Starting phenix.real_space_refine on Tue Sep 15 11:18:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.cif Found real_map, /net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6von_21270/09_2026/6von_21270.cif" } resolution = 3.35 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 130 5.16 5 C 24851 2.51 5 N 6676 2.21 5 O 7490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39163 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3850 Classifications: {'peptide': 501} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain: "B" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3854 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 17, 'TRANS': 484} Chain: "C" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3843 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "D" Number of atoms: 3619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3619 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 452} Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3645 Classifications: {'peptide': 481} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 455} Chain: "F" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3636 Classifications: {'peptide': 480} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 454} Chain: "d" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1384 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 4, 'TRANS': 174} Chain: "g" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2502 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "e" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 1237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1237 Classifications: {'peptide': 153} Link IDs: {'TRANS': 152} Chain: "J" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1018 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain: "a" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1741 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "X" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Y" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 544 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'ATP': 1, 'TTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.83, per 1000 atoms: 0.23 Number of scatterers: 39163 At special positions: 0 Unit cell: (229.554, 142.155, 148.473, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 130 16.00 P 16 15.00 O 7490 8.00 N 6676 7.00 C 24851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.8 seconds 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9422 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 24 sheets defined 60.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.781A pdb=" N MET A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix removed outlier: 3.764A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 278 removed outlier: 3.755A pdb=" N GLN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.596A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.545A pdb=" N THR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.623A pdb=" N PHE A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.040A pdb=" N ALA A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.671A pdb=" N GLN A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.619A pdb=" N LEU A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 Processing helix chain 'A' and resid 483 through 505 Processing helix chain 'B' and resid 9 through 19 removed outlier: 3.862A pdb=" N GLY B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.934A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU B 105 " --> pdb=" O GLU B 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 101 through 105' Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 220 No H-bonds generated for 'chain 'B' and resid 218 through 220' Processing helix chain 'B' and resid 232 through 252 Proline residue: B 240 - end of helix removed outlier: 3.719A pdb=" N PHE B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 278 Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.834A pdb=" N ALA B 286 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 300 removed outlier: 3.840A pdb=" N LEU B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 329 through 339 removed outlier: 3.681A pdb=" N THR B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 373 through 397 removed outlier: 5.134A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.506A pdb=" N THR B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.806A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 469 through 480 removed outlier: 3.956A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 503 removed outlier: 4.248A pdb=" N LEU B 503 " --> pdb=" O GLU B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 101 through 105 removed outlier: 3.509A pdb=" N TYR C 104 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 105 " --> pdb=" O GLU C 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 101 through 105' Processing helix chain 'C' and resid 151 through 158 Processing helix chain 'C' and resid 175 through 187 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 232 through 253 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.636A pdb=" N GLN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 Processing helix chain 'C' and resid 290 through 300 Processing helix chain 'C' and resid 329 through 339 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.140A pdb=" N ALA C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 394 removed outlier: 3.577A pdb=" N LYS C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 378 " --> pdb=" O LYS C 374 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS C 382 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 400 removed outlier: 4.182A pdb=" N GLN C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 418 Processing helix chain 'C' and resid 430 through 444 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 469 through 479 removed outlier: 4.023A pdb=" N GLN C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 479 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.526A pdb=" N THR D 106 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 205 through 220 Processing helix chain 'D' and resid 244 through 263 removed outlier: 3.579A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 289 removed outlier: 3.737A pdb=" N VAL D 279 " --> pdb=" O ILE D 275 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.894A pdb=" N LEU D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 333 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'D' and resid 376 through 402 removed outlier: 7.491A pdb=" N GLU D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU D 383 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 385 " --> pdb=" O GLY D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 409 through 413 removed outlier: 3.699A pdb=" N GLU D 412 " --> pdb=" O GLY D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 463 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 480 through 494 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 178 through 192 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 263 removed outlier: 5.081A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE E 260 " --> pdb=" O MET E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 290 removed outlier: 3.652A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 311 removed outlier: 3.831A pdb=" N LEU E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 333 removed outlier: 3.509A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 381 through 408 removed outlier: 5.029A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 431 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 463 removed outlier: 3.503A pdb=" N LEU E 460 " --> pdb=" O ARG E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 475 removed