Starting phenix.real_space_refine on Sun Aug 24 07:57:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nf8_12298/08_2025/7nf8_12298.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nf8_12298/08_2025/7nf8_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_12298/08_2025/7nf8_12298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nf8_12298/08_2025/7nf8_12298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nf8_12298/08_2025/7nf8_12298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nf8_12298/08_2025/7nf8_12298.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: F, E, G, H Time building chain proxies: 7.51, per 1000 atoms: 0.43 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: 1.78 Conformation dependent library (CDL) restraints added in 773.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.68 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: 3.48 Time building geometry restraints manager: 2.32 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: 10228 26.27 - 52.54: 718 52.54 - 78.81: 84 78.81 - 105.08: 18 105.08 - 131.34: 8 Dihedral angle restraints: 11056 sinusoidal: 4766 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 11053 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: 0.03 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.390 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 17.271 131.344 6996 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 aren 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 covalent geometry : bond 0.00612 (18110) covalent geometry : angle 0.74709 (24644) SS BOND : bond 0.02548 ( 8) SS BOND : angle 1.43062 ( 16) hydrogen bonds : bond 0.30241 ( 742) hydrogen bonds : angle 10.10272 ( 2070) link_BETA1-4 : bond 0.03842 ( 4) link_BETA1-4 : angle 8.31775 ( 12) link_NAG-ASN : bond 0.06076 ( 12) link_NAG-ASN : angle 6.31466 ( 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 : 0.653 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: 0.7029 (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: 0.3560 (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: 0.5970 (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: 0.5415 time to fit residues: 294.1124 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 : 0.682 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4185 r_free = 0.4185 target = 0.184242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105164 restraints weight = 21067.208| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.17 r_work: 0.3038 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 0.035 18134 Z= 0.163 Angle : 0.783 14.937 24708 Z= 0.381 Chirality : 0.048 0.314 2800 Planarity : 0.006 0.040 3040 Dihedral : 10.626 123.680 3110 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 6.36 % Allowed : 23.97 % Favored : 69.67 % 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 aren not related in a simple way. whole: -2.67 (0.16), residues: 2148 helix: -1.81 (0.14), residues: 1012 sheet: -1.92 (0.30), residues: 180 loop : -1.51 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 671 TYR 0.015 0.002 TYR A 65 PHE 0.013 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 covalent geometry : bond 0.00349 (18110) covalent geometry : angle 0.75233 (24644) SS BOND : bond 0.00509 ( 8) SS BOND : angle 1.36894 ( 16) hydrogen bonds : bond 0.05260 ( 742) hydrogen bonds : angle 5.03450 ( 2070) link_BETA1-4 : bond 0.01751 ( 4) link_BETA1-4 : angle 3.86902 ( 12) link_NAG-ASN : bond 0.00897 ( 12) link_NAG-ASN : angle 5.25125 ( 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 374 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 254 time to evaluate : 0.691 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: 0.6592 (ttm) cc_final: 0.6118 (ttp) REVERT: B 111 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7118 (mp) REVERT: B 128 ILE cc_start: 0.7659 (mt) cc_final: 0.7394 (mm) REVERT: B 205 ARG cc_start: 0.6384 (OUTLIER) cc_final: 0.6044 (mtp-110) REVERT: B 212 GLU cc_start: 0.6912 (pm20) cc_final: 0.6602 (pm20) REVERT: B 220 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6968 (p) REVERT: B 233 ASP cc_start: 0.7047 (t70) cc_final: 0.6740 (t70) REVERT: B 258 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6483 (pp) REVERT: B 356 MET cc_start: 0.6556 (mmm) cc_final: 0.5974 (mmt) REVERT: B 390 ILE cc_start: 0.7081 (mm) cc_final: 0.6755 (mm) REVERT: B 454 PHE cc_start: 0.6317 (OUTLIER) cc_final: 0.5828 (t80) REVERT: B 471 MET cc_start: 0.8082 (ppp) cc_final: 0.7272 (pmt) REVERT: B 473 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8079 (mp) REVERT: A 113 LYS cc_start: 0.8094 (mttm) cc_final: 0.7156 (tttm) REVERT: A 250 ILE cc_start: 0.8629 (pp) cc_final: 0.8390 (mm) REVERT: A 363 SER cc_start: 0.8729 (t) cc_final: 0.8525 (m) REVERT: A 423 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8232 (m) REVERT: A 426 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7822 (pp20) REVERT: A 500 THR cc_start: 0.9129 (p) cc_final: 0.8839 (m) REVERT: A 617 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7643 (ttm-80) REVERT: E 71 MET cc_start: 0.6594 (ttm) cc_final: 0.6122 (ttp) REVERT: E 111 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7123 (mp) REVERT: E 128 ILE cc_start: 0.7658 (mt) cc_final: 0.7393 (mm) REVERT: E 205 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.6026 (mtp-110) REVERT: E 212 GLU cc_start: 0.6909 (pm20) cc_final: 0.6598 (pm20) REVERT: E 220 SER cc_start: 0.7204 (OUTLIER) cc_final: 0.6965 (p) REVERT: E 233 ASP cc_start: 0.7052 (t70) cc_final: 0.6745 (t70) REVERT: E 258 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6490 (pp) REVERT: E 356 MET cc_start: 0.6576 (mmm) cc_final: 0.5996 (mmt) REVERT: E 390 ILE cc_start: 0.7085 (mm) cc_final: 0.6760 (mm) REVERT: E 454 PHE cc_start: 0.6315 (OUTLIER) cc_final: 0.5829 (t80) REVERT: E 471 MET cc_start: 0.8081 (ppp) cc_final: 0.7268 (pmt) REVERT: E 473 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 113 LYS cc_start: 0.8098 (mttm) cc_final: 0.7159 (tttm) REVERT: F 250 ILE cc_start: 0.8633 (pp) cc_final: 0.8394 (mm) REVERT: F 363 SER cc_start: 0.8734 (t) cc_final: 0.8529 (m) REVERT: F 423 SER cc_start: 0.8914 (OUTLIER) cc_final: 0.8237 (m) REVERT: F 426 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7832 (pp20) REVERT: F 500 THR cc_start: 0.9133 (p) cc_final: 0.8844 (m) REVERT: F 617 ARG cc_start: 0.8050 (ttt90) cc_final: 0.7645 (ttm-80) outliers start: 120 outliers final: 20 residues processed: 348 average time/residue: 0.4951 time to fit residues: 198.5197 Evaluate side-chains 256 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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 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 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: 0.6980 chunk 29 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 192 optimal weight: 0.0870 chunk 111 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4170 r_free = 0.4170 target = 0.182751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.104054 restraints weight = 21082.622| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.17 r_work: 0.3004 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3097 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= 0.139 Angle : 0.702 16.720 24708 Z= 0.340 Chirality : 0.045 0.331 2800 Planarity : 0.005 0.042 3040 Dihedral : 9.076 124.742 3052 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 4.67 % Allowed : 25.66 % Favored : 69.67 % 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 aren not related in a simple way. whole: -1.67 (0.17), residues: 2148 helix: -0.64 (0.16), residues: 1010 sheet: -1.83 (0.32), residues: 178 loop : -1.35 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 326 TYR 0.013 0.001 TYR F 65 PHE 0.013 0.001 PHE F 407 TRP 0.014 0.001 TRP E 383 HIS 0.005 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00301 (18110) covalent geometry : angle 0.66268 (24644) SS BOND : bond 0.00317 ( 8) SS BOND : angle 1.12946 ( 16) hydrogen bonds : bond 0.04497 ( 742) hydrogen bonds : angle 4.57967 ( 2070) link_BETA1-4 : bond 0.01619 ( 4) link_BETA1-4 : angle 3.85076 ( 12) link_NAG-ASN : bond 0.00898 ( 12) link_NAG-ASN : angle 5.63540 ( 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 330 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 242 time to evaluate : 0.869 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 128 ILE cc_start: 0.7627 (mt) cc_final: 0.7408 (mm) REVERT: B 171 ARG cc_start: 0.5030 (ptm160) cc_final: 0.4380 (mtp-110) REVERT: B 209 ASN cc_start: 0.7174 (p0) cc_final: 0.6884 (t0) REVERT: B 233 ASP cc_start: 0.7194 (t70) cc_final: 0.6821 (t70) REVERT: B 250 ARG cc_start: 0.6405 (mmm-85) cc_final: 0.4909 (tmm-80) REVERT: B 333 ARG cc_start: 0.6471 (mmp80) cc_final: 0.6033 (mmp-170) REVERT: B 337 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6303 (ppp) REVERT: B 348 ARG cc_start: 0.3795 (OUTLIER) cc_final: 0.3361 (mpp-170) REVERT: B 356 MET cc_start: 0.6569 (mmm) cc_final: 0.5972 (mmm) REVERT: B 390 ILE cc_start: 0.6906 (mm) cc_final: 0.6679 (mm) REVERT: B 454 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5790 (t80) REVERT: B 473 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8219 (mp) REVERT: A 113 LYS cc_start: 0.8050 (mttm) cc_final: 0.7517 (tppt) REVERT: A 437 GLU cc_start: 0.7727 (tp30) cc_final: 0.7523 (mm-30) REVERT: A 486 MET cc_start: 0.9272 (mtp) cc_final: 0.9027 (mtm) REVERT: A 500 THR cc_start: 0.9162 (p) cc_final: 0.8878 (m) REVERT: A 524 HIS cc_start: 0.7746 (OUTLIER) cc_final: 0.7042 (p-80) REVERT: A 609 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: A 617 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7692 (ttm-80) REVERT: A 671 ARG cc_start: 0.8182 (ptm160) cc_final: 0.7902 (ptp90) REVERT: E 128 ILE cc_start: 0.7617 (mt) cc_final: 0.7401 (mm) REVERT: E 209 ASN cc_start: 0.7171 (p0) cc_final: 0.6881 (t0) REVERT: E 233 ASP cc_start: 0.7199 (t70) cc_final: 0.6826 (t70) REVERT: E 250 ARG cc_start: 0.6411 (mmm-85) cc_final: 0.4905 (tmm-80) REVERT: E 326 ARG cc_start: 0.6355 (mmt90) cc_final: 0.6028 (mmt90) REVERT: E 333 ARG cc_start: 0.6468 (mmp80) cc_final: 0.6033 (mmp-170) REVERT: E 337 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.6295 (ppp) REVERT: E 348 ARG cc_start: 0.3782 (OUTLIER) cc_final: 0.3353 (mpp-170) REVERT: E 356 MET cc_start: 0.6566 (mmm) cc_final: 0.5967 (mmm) REVERT: E 390 ILE cc_start: 0.6911 (mm) cc_final: 0.6685 (mm) REVERT: E 454 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5790 (t80) REVERT: E 473 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8219 (mp) REVERT: F 113 LYS cc_start: 0.8056 (mttm) cc_final: 0.7523 (tppt) REVERT: F 437 GLU cc_start: 0.7714 (tp30) cc_final: 0.7511 (mm-30) REVERT: F 486 MET cc_start: 0.9270 (mtp) cc_final: 0.9027 (mtm) REVERT: F 500 THR cc_start: 0.9166 (p) cc_final: 0.8881 (m) REVERT: F 524 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7034 (p-80) REVERT: F 609 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: F 617 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7693 (ttm-80) REVERT: F 671 ARG cc_start: 0.8178 (ptm160) cc_final: 0.7899 (ptp90) outliers start: 88 outliers final: 32 residues processed: 304 average time/residue: 0.6988 time to fit residues: 236.2559 Evaluate side-chains 268 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 104 PHE Chi-restraints excluded: chain B residue 304 ILE 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 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 90 ILE Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 304 ILE 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 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: 0.8980 chunk 116 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 474 GLN A 577 ASN E 237 GLN E 474 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.181166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101645 restraints weight = 21072.232| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.62 r_work: 0.2927 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18134 Z= 0.178 Angle : 0.707 15.042 24708 Z= 0.345 Chirality : 0.046 0.331 2800 Planarity : 0.005 0.070 3040 Dihedral : 8.497 125.461 3042 