7470 (m-80) cc_final: 0.7167 (m-80) REVERT: E 397 ARG cc_start: 0.7365 (mmm-85) cc_final: 0.7073 (mmm-85) REVERT: E 415 ILE cc_start: 0.7206 (OUTLIER) cc_final: 0.6978 (tp) REVERT: E 475 MET cc_start: 0.7909 (mtm) cc_final: 0.7478 (ptt) REVERT: F 113 LYS cc_start: 0.8098 (mttm) cc_final: 0.7435 (tppt) REVERT: F 486 MET cc_start: 0.9199 (mtp) cc_final: 0.8786 (mtm) REVERT: F 524 HIS cc_start: 0.7766 (OUTLIER) cc_final: 0.7115 (p-80) REVERT: F 671 ARG cc_start: 0.8177 (ptm160) cc_final: 0.7875 (ptp90) outliers start: 53 outliers final: 32 residues processed: 266 average time/residue: 0.6995 time to fit residues: 206.7547 Evaluate side-chains 250 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 344 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 567 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 276 THR Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 210 ASP Chi-restraints excluded: chain F residue 524 HIS Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 567 ARG Chi-restraints excluded: chain F residue 685 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 126 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 178 optimal weight: 0.0470 chunk 186 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 chunk 190 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 403 GLN A 670 ASN A 679 ASN F 670 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.178117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099145 restraints weight = 21015.058| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.19 r_work: 0.2925 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18134 Z= 0.128 Angle : 0.659 8.992 24708 Z= 0.318 Chirality : 0.044 0.334 2800 Planarity : 0.004 0.038 3040 Dihedral : 6.565 54.985 2454 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 2.65 % Allowed : 29.64 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.30 (0.18), residues: 2148 helix: 0.82 (0.18), residues: 958 sheet: -1.03 (0.36), residues: 160 loop : -1.01 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 671 TYR 0.014 0.001 TYR F 65 PHE 0.015 0.001 PHE A 407 TRP 0.013 0.001 TRP E 383 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (18110) covalent geometry : angle 0.64262 / 0.31 (24644) SS BOND : bond 0.00300 / 0.13 ( 8) SS BOND : angle 1.43915 / 0.86 ( 16) hydrogen bonds : bond 0.03629 / 2.40 ( 742) hydrogen bonds : angle 4.16115 / 2.89 ( 2070) link_BETA1-4 : bond 0.01531 / 0.78 ( 4) link_BETA1-4 : angle 3.39357 / 1.83 ( 12) link_NAG-ASN : bond 0.00665 / 0.35 ( 12) link_NAG-ASN : angle 3.32549 / 2.22 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8691.75 seconds wall clock time: 148 minutes 42.05 seconds (8922.05 seconds total)