outlier: 4.129A pdb=" N PHE E 474 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR E 475 " --> pdb=" O GLU E 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 470 through 475' Processing helix chain 'E' and resid 480 through 496 removed outlier: 3.639A pdb=" N SER E 494 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 153 through 159 Processing helix chain 'F' and resid 178 through 190 Processing helix chain 'F' and resid 206 through 219 Processing helix chain 'F' and resid 226 through 230 removed outlier: 3.548A pdb=" N GLU F 229 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 263 removed outlier: 3.697A pdb=" N ARG F 248 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 289 removed outlier: 3.550A pdb=" N VAL F 279 " --> pdb=" O ILE F 275 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY F 282 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 313 removed outlier: 3.768A pdb=" N LEU F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE F 313 " --> pdb=" O LEU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 333 Processing helix chain 'F' and resid 336 through 344 removed outlier: 3.604A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 358 removed outlier: 3.692A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 401 Processing helix chain 'F' and resid 401 through 409 removed outlier: 3.569A pdb=" N LEU F 408 " --> pdb=" O ILE F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 435 through 437 No H-bonds generated for 'chain 'F' and resid 435 through 437' Processing helix chain 'F' and resid 438 through 443 Processing helix chain 'F' and resid 450 through 463 Processing helix chain 'F' and resid 465 through 469 removed outlier: 4.342A pdb=" N SER F 468 " --> pdb=" O GLU F 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 475 Processing helix chain 'F' and resid 479 through 496 Processing helix chain 'd' and resid 73 through 88 removed outlier: 3.722A pdb=" N ALA d 81 " --> pdb=" O ARG d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 106 removed outlier: 3.909A pdb=" N ARG d 104 " --> pdb=" O GLU d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 116 removed outlier: 4.235A pdb=" N TYR d 112 " --> pdb=" O GLU d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 137 removed outlier: 4.005A pdb=" N VAL d 128 " --> pdb=" O ASN d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing helix chain 'd' and resid 157 through 173 removed outlier: 4.325A pdb=" N GLU d 166 " --> pdb=" O LEU d 162 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL d 168 " --> pdb=" O GLU d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 188 through 203 Processing helix chain 'd' and resid 237 through 249 removed outlier: 3.508A pdb=" N GLU d 249 " --> pdb=" O ALA d 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 100 Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 132 through 151 removed outlier: 3.629A pdb=" N MET g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 171 Processing helix chain 'g' and resid 188 through 203 Processing helix chain 'g' and resid 246 through 251 removed outlier: 3.587A pdb=" N GLU g 251 " --> pdb=" O ASP g 248 " (cutoff:3.500A) Processing helix chain 'g' and resid 287 through 363 Proline residue: g 297 - end of helix Processing helix chain 'e' and resid 88 through 106 removed outlier: 3.728A pdb=" N ALA e 92 " --> pdb=" O ASP e 88 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE e 98 " --> pdb=" O GLN e 94 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG e 104 " --> pdb=" O GLU e 100 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS e 105 " --> pdb=" O ALA e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 129 removed outlier: 3.822A pdb=" N ILE e 113 " --> pdb=" O LYS e 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 159 removed outlier: 3.745A pdb=" N VAL I 36 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP I 51 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR I 115 " --> pdb=" O ILE I 111 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR I 124 " --> pdb=" O GLN I 120 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER I 158 " --> pdb=" O GLY I 154 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N CYS I 159 " --> pdb=" O THR I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 182 removed outlier: 4.150A pdb=" N ASN I 170 " --> pdb=" O LEU I 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 109 Processing helix chain 'J' and resid 110 through 204 removed outlier: 4.064A pdb=" N PHE J 115 " --> pdb=" O PRO J 111 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET J 116 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG J 119 " --> pdb=" O PHE J 115 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE J 123 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG J 178 " --> pdb=" O LEU J 174 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL J 183 " --> pdb=" O LYS J 179 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 211 Processing helix chain 'J' and resid 211 through 219 Processing helix chain 'a' and resid 36 through 57 removed outlier: 3.522A pdb=" N LEU a 40 " --> pdb=" O HIS a 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE a 56 " --> pdb=" O GLY a 52 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA a 57 " --> pdb=" O SER a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 85 Processing helix chain 'a' and resid 91 through 93 No H-bonds generated for 'chain 'a' and resid 91 through 93' Processing helix chain 'a' and resid 94 through 115 Processing helix chain 'a' and resid 129 through 133 removed outlier: 3.572A pdb=" N ASN a 132 " --> pdb=" O ALA a 129 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP a 133 " --> pdb=" O PRO a 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 129 through 133' Processing helix chain 'a' and resid 134 through 156 removed outlier: 5.546A pdb=" N LEU a 140 " --> pdb=" O THR a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 207 removed outlier: 4.676A pdb=" N ILE a 174 " --> pdb=" O ILE a 170 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE a 176 " --> pdb=" O LEU a 172 " (cutoff:3.500A) Proline residue: a 183 - end of helix removed outlier: 4.038A pdb=" N ALA a 196 " --> pdb=" O GLY a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 244 removed outlier: 4.588A pdb=" N VAL a 216 " --> pdb=" O VAL a 212 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE a 218 " --> pdb=" O ILE a 214 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU a 219 " --> pdb=" O PRO a 215 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 19 Processing helix chain 'M' and resid 21 through 42 Processing helix chain 'M' and resid 45 through 76 Processing helix chain 'N' and resid 4 through 22 Processing helix chain 'N' and resid 22 through 42 removed outlier: 4.282A pdb=" N VAL N 26 " --> pdb=" O ILE N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 76 Processing helix chain 'O' and resid 4 through 42 removed outlier: 4.472A pdb=" N GLY O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 24 - end of helix removed outlier: 4.363A pdb=" N THR O 30 " --> pdb=" O VAL O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 76 Processing helix chain 'P' and resid 4 through 22 Processing helix chain 'P' and resid 23 through 42 Processing helix chain 'P' and resid 45 through 76 Processing helix chain 'Q' and resid 4 through 42 removed outlier: 4.677A pdb=" N GLY Q 23 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) Proline residue: Q 24 - end of helix Processing helix chain 'Q' and resid 45 through 76 removed outlier: 4.172A pdb=" N GLY Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 4.683A pdb=" N GLY R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Proline residue: R 24 - end of helix Processing helix chain 'R' and resid 45 through 76 Processing