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 5.94 % Allowed : 24.23 % Favored : 69.83 % 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 aren not related in a simple way. whole: -1.16 (0.17), residues: 2148 helix: -0.19 (0.17), residues: 1004 sheet: -1.24 (0.34), residues: 160 loop : -1.21 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 326 TYR 0.017 0.002 TYR F 65 PHE 0.020 0.002 PHE A 407 TRP 0.014 0.001 TRP E 383 HIS 0.006 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00413 (18110) covalent geometry : angle 0.67385 (24644) SS BOND : bond 0.00608 ( 8) SS BOND : angle 1.22029 ( 16) hydrogen bonds : bond 0.04399 ( 742) hydrogen bonds : angle 4.39207 ( 2070) link_BETA1-4 : bond 0.02015 ( 4) link_BETA1-4 : angle 3.96461 ( 12) link_NAG-ASN : bond 0.00978 ( 12) link_NAG-ASN : angle 5.12812 ( 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 331 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 219 time to evaluate : 0.722 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: 0.7378 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 171 ARG cc_start: 0.4984 (ptm160) cc_final: 0.4175 (mmm-85) REVERT: B 207 PHE cc_start: 0.5470 (OUTLIER) cc_final: 0.3836 (p90) REVERT: B 209 ASN cc_start: 0.7216 (p0) cc_final: 0.6907 (t0) REVERT: B 233 ASP cc_start: 0.7040 (t70) cc_final: 0.6726 (t70) REVERT: B 250 ARG cc_start: 0.6474 (mmm-85) cc_final: 0.4973 (tmm-80) REVERT: B 282 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7130 (pt0) REVERT: B 333 ARG cc_start: 0.6563 (mmp80) cc_final: 0.6137 (mmp-170) REVERT: B 337 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.6089 (ppp) REVERT: B 343 TYR cc_start: 0.6005 (m-10) cc_final: 0.5560 (m-80) REVERT: B 356 MET cc_start: 0.6487 (mmm) cc_final: 0.5938 (mmm) REVERT: B 454 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.6093 (t80) REVERT: B 465 ILE cc_start: 0.7099 (pt) cc_final: 0.6853 (pp) REVERT: A 68 MET cc_start: 0.5221 (mtm) cc_final: 0.4549 (mtm) REVERT: A 113 LYS cc_start: 0.8180 (mttm) cc_final: 0.7680 (mttm) REVERT: A 243 ASN cc_start: 0.8087 (t0) cc_final: 0.7784 (t0) REVERT: A 374 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7346 (pt0) REVERT: A 423 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8225 (m) REVERT: A 426 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7950 (pp20) REVERT: A 437 GLU cc_start: 0.7852 (tp30) cc_final: 0.7633 (mm-30) REVERT: A 486 MET cc_start: 0.9287 (mtp) cc_final: 0.9025 (mtm) REVERT: A 500 THR cc_start: 0.9160 (p) cc_final: 0.8916 (m) REVERT: A 524 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7043 (p-80) REVERT: A 617 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7654 (ttm-80) REVERT: A 639 THR cc_start: 0.7964 (t) cc_final: 0.7736 (m) REVERT: A 671 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7893 (ptp90) REVERT: E 134 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: E 175 TYR cc_start: 0.4394 (t80) cc_final: 0.4153 (t80) REVERT: E 207 PHE cc_start: 0.5478 (OUTLIER) cc_final: 0.3845 (p90) REVERT: E 209 ASN cc_start: 0.7216 (p0) cc_final: 0.6904 (t0) REVERT: E 233 ASP cc_start: 0.7058 (t70) cc_final: 0.6746 (t70) REVERT: E 250 ARG cc_start: 0.6470 (mmm-85) cc_final: 0.4973 (tmm-80) REVERT: E 282 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7142 (pt0) REVERT: E 333 ARG cc_start: 0.6568 (mmp80) cc_final: 0.6144 (mmp-170) REVERT: E 337 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.6077 (ppp) REVERT: E 343 TYR cc_start: 0.6001 (m-10) cc_final: 0.5556 (m-80) REVERT: E 356 MET cc_start: 0.6487 (mmm) cc_final: 0.5937 (mmm) REVERT: E 454 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.6098 (t80) REVERT: E 465 ILE cc_start: 0.7091 (pt) cc_final: 0.6846 (pp) REVERT: F 68 MET cc_start: 0.5230 (mtm) cc_final: 0.4568 (mtm) REVERT: F 113 LYS cc_start: 0.8182 (mttm) cc_final: 0.7679 (mttm) REVERT: F 243 ASN cc_start: 0.8083 (t0) cc_final: 0.7780 (t0) REVERT: F 374 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: F 423 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8229 (m) REVERT: F 426 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7947 (pp20) REVERT: F 437 GLU cc_start: 0.7857 (tp30) cc_final: 0.7639 (mm-30) REVERT: F 486 MET cc_start: 0.9287 (mtp) cc_final: 0.9026 (mtm) REVERT: F 500 THR cc_start: 0.9161 (p) cc_final: 0.8917 (m) REVERT: F 524 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7027 (p-80) REVERT: F 617 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7652 (ttm-80) REVERT: F 639 THR cc_start: 0.7964 (t) cc_final: 0.7737 (m) REVERT: F 671 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7882 (ptp90) outliers start: 112 outliers final: 42 residues processed: 297 average time/residue: 0.6937 time to fit residues: 228.8080 Evaluate side-chains 267 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 279 THR 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 384 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 454 PHE 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 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 279 THR 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 384 LEU Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 454 PHE 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 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: 0.9980 chunk 104 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 131 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 160 optimal weight: 0.6980 chunk 207 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 358 HIS E 237 GLN E 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.181985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104973 restraints weight = 20864.366| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.71 r_work: 0.2946 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18134 Z= 0.127 Angle : 0.661 12.946 24708 Z= 0.321 Chirality : 0.044 0.331 2800 Planarity : 0.004 0.038 3040 Dihedral : 8.156 125.831 3038 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 5.14 % Allowed : 25.56 % Favored : 69.30 % 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 