helix chain 'S' and resid 4 through 42 removed outlier: 4.823A pdb=" N GLY S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Proline residue: S 24 - end of helix Processing helix chain 'S' and resid 45 through 76 Processing helix chain 'T' and resid 4 through 42 removed outlier: 4.033A pdb=" N GLY T 23 " --> pdb=" O LEU T 19 " (cutoff:3.500A) Proline residue: T 24 - end of helix Processing helix chain 'T' and resid 45 through 76 Processing helix chain 'U' and resid 4 through 22 Processing helix chain 'U' and resid 22 through 42 removed outlier: 3.879A pdb=" N VAL U 26 " --> pdb=" O ILE U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 76 Processing helix chain 'V' and resid 4 through 42 removed outlier: 4.482A pdb=" N SER V 9 " --> pdb=" O ILE V 5 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL V 10 " --> pdb=" O ALA V 6 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE V 22 " --> pdb=" O GLY V 18 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY V 23 " --> pdb=" O LEU V 19 " (cutoff:3.500A) Proline residue: V 24 - end of helix removed outlier: 3.663A pdb=" N GLY V 27 " --> pdb=" O GLY V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 77 removed outlier: 3.884A pdb=" N VAL V 70 " --> pdb=" O TYR V 66 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU V 75 " --> pdb=" O ALA V 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 23 removed outlier: 3.984A pdb=" N GLY W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 42 removed outlier: 4.034A pdb=" N GLY W 27 " --> pdb=" O GLY W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 76 removed outlier: 4.167A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 42 removed outlier: 4.700A pdb=" N GLY X 23 " --> pdb=" O LEU X 19 " (cutoff:3.500A) Proline residue: X 24 - end of helix Processing helix chain 'X' and resid 45 through 76 Processing helix chain 'Y' and resid 4 through 42 removed outlier: 3.752A pdb=" N GLY Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Proline residue: Y 24 - end of helix Processing helix chain 'Y' and resid 45 through 76 Processing helix chain 'Z' and resid 4 through 42 removed outlier: 4.669A pdb=" N GLY Z 23 " --> pdb=" O LEU Z 19 " (cutoff:3.500A) Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 45 through 76 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 4.398A pdb=" N GLU A 52 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 53 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ALA A 64 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU F 90 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN F 67 " --> pdb=" O ARG F 75 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP F 32 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109 removed outlier: 5.811A pdb=" N ILE A 109 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N CYS A 194 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL A 225 " --> pdb=" O CYS A 194 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR A 196 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLU A 227 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA A 198 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 321 removed outlier: 7.941A pdb=" N VAL A 320 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE A 168 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 167 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 67 removed outlier: 4.268A pdb=" N GLU B 52 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 53 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL D 61 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG D 75 " --> pdb=" O GLN D 66 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU D 68 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ARG D 73 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL D 30 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ILE D 26 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP D 32 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 100 removed outlier: 3.966A pdb=" N ILE B 98 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 127 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 100 " --> pdb=" O SER B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AA7, first strand: chain 'B' and resid 319 through 321 removed outlier: 6.234A pdb=" N ILE B 168 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 167 " --> pdb=" O ILE B 343 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 90 through 93 removed outlier: 7.156A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE d 221 " --> pdb=" O MET d 235 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR d 222 " --> pdb=" O THR d 181 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL d 212 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER d 182 " --> pdb=" O VAL d 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 93 removed outlier: 4.319A pdb=" N GLU E 90 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LEU E 68 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ARG E 73 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE E 26 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP E 32 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG C 41 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.563A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 5.884A pdb=" N ILE C 109 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 199 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 319 through 321 removed outlier: 6.685A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 111 removed outlier: 6.434A pdb=" N PHE D 111 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA D 233 " --> pdb=" O SER D 197 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA D 326 " --> pdb=" O LEU D 270 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE D 272 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N TYR D 328 " --> pdb=" O ILE D 272 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL D 327 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU D 170 " --> pdb=" O VAL D 327 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 148 through 149 removed outlier: 4.677A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AB8, first strand: chain 'E' and resid 110 through 111 removed outlier: 6.170A pdb=" N PHE E 111 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLN E 238 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 268 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE E 324 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS E 167 " --> pdb=" O ASP E 347 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N THR E 349 " --> pdb=" O LYS E 167 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY E 169 " --> pdb=" O THR E 349 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 148 through 149 removed outlier: 4.114A pdb=" N TYR E 162 " --> pdb=" O PHE E 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC2, first strand: chain 'F' and resid 232 through 237 removed outlier: 6.502A pdb=" N ILE F 168 " --> pdb=" O GLN F 325 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL F 327 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N LEU F 170 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'g' and resid 157 through 159 removed outlier: 7.405A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 256 through 259 Processing sheet with id=AC5, first strand: chain 'e' and resid 13 through 15 removed outlier: 3.729A pdb=" N TRP e 15 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN e 4 " --> pdb=" O ILE e 74 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE e 76 " --> pdb=" O ASN e 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS e 6 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL e 78 " --> pdb=" O CYS e 6 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU e 8 " --> pdb=" O VAL e 78 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY e 65 " --> pdb=" O VAL e 44 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL e 44 " --> pdb=" O GLY e 65 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 30 through 33 removed outlier: 4.153A pdb=" N ILE e 22 " --> pdb=" O VAL e 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER e 25 " --> pdb=" O ILE e 48 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE e 48 " --> pdb=" O SER e 25 " (cutoff:3.500A) 2498 hydrogen bonds defined for protein. 7362 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: 8.65 Time building geometry restraints manager: 4.60 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: 6884 1.32 - 1.45: 9140 1.45 - 1.57: 23417 1.57 - 1.69: 26 1.69 - 1.82: 248 Bond restraints: 39715 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.32e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.04e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C4 ATP D 502 " pdb=" C5 ATP D 502 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.85e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.05e+01 ... (remaining 39710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 53560 4.30 - 8.59: 277 8.59 - 12.89: 17 12.89 - 17.19: 3 17.19 - 21.48: 4 Bond angle restraints: 53861 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 118.39 21.48 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 120.64 19.23 1.00e+00 1.00e+00 3.70e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.83 18.04 1.00e+00 1.00e+00 3.26e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 120.02 16.81 1.00e+00 1.00e+00 2.82e+02 ... (remaining 53856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.17: 22759 26.17 - 52.34: 1151 52.34 - 78.51: 125 78.51 - 104.68: 25 104.68 - 130.85: 1 Dihedral angle restraints: 24061 sinusoidal: 9351 harmonic: 14710 Sorted by residual: dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 dihedral pdb=" CA LEU g 129 " pdb=" C LEU g 129 " pdb=" N CYS g 130 " pdb=" CA CYS g 130 " ideal model delta harmonic sigma weight residual 180.00 138.85 41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA ASP g 104 " pdb=" C ASP g 104 " pdb=" N VAL g 105 " pdb=" CA VAL g 105 " ideal model delta harmonic sigma weight residual -180.00 -142.75 -37.25 0 5.00e+00 4.00e-02 5.55e+01 ... (remaining 24058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5927 0.090 - 0.179: 499 0.179 - 0.269: 8 0.269 - 0.359: 1 0.359 - 0.449: 1 Chirality restraints: 6436 Sorted by residual: chirality pdb=" C9 TTX D 501 " pdb=" C10 TTX D 501 " pdb=" C8 TTX D 501 " pdb=" N3 TTX D 501 " both_signs ideal model delta sigma weight residual False -2.28 -2.73 0.45 2.00e-01 2.50e+01 5.03e+00 chirality pdb=" CB VAL a 208 " pdb=" CA VAL a 208 " pdb=" CG1 VAL a 208 " pdb=" CG2 VAL a 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA LEU g 231 " pdb=" N LEU g 231 " pdb=" C LEU g 231 " pdb=" CB LEU g 231 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 6433 not shown) Planarity restraints: 6946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 176 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LYS B 176 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS B 176 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 177 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN X 42 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO X 43 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO X 43 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO X 43 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 178 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C LYS F 178 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS F 178 " -0.020 2.00e-02 2.50e+03 pdb=" N THR F 179 " -0.018 2.00e-02 2.50e+03 ... (remaining 6943 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 735 2.69 - 3.24: 39380 3.24 - 3.79: 63913 3.79 - 4.35: 86314 4.35 - 4.90: 139222 Nonbonded interactions: 329564 Sorted by model distance: nonbonded pdb=" O GLN a 38 " pdb=" OG1 THR a 42 " model vdw 2.133 3.040 nonbonded pdb=" OG1 THR C 228 " pdb=" OD1 ASP C 230 " model vdw 2.161 3.040 nonbonded pdb=" O ALA C 218 " pdb=" OG1 THR C 222 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR B 196 " pdb=" OD2 ASP B 262 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR B 228 " pdb=" OD1 ASP B 230 " model vdw 2.207 3.040 ... (remaining 329559 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 503 or resid 601)) selection = (chain 'B' and resid 6 through 601) selection = (chain 'C' and (resid 6 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and resid 17 through 494) selection = (chain 'E' and resid 17 through 494) selection = (chain 'F' and resid 17 through 494) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 6.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.750 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 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 : 0.005 0.093 39715 Z= 0.283 Angle : 0.908 21.482 53861 Z= 0.540 Chirality : 0.050 0.449 6436 Planarity : 0.006 0.077 6946 Dihedral : 15.221 130.850 14639 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.08 % Rotamer: Outliers : 0.05 % Allowed : 6.63 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.10), residues: 5134 helix: -1.41 (0.08), residues: 2771 sheet: -2.43 (0.18), residues: 630 loop : -2.75 (0.13), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 14 TYR 0.018 0.002 TYR a 27 PHE 0.021 0.002 PHE g 85 TRP 0.006 0.001 TRP a 28 HIS 0.006 0.001 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.28 (39715) covalent geometry : angle 0.90771 / 0.54 (53861) hydrogen bonds : bond 0.12290 / 8.26 ( 2489) hydrogen bonds : angle 6.18608 / 4.33 ( 7362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 749 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5882 (mm-30) cc_final: 0.5299 (mm-30) REVERT: A 141 ARG cc_start: 0.7617 (ttt180) cc_final: 0.7409 (ttm170) REVERT: A 279 ARG cc_start: 0.7551 (mmt90) cc_final: 0.7346 (mmm160) REVERT: A 290 ASP cc_start: 0.8111 (p0) cc_final: 0.7854 (p0) REVERT: A 413 ARG cc_start: 0.7005 (ttm170) cc_final: 0.6474 (ttp80) REVERT: A 498 MET cc_start: 0.8283 (tpt) cc_final: 0.7888 (tpp) REVERT: B 90 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7770 (mmtm) REVERT: B 285 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7750 (mt-10) REVERT: C 362 ILE cc_start: 0.8378 (tp) cc_final: 0.8085 (tt) REVERT: C 455 ARG cc_start: 0.6831 (ttm-80) cc_final: 0.6599 (ptp-110) REVERT: D 127 ARG cc_start: 0.5997 (mtm110) cc_final: 0.5752 (mtm110) REVERT: D 411 ASP cc_start: 0.7029 (m-30) cc_final: 0.6800 (m-30) REVERT: E 48 ILE cc_start: 0.8698 (pt) cc_final: 0.8401 (mt) REVERT: E 247 MET cc_start: 0.8093 (ttp) cc_final: 0.7871 (ttp) REVERT: E 387 ILE cc_start: 0.8326 (tt) cc_final: 0.7805 (mm) REVERT: E 453 GLU cc_start: 0.6680 (mp0) cc_final: 0.6444 (mp0) REVERT: F 32 ASP cc_start: 0.8349 (p0) cc_final: 0.8139 (p0) REVERT: F 53 ASP cc_start: 0.6694 (t0) cc_final: 0.6341 (t0) REVERT: F 143 ASP cc_start: 0.7062 (t0) cc_final: 0.6551 (t0) REVERT: F 248 ARG cc_start: 0.7867 (mmt-90) cc_final: 0.7651 (mmt-90) REVERT: F 369 ASP cc_start: 0.7316 (t70) cc_final: 0.7044 (t70) REVERT: F 382 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6689 (tp30) REVERT: F 462 LEU cc_start: 0.7797 (pp) cc_final: 0.7580 (pp) REVERT: d 171 LYS cc_start: 0.6907 (mmtm) cc_final: 0.6425 (tppt) REVERT: g 160 ILE cc_start: 0.8077 (mm) cc_final: 0.7869 (mm) REVERT: g 238 GLU cc_start: 0.4401 (mp0) cc_final: 0.4001 (mt-10) REVERT: g 353 ILE cc_start: 0.8827 (mt) cc_final: 0.8381 (pt) REVERT: e 111 GLN cc_start: 0.5081 (mp10) cc_final: 0.4435 (mp10) REVERT: I 122 GLU cc_start: 0.3799 (mm-30) cc_final: 0.3446 (tp30) REVERT: J 116 MET cc_start: -0.2227 (ptt) cc_final: -0.2667 (ptt) REVERT: a 191 PHE cc_start: 0.3965 (m-80) cc_final: 