aren not related in a simple way. whole: -0.88 (0.18), residues: 2148 helix: 0.11 (0.17), residues: 972 sheet: -1.07 (0.35), residues: 160 loop : -1.12 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 326 TYR 0.018 0.001 TYR A 65 PHE 0.016 0.001 PHE B 249 TRP 0.014 0.001 TRP E 383 HIS 0.007 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00279 (18110) covalent geometry : angle 0.63133 (24644) SS BOND : bond 0.00196 ( 8) SS BOND : angle 0.74278 ( 16) hydrogen bonds : bond 0.03781 ( 742) hydrogen bonds : angle 4.27351 ( 2070) link_BETA1-4 : bond 0.01421 ( 4) link_BETA1-4 : angle 3.73460 ( 12) link_NAG-ASN : bond 0.00862 ( 12) link_NAG-ASN : angle 4.70384 ( 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 311 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 214 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 175 TYR cc_start: 0.3741 (OUTLIER) cc_final: 0.3204 (t80) REVERT: B 207 PHE cc_start: 0.5608 (OUTLIER) cc_final: 0.3963 (p90) REVERT: B 209 ASN cc_start: 0.7312 (p0) cc_final: 0.7023 (t0) REVERT: B 233 ASP cc_start: 0.7057 (t70) cc_final: 0.6748 (t70) REVERT: B 250 ARG cc_start: 0.6594 (mmm-85) cc_final: 0.4986 (tmm-80) REVERT: B 282 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6689 (pt0) REVERT: B 333 ARG cc_start: 0.6583 (mmp80) cc_final: 0.6177 (mmp-170) REVERT: B 343 TYR cc_start: 0.6054 (m-10) cc_final: 0.5593 (m-80) REVERT: B 356 MET cc_start: 0.6329 (mmm) cc_final: 0.5783 (mmm) REVERT: B 454 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.5824 (t80) REVERT: B 474 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6163 (tt0) REVERT: A 68 MET cc_start: 0.5369 (mtm) cc_final: 0.4225 (mtm) REVERT: A 113 LYS cc_start: 0.8243 (mttm) cc_final: 0.7783 (mttm) REVERT: A 243 ASN cc_start: 0.8057 (t0) cc_final: 0.7751 (t0) REVERT: A 374 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: A 486 MET cc_start: 0.9301 (mtp) cc_final: 0.8905 (mtm) REVERT: A 500 THR cc_start: 0.9148 (p) cc_final: 0.8927 (m) REVERT: A 521 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6875 (tp30) REVERT: A 617 ARG cc_start: 0.7995 (ttt90) cc_final: 0.7694 (ttm-80) REVERT: A 671 ARG cc_start: 0.8225 (ptm160) cc_final: 0.7957 (ptp90) REVERT: E 207 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.3976 (p90) REVERT: E 209 ASN cc_start: 0.7309 (p0) cc_final: 0.7018 (t0) REVERT: E 233 ASP cc_start: 0.7067 (t70) cc_final: 0.6758 (t70) REVERT: E 250 ARG cc_start: 0.6587 (mmm-85) cc_final: 0.4989 (tmm-80) REVERT: E 282 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6690 (pt0) REVERT: E 333 ARG cc_start: 0.6586 (mmp80) cc_final: 0.6181 (mmp-170) REVERT: E 356 MET cc_start: 0.6329 (mmm) cc_final: 0.5778 (mmm) REVERT: E 454 PHE cc_start: 0.6615 (OUTLIER) cc_final: 0.5827 (t80) REVERT: F 113 LYS cc_start: 0.8248 (mttm) cc_final: 0.7793 (mttm) REVERT: F 243 ASN cc_start: 0.8066 (t0) cc_final: 0.7762 (t0) REVERT: F 374 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7396 (pt0) REVERT: F 486 MET cc_start: 0.9300 (mtp) cc_final: 0.8912 (mtm) REVERT: F 500 THR cc_start: 0.9151 (p) cc_final: 0.8928 (m) REVERT: F 521 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6867 (tp30) REVERT: F 617 ARG cc_start: 0.8000 (ttt90) cc_final: 0.7700 (ttm-80) REVERT: F 671 ARG cc_start: 0.8226 (ptm160) cc_final: 0.7959 (ptp90) outliers start: 97 outliers final: 40 residues processed: 279 average time/residue: 0.7421 time to fit residues: 228.7820 Evaluate side-chains 256 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 204 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 175 TYR 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 304 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 474 GLN 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 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 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 304 ILE Chi-restraints excluded: chain E residue 314 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 391 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 314 ASN A 516 ASN E 237 GLN E 474 GLN F 314 ASN F 516 ASN F 577 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.179232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108516 restraints weight = 20823.270| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.91 r_work: 0.2895 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18134 Z= 0.257 Angle : 0.747 12.433 24708 Z= 0.366 Chirality : 0.049 0.342 2800 Planarity : 0.005 0.042 3040 Dihedral : 8.453 128.489 3038 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 5.83 % Allowed : 24.55 % Favored : 69.62 % 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 aren not related in a simple way. whole: -0.96 (0.18), residues: 2148 helix: 0.06 (0.17), residues: 998 sheet: -1.26 (0.34), residues: 180 loop : -1.18 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 326 TYR 0.020 0.002 TYR A 259 PHE 0.027 0.002 PHE F 407 TRP 0.014 0.002 TRP E 383 HIS 0.009 0.002 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00610 (18110) covalent geometry : angle 0.72115 (24644) SS BOND : bond 0.00890 ( 8) SS BOND : angle 1.71970 ( 16) hydrogen bonds : bond 0.04881 ( 742) hydrogen bonds : angle 4.46691 ( 2070) link_BETA1-4 : bond 0.01800 ( 4) link_BETA1-4 : angle 3.88384 ( 12) link_NAG-ASN : bond 0.00793 ( 12) link_NAG-ASN : angle 4.52535 ( 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 331 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 221 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.4272 (p90) REVERT: B 209 ASN cc_start: 0.7295 (p0) cc_final: 0.7036 (t0) REVERT: B 233 ASP cc_start: 0.7035 (t70) cc_final: 0.6761 (t70) REVERT: B 250 ARG cc_start: 0.6498 (mmm-85) cc_final: 0.4907 (tmm-80) REVERT: B 282 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: B 333 ARG cc_start: 0.6423 (mmp80) cc_final: 0.6080 (mmp-170) REVERT: B 343 TYR cc_start: 0.6015 (m-10) cc_final: 0.5556 (m-80) REVERT: B 356 MET cc_start: 0.6359 (mmm) cc_final: 0.5933 (mmt) REVERT: B 474 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6396 (tt0) REVERT: A 68 MET cc_start: 0.5678 (mtm) cc_final: 0.4447 (mtm) REVERT: A 113 LYS cc_start: 0.8315 (mttm) cc_final: 0.7562 (tptt) REVERT: A 243 ASN cc_start: 0.7758 (t0) cc_final: 0.7505 (t0) REVERT: A 374 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7508 (pt0) REVERT: A 486 MET cc_start: 0.9303 (mtp) cc_final: 0.9059 (mtm) REVERT: A 524 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7126 (p-80) REVERT: A 617 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7667 (ttm-80) REVERT: A 619 ARG cc_start: 0.7451 (ttp80) cc_final: 0.7193 (ttp80) REVERT: A 671 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7996 (ptp90) REVERT: E 207 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.4278 (p90) REVERT: E 209 ASN cc_start: 0.7245 (p0) cc_final: 0.6977 (t0) REVERT: E 233 ASP cc_start: 0.7043 (t70) cc_final: 0.6770 (t70) REVERT: E 250 ARG cc_start: 0.6505 (mmm-85) cc_final: 0.4907 (tmm-80) REVERT: E 282 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6688 (pt0) REVERT: E 333 ARG cc_start: 0.6419 (mmp80) cc_final: 0.6075 (mmp-170) REVERT: E 343 TYR cc_start: 0.5989 (m-10) cc_final: 0.5562 (m-80) REVERT: E 356 MET cc_start: 0.6363 (mmm) cc_final: 0.5932 (mmt) REVERT: E 474 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.6456 (tt0) REVERT: F 68 MET cc_start: 0.5023 (mtm) cc_final: 0.3482 (mpt) REVERT: F 113 LYS cc_start: 0.8312 (mttm) cc_final: 0.7558 (tptt) REVERT: F 243 ASN cc_start: 0.7761 (t0) cc_final: 0.7510 (t0) REVERT: F 374 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: F 486 MET cc_start: 0.9305 (mtp) cc_final: 0.9064 (mtm) REVERT: F 524 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7131 (p-80) REVERT: F 617 ARG cc_start: 0.7953 (ttt90) cc_final: 0.7664 (ttm-80) REVERT: F 619 ARG cc_start: 0.7451 (ttp80) cc_final: 0.7192 (ttp80) REVERT: F 671 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7992 (ptp90) outliers start: 110 outliers final: 50 residues processed: 293 average time/residue: 0.7007 time to fit residues: 227.9870 Evaluate side-chains 274 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 THR 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 304 ILE 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 384 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 474 GLN 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 638 VAL Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain E residue 77 THR 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 304 ILE 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 384 LEU Chi-restraints excluded: chain E residue 391 THR Chi-restraints excluded: chain E residue 474 GLN 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 638 VAL Chi-restraints excluded: chain F residue 671 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: 0.9980 chunk 107 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN E 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.180797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104659 restraints weight = 20836.839| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.64 r_work: 0.2908 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4274 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= 0.144 Angle : 0.681 11.240 24708 Z= 0.331 Chirality : 0.045 0.334 2800 Planarity : 0.004 0.043 3040 Dihedral : 8.168 126.739 3034 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 4.19 % Allowed : 27.47 % 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 aren not related in a simple way. whole: -0.76 (0.18), residues: 2148 helix: 0.30 (0.17), residues: 970 sheet: -1.10 (0.36), residues: 160 loop : -1.14 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 326 TYR 0.019 0.001 TYR F 65 PHE 0.015 0.001 PHE A 407 TRP 0.015 0.001 TRP E 383 HIS 0.006 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00326 (18110) covalent geometry : angle 0.65615 (24644) SS BOND : bond 0.00665 ( 8) SS BOND : angle 1.66271 ( 16) hydrogen bonds : bond 0.03965 ( 742) hydrogen bonds : angle 4.32401 ( 2070) link_BETA1-4 : bond 0.01793 ( 4) link_BETA1-4 : angle 3.67803 ( 12) link_NAG-ASN : bond 0.00780 ( 12) link_NAG-ASN : angle 4.21600 ( 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 289 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 210 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6664 (mmp) cc_final: 0.6447 (mmm) REVERT: B 207 PHE cc_start: 0.5772 (OUTLIER) cc_final: 0.4095 (p90) REVERT: B 209 ASN cc_start: 0.7247 (p0) cc_final: 0.6989 (t0) REVERT: B 233 ASP cc_start: 0.7079 (t70) cc_final: 0.6805 (t70) REVERT: B 241 ILE cc_start: 0.6740 (mt) cc_final: 0.6517 (tp) REVERT: B 250 ARG cc_start: 0.6367 (mmm-85) cc_final: 0.5020 (tmm-80) REVERT: B 282 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6592 (pt0) REVERT: B 333 ARG cc_start: 0.6485 (mmp80) cc_final: 0.6142 (mmp-170) REVERT: B 343 TYR cc_start: 0.6043 (m-10) cc_final: 0.5497 (m-80) REVERT: B 356 MET cc_start: 0.6432 (mmm) cc_final: 0.5943 (mmm) REVERT: B 397 ARG cc_start: 0.7731 (mmm160) cc_final: 0.7340 (mmm-85) REVERT: A 68 MET cc_start: 0.5414 (mtm) cc_final: 0.4632 (mtm) REVERT: A 113 LYS cc_start: 0.8293 (mttm) cc_final: 0.7561 (tptt) REVERT: A 374 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: A 486 MET cc_start: 0.9290 (mtp) cc_final: 0.8909 (mtm) REVERT: A 524 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7106 (p-80) REVERT: A 617 ARG cc_start: 0.7952 (ttt90) cc_final: 0.7729 (ttm-80) REVERT: A 671 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8016 (ptp90) REVERT: E 59 MET cc_start: 0.6653 (mmp) cc_final: 0.6438 (mmm) REVERT: E 207 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.4099 (p90) REVERT: E 209 ASN cc_start: 0.7246 (p0) cc_final: 0.6986 (t0) REVERT: E 233 ASP cc_start: 0.7075 (t70) cc_final: 0.6802 (t70) REVERT: E 241 ILE cc_start: 0.6747 (mt) cc_final: 0.6522 (tp) REVERT: E 250 ARG cc_start: 0.6370 (mmm-85) cc_final: 0.5017 (tmm-80) REVERT: E 282 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6582 (pt0) REVERT: E 333 ARG cc_start: 0.6487 (mmp80) cc_final: 0.6143 (mmp-170) REVERT: E 356 MET cc_start: 0.6427 (mmm) cc_final: 0.5934 (mmm) REVERT: E 397 