0.3740 (m-80) REVERT: N 15 LEU cc_start: 0.5152 (pp) cc_final: 0.4948 (pp) REVERT: N 34 GLN cc_start: 0.4894 (mt0) cc_final: 0.4569 (mt0) REVERT: N 60 MET cc_start: 0.2620 (mtp) cc_final: 0.2302 (mmm) REVERT: W 59 PHE cc_start: 0.4513 (m-80) cc_final: 0.4171 (m-80) outliers start: 2 outliers final: 0 residues processed: 751 average time/residue: 0.2852 time to fit residues: 336.1391 Evaluate side-chains 555 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 494 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 43 HIS A 201 GLN A 208 GLN A 351 ASN A 359 ASN A 409 ASN A 468 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN B 84 GLN B 212 ASN B 425 GLN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 GLN E 45 ASN E 66 GLN E 225 GLN E 389 GLN E 472 GLN F 19 ASN F 141 GLN F 389 GLN F 489 ASN d 227 ASN g 135 ASN g 192 GLN g 228 HIS g 346 GLN I 55 ASN I 66 ASN I 112 ASN I 139 GLN ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS a 69 GLN a 70 ASN a 86 GLN M 28 GLN M 78 ASN P 34 GLN R 42 GLN S 28 GLN U 42 GLN V 42 GLN W 34 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.184319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143709 restraints weight = 54572.038| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.51 r_work: 0.3285 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39715 Z= 0.184 Angle : 0.678 10.545 53861 Z= 0.347 Chirality : 0.045 0.227 6436 Planarity : 0.006 0.084 6946 Dihedral : 6.276 115.437 5582 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.84 % Favored : 94.08 % Rotamer: Outliers : 1.69 % Allowed : 12.71 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.11), residues: 5134 helix: -0.10 (0.09), residues: 2831 sheet: -2.05 (0.18), residues: 648 loop : -2.23 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG e 121 TYR 0.017 0.002 TYR a 27 PHE 0.015 0.001 PHE g 85 TRP 0.006 0.001 TRP e 15 HIS 0.006 0.001 HIS e 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (39715) covalent geometry : angle 0.67753 / 0.35 (53861) hydrogen bonds : bond 0.05267 / 3.60 ( 2489) hydrogen bonds : angle 5.09726 / 3.54 ( 7362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 595 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8400 (p0) cc_final: 0.8178 (p0) REVERT: A 413 ARG cc_start: 0.7265 (ttm170) cc_final: 0.6349 (ttp80) REVERT: A 498 MET cc_start: 0.8487 (tpt) cc_final: 0.8096 (tpp) REVERT: B 41 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7701 (mmm160) REVERT: B 90 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7824 (mmtm) REVERT: B 216 ARG cc_start: 0.8028 (mtt-85) cc_final: 0.7557 (mmm160) REVERT: B 285 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8238 (mt-10) REVERT: B 419 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6715 (tp30) REVERT: C 227 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 362 ILE cc_start: 0.8581 (tp) cc_final: 0.8257 (tt) REVERT: D 32 ASP cc_start: 0.8643 (p0) cc_final: 0.8440 (p0) REVERT: D 120 ASN cc_start: 0.7834 (m-40) cc_final: 0.7613 (m-40) REVERT: D 127 ARG cc_start: 0.6376 (mtm110) cc_final: 0.6089 (mtm110) REVERT: D 225 GLN cc_start: 0.6894 (mm110) cc_final: 0.6622 (mp10) REVERT: E 47 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8691 (pp) REVERT: E 141 GLN cc_start: 0.8065 (tt0) cc_final: 0.7852 (tt0) REVERT: E 265 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: E 280 GLN cc_start: 0.7468 (tm-30) cc_final: 0.6959 (tt0) REVERT: E 453 GLU cc_start: 0.7277 (mp0) cc_final: 0.7068 (mt-10) REVERT: F 53 ASP cc_start: 0.6898 (t0) cc_final: 0.6438 (t0) REVERT: F 73 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7849 (mtt90) REVERT: F 143 ASP cc_start: 0.7548 (t0) cc_final: 0.7094 (t0) REVERT: F 369 ASP cc_start: 0.7793 (t70) cc_final: 0.7484 (t70) REVERT: d 171 LYS cc_start: 0.6862 (mmtm) cc_final: 0.6297 (tppt) REVERT: g 84 PRO cc_start: 0.7587 (Cg_exo) cc_final: 0.7301 (Cg_endo) REVERT: g 121 MET cc_start: 0.7646 (ttm) cc_final: 0.7384 (ttm) REVERT: g 192 GLN cc_start: 0.7618 (mt0) cc_final: 0.6949 (tp40) REVERT: g 353 ILE cc_start: 0.8812 (mt) cc_final: 0.8507 (pt) REVERT: I 122 GLU cc_start: 0.4019 (mm-30) cc_final: 0.3668 (tp30) REVERT: J 116 MET cc_start: -0.3479 (ptt) cc_final: -0.3774 (ptt) REVERT: a 191 PHE cc_start: 0.4646 (m-80) cc_final: 0.4272 (m-80) REVERT: N 34 GLN cc_start: 0.5659 (mt0) cc_final: 0.5288 (mt0) REVERT: O 24 PRO cc_start: 0.4420 (Cg_exo) cc_final: 0.4163 (Cg_endo) REVERT: O 50 ARG cc_start: 0.5390 (mtm180) cc_final: 0.4196 (ptm160) REVERT: V 37 GLU cc_start: 0.6284 (tt0) cc_final: 0.6021 (mt-10) REVERT: V 75 LEU cc_start: 0.0415 (tt) cc_final: 0.0154 (tt) REVERT: W 59 PHE cc_start: 0.5059 (m-80) cc_final: 0.4344 (m-80) outliers start: 69 outliers final: 38 residues processed: 641 average time/residue: 0.2623 time to fit residues: 267.3432 Evaluate side-chains 569 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 529 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 141 GLN Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 237 VAL Chi-restraints excluded: chain g residue 258 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 113 ILE Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 417 optimal weight: 1.9990 chunk 233 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 378 optimal weight: 0.8980 chunk 470 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 476 optimal weight: 9.9990 chunk 380 optimal weight: 1.9990 chunk 461 optimal weight: 5.9990 chunk 219 optimal weight: 0.7980 chunk 367 optimal weight: 7.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 359 ASN ** A 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 GLN B 208 GLN C 43 HIS C 214 GLN C 273 GLN C 425 GLN C 434 GLN ** D 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN E 389 GLN F 389 GLN g 325 ASN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN R 42 GLN T 28 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.184403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145517 restraints weight = 54767.831| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.48 r_work: 0.3299 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39715 Z= 0.196 Angle : 0.671 11.321 53861 Z= 0.342 Chirality : 0.045 0.244 6436 Planarity : 0.005 0.071 6946 Dihedral : 6.129 106.304 5582 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 2.57 % Allowed : 15.04 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.11), residues: 5134 helix: 0.32 (0.09), residues: 2859 sheet: -1.81 (0.19), residues: 646 loop : -2.06 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.028 0.002 TYR O 66 PHE 0.033 0.002 PHE V 59 TRP 0.009 0.001 TRP a 28 HIS 0.007 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (39715) covalent geometry : angle 0.67131 / 0.34 (53861) hydrogen bonds : bond 0.05156 / 3.52 ( 2489) hydrogen bonds : angle 4.95935 / 3.44 ( 7362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 544 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6348 (mm-30) cc_final: 0.5944 (mm-30) REVERT: A 408 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7449 (mt0) REVERT: A 413 ARG cc_start: 0.7364 (ttm170) cc_final: 0.6508 (ttp80) REVERT: A 498 MET cc_start: 0.8397 (tpt) cc_final: 0.8103 (tpp) REVERT: B 79 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6428 (p0) REVERT: B 90 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7851 (mmtm) REVERT: B 109 ILE cc_start: 0.8550 (mm) cc_final: 0.8127 (mt) REVERT: B 216 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7528 (mmm160) REVERT: C 94 ARG cc_start: 0.7274 (mtm180) cc_final: 0.7073 (mtp-110) REVERT: C 362 ILE cc_start: 0.8569 (tp) cc_final: 0.8232 (tt) REVERT: D 32 ASP cc_start: 0.8695 (p0) cc_final: 0.8485 (p0) REVERT: D 120 ASN cc_start: 0.7903 (m-40) cc_final: 0.7660 (m-40) REVERT: D 127 ARG cc_start: 0.6412 (mtm110) cc_final: 0.6191 (mtm110) REVERT: E 248 ARG cc_start: 0.7608 (mmt180) cc_final: 0.7388 (mmt180) REVERT: E 280 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6989 (tt0) REVERT: E 385 TYR cc_start: 0.8107 (t80) cc_final: 0.7796 (t80) REVERT: E 488 MET cc_start: 0.6168 (mtm) cc_final: 0.5782 (ptp) REVERT: F 53 ASP cc_start: 0.6976 (t0) cc_final: 0.6578 (t0) REVERT: F 73 ARG cc_start: 0.8372 (mtt90) cc_final: 0.7865 (mtt90) REVERT: F 143 ASP cc_start: 0.7286 (t0) cc_final: 0.6917 (t0) REVERT: F 369 ASP cc_start: 0.7855 (t70) cc_final: 0.7434 (t70) REVERT: d 171 LYS cc_start: 0.6959 (mmtm) cc_final: 0.6396 (tppt) REVERT: g 84 PRO cc_start: 0.7291 (Cg_exo) cc_final: 0.6981 (Cg_endo) REVERT: g 353 ILE cc_start: 0.8823 (mt) cc_final: 0.8622 (pt) REVERT: I 122 GLU cc_start: 0.3952 (mm-30) cc_final: 0.3580 (tp30) REVERT: I 181 GLU cc_start: 0.5343 (OUTLIER) cc_final: 0.5037 (mp0) REVERT: J 116 MET cc_start: -0.3303 (ptt) cc_final: -0.3626 (ptt) REVERT: a 191 PHE cc_start: 0.4733 (m-80) cc_final: 0.4401 (m-80) REVERT: N 60 MET cc_start: 0.3460 (mtp) cc_final: 0.3138 (mmm) REVERT: O 50 ARG cc_start: 0.5606 (mtm180) cc_final: 0.4433 (ptm160) REVERT: Q 60 MET cc_start: 0.1843 (ptp) cc_final: 0.1603 (tmm) REVERT: V 75 LEU cc_start: 0.0984 (tt) cc_final: 0.0693 (tt) REVERT: W 59 PHE cc_start: 0.4998 (m-80) cc_final: 0.4218 (m-80) REVERT: Y 60 MET cc_start: 0.2812 (ppp) cc_final: 0.2406 (mpp) outliers start: 105 outliers final: 58 residues processed: 616 average time/residue: 0.2629 time to fit residues: 260.0341 Evaluate side-chains 579 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 519 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain C residue 415 GLN Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 238 GLN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 404 ILE Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain g residue 122 VAL Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 33 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 181 GLU Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 146 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 40 optimal weight: 0.6980 chunk 384 optimal weight: 7.9990 chunk 296 optimal weight: 0.6980 chunk 185 optimal weight: 0.0980 chunk 79 optimal weight: 0.5980 chunk 436 optimal weight: 0.9990 chunk 370 optimal weight: 0.6980 chunk 354 optimal weight: 3.9990 chunk 179 optimal weight: 0.2980 chunk 287 optimal weight: 0.2980 chunk 252 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 359 ASN A 398 GLN A 468 ASN C 398 GLN D 45 ASN D 72 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 225 GLN E 238 GLN E 389 GLN F 25 GLN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN R 42 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.187148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148553 restraints weight = 54551.084| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.39 r_work: 0.3343 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39715 Z= 0.131 Angle : 0.612 12.635 53861 Z= 0.310 Chirality : 0.043 0.206 6436 Planarity : 0.005 0.067 6946 Dihedral : 5.763 100.487 5582 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.68 % Rotamer: Outliers : 2.40 % Allowed : 16.53 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.12), residues: 5134 helix: 0.82 (0.10), residues: 2832 sheet: -1.67 (0.19), residues: 656 loop : -1.78 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.030 0.001 TYR O 66 PHE 0.014 0.001 PHE g 133 TRP 0.008 0.001 TRP a 28 HIS 0.018 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (39715) covalent geometry : angle 0.61211 / 0.31 (53861) hydrogen bonds : bond 0.04619 / 3.14 ( 2489) hydrogen bonds : angle 4.70301 / 3.26 ( 7362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 571 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5750 (mm-30) REVERT: A 408 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7350 (mt0) REVERT: A 413 ARG cc_start: 0.7359 (ttm170) cc_final: 0.6524 (ttp80) REVERT: B 79 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.6340 (p0) REVERT: B 90 LYS cc_start: 0.8241 (mtmt) cc_final: 0.7894 (mmtp) REVERT: B 216 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7517 (mmm160) REVERT: B 466 LYS cc_start: 0.7776 (mmtt) cc_final: 0.7558 (mmtm) REVERT: C 362 ILE cc_start: 0.8562 (tp) cc_final: 0.8210 (tt) REVERT: D 120 ASN cc_start: 0.7892 (m-40) cc_final: 0.7655 (m-40) REVERT: D 311 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7186 (mm-30) REVERT: E 47 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8557 (pp) REVERT: E 184 GLU cc_start: 0.7731 (tp30) cc_final: 0.7528 (tp30) REVERT: E 280 GLN cc_start: 0.7592 (tm-30) cc_final: 0.7039 (tt0) REVERT: E 385 TYR cc_start: 0.7995 (t80) cc_final: 0.7704 (t80) REVERT: E 488 MET cc_start: 0.6260 (mtm) cc_final: 0.5886 (ptp) REVERT: F 53 ASP cc_start: 0.6738 (t0) cc_final: 0.6327 (t0) REVERT: F 73 ARG cc_start: 0.8296 (mtt90) cc_final: 0.7802 (mtt90) REVERT: F 143 ASP cc_start: 0.7281 (t0) cc_final: 0.6932 (t0) REVERT: F 214 MET cc_start: 0.7661 (mmt) cc_final: 0.7251 (mtt) REVERT: F 369 ASP cc_start: 0.7735 (t70) cc_final: 0.7430 (t70) REVERT: F 378 ARG cc_start: 0.7538 (mtt90) cc_final: 0.7260 (mtt90) REVERT: d 115 PHE cc_start: 0.6793 (m-80) cc_final: 0.6340 (m-80) REVERT: d 171 LYS cc_start: 0.6992 (mmtm) cc_final: 0.6346 (tppt) REVERT: g 84 PRO cc_start: 0.7425 (Cg_exo) cc_final: 0.7089 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7685 (mt0) cc_final: 0.6961 (tp40) REVERT: g 292 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7850 (mt) REVERT: g 353 ILE cc_start: 0.8764 (mt) cc_final: 0.8553 (pt) REVERT: e 45 ASP cc_start: 0.7093 (p0) cc_final: 0.6882 (p0) REVERT: e 76 ILE cc_start: 0.7577 (mp) cc_final: 0.7134 (mt) REVERT: J 116 MET cc_start: -0.3228 (ptt) cc_final: -0.3522 (ptt) REVERT: a 191 PHE cc_start: 0.4616 (m-80) cc_final: 0.4348 (m-80) REVERT: N 60 MET cc_start: 0.3513 (mtp) cc_final: 0.3143 (mmm) REVERT: O 50 ARG cc_start: 0.5661 (mtm180) cc_final: 0.4550 (ptm160) REVERT: P 63 LEU cc_start: 0.1177 (OUTLIER) cc_final: 0.0814 (mt) REVERT: Q 60 MET cc_start: 0.1782 (ptp) cc_final: 0.1564 (tmm) REVERT: S 60 MET cc_start: 0.2877 (OUTLIER) cc_final: 0.2072 (tpp) REVERT: V 75 LEU cc_start: 0.0799 (tt) cc_final: 0.0548 (tt) REVERT: W 59 PHE cc_start: 0.4832 (m-80) cc_final: 0.4012 (m-80) outliers start: 98 outliers final: 55 residues processed: 644 average time/residue: 0.2493 time to fit residues: 259.0798 Evaluate side-chains 573 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 513 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 404 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 212 MET Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 80 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 124 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 235 optimal weight: 0.9990 chunk 239 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 448 optimal weight: 7.9990 chunk 364 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 ASN A 359 ASN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN C 43 HIS C 504 GLN D 225 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 GLN E 389 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN F 396 GLN d 139 GLN e 54 ASN P 28 GLN R 42 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.184727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158165 restraints weight = 53254.850| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.77 r_work: 0.3414 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 39715 Z= 0.164 Angle : 0.632 12.789 53861 Z= 0.320 Chirality : 0.044 0.308 6436 Planarity : 0.005 0.068 6946 Dihedral : 5.766 100.380 5582 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 2.89 % Allowed : 17.56 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 5134 helix: 0.92 (0.10), residues: 2834 sheet: -1.60 (0.19), residues: 665 loop : -1.71 