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7258 (mmm-85) REVERT: E 478 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5315 (pm20) REVERT: F 113 LYS cc_start: 0.8296 (mttm) cc_final: 0.7560 (tptt) REVERT: F 374 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7483 (pt0) REVERT: F 486 MET cc_start: 0.9289 (mtp) cc_final: 0.8914 (mtm) REVERT: F 524 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7106 (p-80) REVERT: F 617 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7730 (ttm-80) REVERT: F 671 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8022 (ptp90) outliers start: 79 outliers final: 40 residues processed: 265 average time/residue: 0.7610 time to fit residues: 222.3241 Evaluate side-chains 258 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 304 ILE 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 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 536 VAL 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 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 304 ILE 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 478 GLU 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 536 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 130 optimal weight: 0.0170 chunk 119 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 43 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 191 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 403 GLN E 237 GLN F 403 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 = 0.181698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102234 restraints weight = 20766.582| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.17 r_work: 0.2972 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18134 Z= 0.127 Angle : 0.652 11.073 24708 Z= 0.316 Chirality : 0.044 0.331 2800 Planarity : 0.004 0.040 3040 Dihedral : 7.906 125.372 3034 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 3.87 % Allowed : 27.52 % Favored : 68.61 % 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 aren not related in a simple way. whole: -0.59 (0.18), residues: 2148 helix: 0.46 (0.17), residues: 976 sheet: -1.09 (0.36), residues: 160 loop : -1.07 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 326 TYR 0.021 0.001 TYR F 65 PHE 0.012 0.001 PHE A 407 TRP 0.015 0.001 TRP B 383 HIS 0.007 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00283 (18110) covalent geometry : angle 0.62859 (24644) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.24792 ( 16) hydrogen bonds : bond 0.03636 ( 742) hydrogen bonds : angle 4.20655 ( 2070) link_BETA1-4 : bond 0.01582 ( 4) link_BETA1-4 : angle 3.57060 ( 12) link_NAG-ASN : bond 0.00731 ( 12) link_NAG-ASN : angle 3.98953 ( 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 292 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 219 time to evaluate : 0.693 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: B 59 MET cc_start: 0.6646 (mmp) cc_final: 0.6378 (mmm) REVERT: B 77 THR cc_start: 0.5704 (m) cc_final: 0.5336 (p) REVERT: B 171 ARG cc_start: 0.4680 (ptt180) cc_final: 0.4455 (ptt180) REVERT: B 205 ARG cc_start: 0.6957 (mtp-110) cc_final: 0.6688 (mtp-110) REVERT: B 209 ASN cc_start: 0.7247 (p0) cc_final: 0.6997 (t0) REVERT: B 221 ILE cc_start: 0.7072 (mm) cc_final: 0.6792 (mt) REVERT: B 233 ASP cc_start: 0.7196 (t70) cc_final: 0.6944 (t70) REVERT: B 241 ILE cc_start: 0.6929 (mt) cc_final: 0.6713 (tp) REVERT: B 250 ARG cc_start: 0.5818 (mmm-85) cc_final: 0.4990 (tmm-80) REVERT: B 282 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6593 (pt0) REVERT: B 326 ARG cc_start: 0.6645 (mmt90) cc_final: 0.6310 (mpt180) REVERT: B 333 ARG cc_start: 0.6431 (mmp80) cc_final: 0.6111 (mmp-170) REVERT: B 343 TYR cc_start: 0.6040 (m-10) cc_final: 0.5489 (m-80) REVERT: B 356 MET cc_start: 0.6414 (mmm) cc_final: 0.6047 (mmm) REVERT: B 397 ARG cc_start: 0.7810 (mmm160) cc_final: 0.7402 (mmm-85) REVERT: B 415 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.7034 (tp) REVERT: A 68 MET cc_start: 0.5482 (mtm) cc_final: 0.4571 (mtm) REVERT: A 113 LYS cc_start: 0.8155 (mttm) cc_final: 0.7478 (tptt) REVERT: A 486 MET cc_start: 0.9277 (mtp) cc_final: 0.8891 (mtm) REVERT: A 644 GLU cc_start: 0.8793 (tp30) cc_final: 0.8538 (tp30) REVERT: A 658 ARG cc_start: 0.7872 (mmp80) cc_final: 0.7588 (mmp-170) REVERT: A 671 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7984 (ptp90) REVERT: E 59 MET cc_start: 0.6653 (mmp) cc_final: 0.6384 (mmm) REVERT: E 77 THR cc_start: 0.5697 (m) cc_final: 0.5335 (p) REVERT: E 205 ARG cc_start: 0.6957 (mtp-110) cc_final: 0.6690 (mtp-110) REVERT: E 209 ASN cc_start: 0.7246 (p0) cc_final: 0.6994 (t0) REVERT: E 221 ILE cc_start: 0.7073 (mm) cc_final: 0.6795 (mt) REVERT: E 233 ASP cc_start: 0.7190 (t70) cc_final: 0.6938 (t70) REVERT: E 241 ILE cc_start: 0.6931 (mt) cc_final: 0.6714 (tp) REVERT: E 250 ARG cc_start: 0.5819 (mmm-85) cc_final: 0.4988 (tmm-80) REVERT: E 282 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6580 (pt0) REVERT: E 333 ARG cc_start: 0.6436 (mmp80) cc_final: 0.6114 (mmp-170) REVERT: E 348 ARG cc_start: 0.3696 (OUTLIER) cc_final: 0.3447 (mpp-170) REVERT: E 356 MET cc_start: 0.6411 (mmm) cc_final: 0.6043 (mmm) REVERT: E 397 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7380 (mmm-85) REVERT: E 398 PHE cc_start: 0.6406 (t80) cc_final: 0.5809 (t80) REVERT: E 415 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.7031 (tp) REVERT: F 113 LYS cc_start: 0.8177 (mttm) cc_final: 0.7500 (tptt) REVERT: F 486 MET cc_start: 0.9276 (mtp) cc_final: 0.8894 (mtm) REVERT: F 644 GLU cc_start: 0.8791 (tp30) cc_final: 0.8534 (tp30) REVERT: F 671 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7991 (ptp90) outliers start: 73 outliers final: 41 residues processed: 273 average time/residue: 0.7170 time to fit residues: 217.6917 Evaluate side-chains 255 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 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 344 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 426 LEU 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 417 ASP Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 