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 455 TYR 0.030 0.001 TYR O 66 PHE 0.026 0.001 PHE V 59 TRP 0.006 0.001 TRP a 28 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (39715) covalent geometry : angle 0.63180 / 0.32 (53861) hydrogen bonds : bond 0.04727 / 3.22 ( 2489) hydrogen bonds : angle 4.70064 / 3.25 ( 7362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 529 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6059 (mm-30) REVERT: A 408 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7457 (mt0) REVERT: A 413 ARG cc_start: 0.7448 (ttm170) cc_final: 0.6749 (ttp80) REVERT: B 79 ASP cc_start: 0.6734 (OUTLIER) cc_final: 0.6485 (p0) REVERT: B 90 LYS cc_start: 0.8348 (mtmt) cc_final: 0.8006 (mmtm) REVERT: B 216 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7590 (mmm160) REVERT: B 355 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6745 (mmp-170) REVERT: B 466 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7637 (mmtm) REVERT: C 362 ILE cc_start: 0.8618 (tp) cc_final: 0.8287 (tt) REVERT: C 415 GLN cc_start: 0.7739 (tt0) cc_final: 0.7483 (tt0) REVERT: D 311 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7376 (mm-30) REVERT: E 47 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8599 (pp) REVERT: E 280 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7074 (tt0) REVERT: E 385 TYR cc_start: 0.8076 (t80) cc_final: 0.7813 (t80) REVERT: E 488 MET cc_start: 0.6344 (mtm) cc_final: 0.5903 (ptp) REVERT: F 53 ASP cc_start: 0.6787 (t0) cc_final: 0.6454 (t0) REVERT: F 73 ARG cc_start: 0.8393 (mtt90) cc_final: 0.7878 (mtt90) REVERT: F 143 ASP cc_start: 0.7410 (t0) cc_final: 0.7060 (t0) REVERT: F 204 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6865 (pp20) REVERT: F 214 MET cc_start: 0.7937 (mmt) cc_final: 0.7464 (mtt) REVERT: F 369 ASP cc_start: 0.8034 (t70) cc_final: 0.7654 (t70) REVERT: F 378 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7383 (mtt90) REVERT: d 171 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6441 (tppt) REVERT: g 84 PRO cc_start: 0.7314 (Cg_exo) cc_final: 0.6894 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7765 (mt0) cc_final: 0.7009 (tp40) REVERT: e 36 ASN cc_start: 0.7272 (m-40) cc_final: 0.6067 (t0) REVERT: e 45 ASP cc_start: 0.7306 (p0) cc_final: 0.7088 (p0) REVERT: e 76 ILE cc_start: 0.7634 (mp) cc_final: 0.7245 (mt) REVERT: J 116 MET cc_start: -0.3131 (ptt) cc_final: -0.3490 (ptt) REVERT: a 191 PHE cc_start: 0.4648 (m-80) cc_final: 0.4349 (m-80) REVERT: N 15 LEU cc_start: 0.5542 (mt) cc_final: 0.5294 (mt) REVERT: N 60 MET cc_start: 0.3541 (mtp) cc_final: 0.3325 (mmm) REVERT: O 50 ARG cc_start: 0.5758 (mtm180) cc_final: 0.4729 (ptm160) REVERT: P 63 LEU cc_start: 0.1281 (OUTLIER) cc_final: 0.0912 (mt) REVERT: S 60 MET cc_start: 0.3079 (OUTLIER) cc_final: 0.2205 (tpp) REVERT: V 75 LEU cc_start: 0.1040 (tt) cc_final: 0.0757 (tt) REVERT: W 59 PHE cc_start: 0.5142 (m-80) cc_final: 0.4319 (m-80) REVERT: Y 60 MET cc_start: 0.3042 (ppp) cc_final: 0.2356 (mpp) outliers start: 118 outliers final: 84 residues processed: 616 average time/residue: 0.2551 time to fit residues: 254.4411 Evaluate side-chains 602 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 512 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 43 HIS Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 212 MET Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 130 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 349 optimal weight: 0.6980 chunk 426 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 452 optimal weight: 1.9990 chunk 327 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 174 optimal weight: 0.2980 chunk 93 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 497 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 225 GLN E 389 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN e 54 ASN e 111 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148392 restraints weight = 53463.416| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.10 r_work: 0.3336 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39715 Z= 0.142 Angle : 0.612 10.758 53861 Z= 0.310 Chirality : 0.043 0.222 6436 Planarity : 0.005 0.070 6946 Dihedral : 5.649 98.211 5582 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 2.93 % Allowed : 18.00 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 5134 helix: 1.07 (0.10), residues: 2832 sheet: -1.52 (0.19), residues: 667 loop : -1.63 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.031 0.001 TYR O 66 PHE 0.022 0.001 PHE V 59 TRP 0.006 0.001 TRP a 28 HIS 0.012 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (39715) covalent geometry : angle 0.61162 / 0.31 (53861) hydrogen bonds : bond 0.04579 / 3.11 ( 2489) hydrogen bonds : angle 4.62720 / 3.20 ( 7362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 522 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6691 (mm-30) cc_final: 0.6197 (mm-30) REVERT: A 408 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7392 (mt0) REVERT: A 413 ARG cc_start: 0.7545 (ttm170) cc_final: 0.6709 (ttp80) REVERT: B 79 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6549 (p0) REVERT: B 90 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8018 (mmtp) REVERT: B 216 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7580 (mmm160) REVERT: B 466 LYS cc_start: 0.7888 (mmtt) cc_final: 0.7617 (mmtm) REVERT: C 362 ILE cc_start: 0.8643 (tp) cc_final: 0.8306 (tt) REVERT: E 47 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8584 (pp) REVERT: E 280 GLN cc_start: 0.7790 (tm-30) cc_final: 0.7175 (tt0) REVERT: E 385 TYR cc_start: 0.8131 (t80) cc_final: 0.7830 (t80) REVERT: E 488 MET cc_start: 0.6144 (mtm) cc_final: 0.5762 (ptp) REVERT: F 53 ASP cc_start: 0.6631 (t0) cc_final: 0.6264 (t0) REVERT: F 73 ARG cc_start: 0.8445 (mtt90) cc_final: 0.7913 (mtt90) REVERT: F 143 ASP cc_start: 0.7489 (t0) cc_final: 0.7179 (t0) REVERT: F 204 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6878 (pp20) REVERT: F 214 MET cc_start: 0.7982 (mmt) cc_final: 0.7424 (mtt) REVERT: F 369 ASP cc_start: 0.8107 (t70) cc_final: 0.7764 (t70) REVERT: d 115 PHE cc_start: 0.6803 (m-80) cc_final: 0.6387 (m-80) REVERT: d 171 LYS cc_start: 0.6927 (mmtm) cc_final: 0.6338 (tppt) REVERT: g 84 PRO cc_start: 0.7455 (Cg_exo) cc_final: 0.7172 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7756 (mt0) cc_final: 0.6959 (tp40) REVERT: g 292 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7881 (mt) REVERT: e 36 ASN cc_start: 0.7304 (m-40) cc_final: 0.5934 (t0) REVERT: e 45 ASP cc_start: 0.7305 (p0) cc_final: 0.7072 (p0) REVERT: e 76 ILE cc_start: 0.7610 (mp) cc_final: 0.7264 (mt) REVERT: J 116 MET cc_start: -0.3467 (ptt) cc_final: -0.3749 (ptt) REVERT: N 60 MET cc_start: 0.3657 (mtp) cc_final: 0.3437 (mmm) REVERT: O 50 ARG cc_start: 0.5663 (mtm180) cc_final: 0.4621 (ptm160) REVERT: P 63 LEU cc_start: 0.1093 (OUTLIER) cc_final: 0.0755 (mt) REVERT: S 60 MET cc_start: 0.3025 (OUTLIER) cc_final: 0.2398 (tpp) REVERT: T 60 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3403 (tpp) REVERT: V 75 LEU cc_start: 0.0287 (tt) cc_final: 0.0067 (tt) REVERT: W 59 PHE cc_start: 0.5256 (m-80) cc_final: 0.4446 (m-80) REVERT: Y 60 MET cc_start: 0.2753 (ppp) cc_final: 0.2305 (mpp) outliers start: 120 outliers final: 81 residues processed: 610 average time/residue: 0.2560 time to fit residues: 252.3714 Evaluate side-chains 587 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 499 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 212 MET Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 57 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 258 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 387 optimal weight: 3.9990 chunk 410 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 188 optimal weight: 0.5980 chunk 294 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 