631 ARG Chi-restraints excluded: chain A residue 665 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 176 VAL 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 344 ILE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 348 ARG Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 426 LEU 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 417 ASP Chi-restraints excluded: chain F residue 536 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 13 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 22 optimal weight: 0.0010 chunk 96 optimal weight: 3.9990 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 403 GLN E 237 GLN F 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.182741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110602 restraints weight = 20899.185| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.92 r_work: 0.2980 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18134 Z= 0.110 Angle : 0.648 10.872 24708 Z= 0.311 Chirality : 0.043 0.329 2800 Planarity : 0.004 0.066 3040 Dihedral : 7.712 123.784 3034 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.04 % Rotamer: Outliers : 2.97 % Allowed : 28.74 % Favored : 68.29 % 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 aren not related in a simple way. whole: -0.40 (0.18), residues: 2148 helix: 0.69 (0.18), residues: 964 sheet: -1.13 (0.36), residues: 160 loop : -1.01 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 296 TYR 0.017 0.001 TYR A 65 PHE 0.011 0.001 PHE A 570 TRP 0.015 0.001 TRP E 383 HIS 0.007 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00237 (18110) covalent geometry : angle 0.62760 (24644) SS BOND : bond 0.00244 ( 8) SS BOND : angle 1.05646 ( 16) hydrogen bonds : bond 0.03399 ( 742) hydrogen bonds : angle 4.17217 ( 2070) link_BETA1-4 : bond 0.01556 ( 4) link_BETA1-4 : angle 3.49981 ( 12) link_NAG-ASN : bond 0.00722 ( 12) link_NAG-ASN : angle 3.77165 ( 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 277 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 MET cc_start: 0.6608 (mmp) cc_final: 0.6335 (mmm) REVERT: B 77 THR cc_start: 0.5757 (m) cc_final: 0.5405 (p) REVERT: B 209 ASN cc_start: 0.7263 (p0) cc_final: 0.7038 (t0) REVERT: B 221 ILE cc_start: 0.7114 (mm) cc_final: 0.6831 (mt) REVERT: B 233 ASP cc_start: 0.7148 (t70) cc_final: 0.6903 (t70) REVERT: B 241 ILE cc_start: 0.6922 (mt) cc_final: 0.6713 (tp) REVERT: B 250 ARG cc_start: 0.5815 (mmm-85) cc_final: 0.4985 (tmm-80) REVERT: B 282 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6498 (pt0) REVERT: B 326 ARG cc_start: 0.6657 (mmt90) cc_final: 0.6314 (mpt180) REVERT: B 333 ARG cc_start: 0.6316 (mmp80) cc_final: 0.5945 (mmp-170) REVERT: B 343 TYR cc_start: 0.6075 (m-10) cc_final: 0.5534 (m-80) REVERT: B 356 MET cc_start: 0.6388 (mmm) cc_final: 0.6033 (mmm) REVERT: B 397 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7437 (mmm-85) REVERT: B 415 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.7010 (tp) REVERT: A 68 MET cc_start: 0.5606 (mtm) cc_final: 0.4854 (mtm) REVERT: A 113 LYS cc_start: 0.8106 (mttm) cc_final: 0.7562 (mttm) REVERT: A 486 MET cc_start: 0.9267 (mtp) cc_final: 0.8877 (mtm) REVERT: A 613 ASN cc_start: 0.8065 (t0) cc_final: 0.7839 (t0) REVERT: A 658 ARG cc_start: 0.7752 (mmp80) cc_final: 0.7483 (mmp-170) REVERT: A 671 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7951 (ptp90) REVERT: E 59 MET cc_start: 0.6611 (mmp) cc_final: 0.6340 (mmm) REVERT: E 77 THR cc_start: 0.5727 (m) cc_final: 0.5364 (p) REVERT: E 209 ASN cc_start: 0.7265 (p0) cc_final: 0.7036 (t0) REVERT: E 221 ILE cc_start: 0.7123 (mm) cc_final: 0.6840 (mt) REVERT: E 233 ASP cc_start: 0.7144 (t70) cc_final: 0.6895 (t70) REVERT: E 241 ILE cc_start: 0.6924 (mt) cc_final: 0.6714 (tp) REVERT: E 250 ARG cc_start: 0.5800 (mmm-85) cc_final: 0.4958 (tmm-80) REVERT: E 282 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6492 (pt0) REVERT: E 333 ARG cc_start: 0.6353 (mmp80) cc_final: 0.5989 (mmp-170) REVERT: E 356 MET cc_start: 0.6393 (mmm) cc_final: 0.6037 (mmm) REVERT: E 397 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7405 (mmm-85) REVERT: E 398 PHE cc_start: 0.6358 (t80) cc_final: 0.5771 (t80) REVERT: E 415 ILE cc_start: 0.7248 (OUTLIER) cc_final: 0.7011 (tp) REVERT: F 113 LYS cc_start: 0.8109 (mttm) cc_final: 0.7566 (mttm) REVERT: F 486 MET cc_start: 0.9262 (mtp) cc_final: 0.8876 (mtm) REVERT: F 613 ASN cc_start: 0.8065 (t0) cc_final: 0.7838 (t0) REVERT: F 671 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7954 (ptp90) outliers start: 56 outliers final: 30 residues processed: 264 average time/residue: 0.7252 time to fit residues: 211.7887 Evaluate side-chains 246 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 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 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 536 VAL 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 90 ILE 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 344 ILE Chi-restraints excluded: chain E residue 407 ILE 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 536 VAL Chi-restraints excluded: chain F residue 631 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: 0.0170 chunk 177 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 150 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 145 optimal weight: 0.0040 chunk 161 optimal weight: 0.0570 chunk 94 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.4152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 679 ASN E 58 ASN E 472 HIS F 403 GLN F 679 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.182607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103675 restraints weight = 20692.357| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.18 r_work: 0.2996 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18134 Z= 0.114 Angle : 0.656 10.839 24708 Z= 0.313 Chirality : 0.043 0.328 2800 Planarity : 0.004 0.062 3040 Dihedral : 7.618 122.840 3032 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 2.44 % Allowed : 29.64 % Favored : 67.92 % 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 aren not related in a simple way. whole: -0.33 (0.18), residues: 2148 helix: 0.72 (0.17), residues: 988 sheet: -1.12 (0.36), residues: 160 loop : -0.98 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 326 TYR 0.017 0.001 TYR F 65 PHE 0.012 0.001 PHE A 570 TRP 0.014 0.001 TRP E 383 HIS 0.007 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00248 (18110) covalent geometry : angle 0.63590 (24644) SS BOND : bond 0.00419 ( 8) SS BOND : angle 1.27102 ( 16) hydrogen bonds : bond 0.03468 ( 742) hydrogen bonds : angle 4.13801 ( 2070) link_BETA1-4 : bond 0.01556 ( 4) link_BETA1-4 : angle 3.52505 ( 12) link_NAG-ASN : bond 0.00691 ( 12) link_NAG-ASN : angle 3.66554 ( 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: 46 poor density : 227 time to evaluate : 0.739 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: B 59 MET cc_start: 0.6640 (mmp) cc_final: 0.6367 (mmm) REVERT: B 77 THR cc_start: 0.5789 (m) cc_final: 0.5480 (p) REVERT: B 104 PHE cc_start: 0.6421 (t80) cc_final: 0.6216 (t80) REVERT: B 209 ASN cc_start: 0.7265 (p0) cc_final: 0.7035 (t0) REVERT: B 221 ILE cc_start: 0.7119 (mm) cc_final: 0.6836 (mt) REVERT: B 233 ASP cc_start: 0.7167 (t70) cc_final: 0.6923 (t70) REVERT: B 241 ILE cc_start: 0.6935 (mt) cc_final: 0.6714 (tp) REVERT: B 250 ARG cc_start: 0.5847 (mmm-85) cc_final: 0.5016 (tmm-80) REVERT: B 282 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6485 (pt0) REVERT: B 326 ARG cc_start: 0.6798 (mmt90) cc_final: 0.6456 (mpt180) REVERT: B 333 ARG cc_start: 0.6385 (mmp80) cc_final: 0.5972 (mmp-170) REVERT: B 356 MET cc_start: 0.6464 (mmm) cc_final: 0.6117 (mmm) REVERT: B 397 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7395 (mmm-85) REVERT: B 398 PHE cc_start: 0.6167 (t80) cc_final: 0.5797 (t80) REVERT: B 415 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.7002 (tp) REVERT: A 113 LYS cc_start: 0.8122 (mttm) cc_final: 0.7595 (mttm) REVERT: A 486 MET cc_start: 0.9281 (mtp) cc_final: 0.8904 (mtm) REVERT: A 524 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7061 (p-80) REVERT: A 613 ASN cc_start: 0.7959 (t0) cc_final: 0.7640 (t0) REVERT: A 644 GLU cc_start: 0.8769 (tp30) cc_final: 0.8543 (tp30) REVERT: A 658 ARG cc_start: 0.7806 (mmp80) cc_final: 0.7532 (mmp-170) REVERT: A 671 ARG cc_start: 0.8232 (ptm160) cc_final: 0.7965 (ptp90) REVERT: E 59 MET cc_start: 0.6646 (mmp) cc_final: 0.6373 (mmm) REVERT: E 77 THR cc_start: 0.5767 (m) cc_final: 0.5406 (p) REVERT: E 104 PHE cc_start: 0.6427 (t80) cc_final: 0.6221 (t80) REVERT: E 209 ASN cc_start: 0.7263 (p0) cc_final: 0.7036 (t0) REVERT: E 221 ILE cc_start: 0.7123 (mm) cc_final: 0.6841 (mt) REVERT: E 233 ASP cc_start: 0.7164 (t70) cc_final: 0.6920 (t70) REVERT: E 241 ILE cc_start: 0.6940 (mt) cc_final: 0.6717 (tp) REVERT: E 250 ARG cc_start: 0.5852 (mmm-85) cc_final: 0.5017 (tmm-80) REVERT: E 282 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6470 (pt0) REVERT: E 333 ARG cc_start: 0.6389 (mmp80) cc_final: 0.5976 (mmp-170) REVERT: E 356 MET cc_start: 0.6467 (mmm) cc_final: 0.6122 (mmm) REVERT: E 397 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7365 (mmm-85) REVERT: E 398 PHE cc_start: 0.6360 (t80) cc_final: 0.5774 (t80) REVERT: E 415 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.7006 (tp) REVERT: E 475 MET cc_start: 0.7164 (ptt) cc_final: 0.6594 (pmm) REVERT: F 113 LYS cc_start: 0.8115 (mttm) cc_final: 0.7594 (mttm) REVERT: F 203 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.8312 (mmtp) REVERT: F 486 MET cc_start: 0.9280 (mtp) cc_final: 0.8907 (mtm) REVERT: F 613 ASN cc_start: 0.7967 (t0) cc_final: 0.7649 (t0) REVERT: F 644 GLU cc_start: 0.8782 (tp30) cc_final: 0.8556 (tp30) REVERT: F 671 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7967 (ptp90) outliers start: 46 outliers final: 31 residues processed: 264 average time/residue: 0.7334 time to fit residues: 214.2235 Evaluate side-chains 257 residues out of total 1886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 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 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 141 ASP Chi-restraints excluded: chain A residue 524 HIS Chi-restraints excluded: chain A residue 536 VAL 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 90 ILE 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 344 ILE 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 141 ASP Chi-restraints excluded: chain F residue 203 LYS Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 631 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: 0.9980 chunk 182 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 141 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN A 403 GLN F 403 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.181505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107726 restraints weight = 20784.312| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.72 r_work: 0.2944 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4691 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= 0.150 Angle : 0.700 21.515 24708 Z= 0.336 Chirality : 0.045 0.334 2800 Planarity : 0.004 0.040 3040 Dihedral : 7.711 123.144 3032 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer: Outliers : 2.97 % Allowed : 29.32 % 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 aren not related in a simple way. whole: -0.34 (0.18), residues: 2148 helix: 0.75 (0.17), residues: 984 sheet: -1.00 (0.37), residues: 160 loop : -1.05 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 326 TYR 0.021 0.001 TYR F 65 PHE 0.019 0.001 PHE F 407 TRP 0.011 0.001 TRP B 383 HIS 0.006 0.001 HIS F 175 Details of bonding type rmsd covalent geometry : bond 0.00345 (18110) covalent geometry : angle 0.68018 (24644) SS BOND : bond 0.01240 ( 8) SS BOND : angle 2.20627 ( 16) hydrogen bonds : bond 0.03841 ( 742) hydrogen bonds : angle 4.19900 ( 2070) link_BETA1-4 : bond 0.01584 ( 4) link_BETA1-4 : angle 3.58795 ( 12) link_NAG-ASN : bond 0.00650 ( 12) link_NAG-ASN : angle 3.59849 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8787.30 seconds wall clock time: 150 minutes 23.26 seconds (9023.26 seconds total)