497 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN d 139 GLN e 30 GLN e 54 ASN e 111 GLN P 28 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.185133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.158100 restraints weight = 53094.043| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.86 r_work: 0.3429 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39715 Z= 0.152 Angle : 0.621 12.743 53861 Z= 0.313 Chirality : 0.043 0.217 6436 Planarity : 0.005 0.071 6946 Dihedral : 5.608 96.884 5582 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.20 % Rotamer: Outliers : 2.91 % Allowed : 18.58 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 5134 helix: 1.11 (0.10), residues: 2835 sheet: -1.47 (0.19), residues: 662 loop : -1.58 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 418 TYR 0.039 0.001 TYR O 66 PHE 0.021 0.001 PHE V 59 TRP 0.005 0.001 TRP a 28 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (39715) covalent geometry : angle 0.62069 / 0.31 (53861) hydrogen bonds : bond 0.04578 / 3.11 ( 2489) hydrogen bonds : angle 4.60577 / 3.19 ( 7362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 512 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5642 (mm-30) REVERT: A 408 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7311 (mt0) REVERT: A 413 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6688 (ttp80) REVERT: B 79 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.6101 (p0) REVERT: B 216 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7482 (mmm160) REVERT: B 466 LYS cc_start: 0.7835 (mmtt) cc_final: 0.7562 (mmtm) REVERT: C 362 ILE cc_start: 0.8543 (tp) cc_final: 0.8187 (tt) REVERT: E 47 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8513 (pp) REVERT: E 280 GLN cc_start: 0.7405 (tm-30) cc_final: 0.7166 (tt0) REVERT: E 385 TYR cc_start: 0.7936 (t80) cc_final: 0.7693 (t80) REVERT: E 488 MET cc_start: 0.6119 (mtm) cc_final: 0.5870 (ptp) REVERT: F 73 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7666 (mtt90) REVERT: F 143 ASP cc_start: 0.7125 (t0) cc_final: 0.6760 (t0) REVERT: F 204 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6588 (pp20) REVERT: F 214 MET cc_start: 0.7549 (mmt) cc_final: 0.7226 (mtt) REVERT: F 369 ASP cc_start: 0.7689 (t70) cc_final: 0.7414 (t70) REVERT: d 115 PHE cc_start: 0.6566 (m-80) cc_final: 0.6152 (m-80) REVERT: d 171 LYS cc_start: 0.6869 (mmtm) cc_final: 0.6345 (tppt) REVERT: g 84 PRO cc_start: 0.7332 (Cg_exo) cc_final: 0.7063 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7676 (mt0) cc_final: 0.6968 (tp40) REVERT: g 292 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7814 (mt) REVERT: e 36 ASN cc_start: 0.7246 (m-40) cc_final: 0.5872 (t0) REVERT: e 76 ILE cc_start: 0.7454 (mp) cc_final: 0.7108 (mt) REVERT: J 116 MET cc_start: -0.2371 (ptt) cc_final: -0.2828 (ptt) REVERT: a 191 PHE cc_start: 0.4567 (m-80) cc_final: 0.4355 (m-80) REVERT: O 50 ARG cc_start: 0.6090 (mtm180) cc_final: 0.5014 (ptm160) REVERT: P 63 LEU cc_start: 0.0926 (OUTLIER) cc_final: 0.0695 (mt) REVERT: Q 60 MET cc_start: 0.1526 (ptp) cc_final: 0.0984 (tmm) REVERT: S 60 MET cc_start: 0.3381 (OUTLIER) cc_final: 0.2660 (tpp) REVERT: T 60 MET cc_start: 0.3791 (OUTLIER) cc_final: 0.3515 (tpp) REVERT: V 75 LEU cc_start: 0.1535 (tt) cc_final: 0.1207 (tt) REVERT: W 59 PHE cc_start: 0.4975 (m-80) cc_final: 0.4215 (m-80) REVERT: Y 60 MET cc_start: 0.2518 (ppp) cc_final: 0.2108 (mpp) outliers start: 119 outliers final: 88 residues processed: 599 average time/residue: 0.2499 time to fit residues: 242.2336 Evaluate side-chains 587 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 492 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 217 MET Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 14 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 63 optimal weight: 0.0170 chunk 370 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 chunk 490 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 114 optimal weight: 0.0370 chunk 324 optimal weight: 0.0030 chunk 227 optimal weight: 0.9980 overall best weight: 0.3906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 84 GLN A 359 ASN A 497 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 389 GLN F 67 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN e 54 ASN e 111 GLN P 28 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.186351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151015 restraints weight = 53576.953| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.25 r_work: 0.3348 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39715 Z= 0.128 Angle : 0.608 12.592 53861 Z= 0.306 Chirality : 0.042 0.251 6436 Planarity : 0.005 0.072 6946 Dihedral : 5.474 94.548 5582 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 2.69 % Allowed : 19.17 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.12), residues: 5134 helix: 1.24 (0.10), residues: 2828 sheet: -1.32 (0.20), residues: 643 loop : -1.51 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 455 TYR 0.042 0.001 TYR O 66 PHE 0.015 0.001 PHE B 390 TRP 0.005 0.001 TRP a 28 HIS 0.004 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (39715) covalent geometry : angle 0.60760 / 0.31 (53861) hydrogen bonds : bond 0.04394 / 2.99 ( 2489) hydrogen bonds : angle 4.53126 / 3.13 ( 7362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 521 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7716 (mmm160) REVERT: A 394 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: A 408 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7259 (mt0) REVERT: A 413 ARG cc_start: 0.7364 (ttm170) cc_final: 0.6676 (ttp80) REVERT: A 497 GLN cc_start: 0.7960 (tp40) cc_final: 0.7728 (tp-100) REVERT: B 79 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6212 (p0) REVERT: B 173 GLN cc_start: 0.7759 (mt0) cc_final: 0.7510 (mm-40) REVERT: B 216 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7529 (mmm160) REVERT: B 466 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7584 (mmtm) REVERT: C 362 ILE cc_start: 0.8577 (tp) cc_final: 0.8217 (tt) REVERT: E 280 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7223 (tt0) REVERT: E 488 MET cc_start: 0.6069 (mtm) cc_final: 0.5764 (ptp) REVERT: F 143 ASP cc_start: 0.7162 (t0) cc_final: 0.6822 (t0) REVERT: F 204 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6586 (pp20) REVERT: F 214 MET cc_start: 0.7617 (mmt) cc_final: 0.7210 (mtt) REVERT: F 369 ASP cc_start: 0.7787 (t70) cc_final: 0.7461 (t70) REVERT: d 115 PHE cc_start: 0.6815 (m-80) cc_final: 0.6338 (m-80) REVERT: d 171 LYS cc_start: 0.6722 (mmtm) cc_final: 0.6169 (tppt) REVERT: d 235 MET cc_start: 0.4208 (OUTLIER) cc_final: 0.3904 (mtt) REVERT: g 84 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.7076 (Cg_endo) REVERT: g 139 LYS cc_start: 0.7857 (ttmt) cc_final: 0.7345 (tmtt) REVERT: g 142 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6306 (mt-10) REVERT: g 192 GLN cc_start: 0.7659 (mt0) cc_final: 0.6884 (tp40) REVERT: g 214 TYR cc_start: 0.8258 (p90) cc_final: 0.8032 (p90) REVERT: g 292 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7798 (mt) REVERT: e 36 ASN cc_start: 0.7176 (m-40) cc_final: 0.5685 (t0) REVERT: e 76 ILE cc_start: 0.7548 (mp) cc_final: 0.7202 (mt) REVERT: I 179 MET cc_start: 0.4681 (tmm) cc_final: 0.4283 (tmm) REVERT: J 116 MET cc_start: -0.3390 (ptt) cc_final: -0.3721 (ptt) REVERT: J 162 MET cc_start: 0.1537 (tmm) cc_final: 0.0924 (tmm) REVERT: a 191 PHE cc_start: 0.4800 (m-80) cc_final: 0.4560 (m-80) REVERT: M 54 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4656 (mt) REVERT: N 60 MET cc_start: 0.3313 (mmm) cc_final: 0.2091 (tpt) REVERT: O 50 ARG cc_start: 0.5741 (mtm180) cc_final: 0.4825 (ptm160) REVERT: P 63 LEU cc_start: 0.0880 (OUTLIER) cc_final: 0.0630 (mt) REVERT: Q 60 MET cc_start: 0.1004 (ptp) cc_final: 0.0614 (tmm) REVERT: S 60 MET cc_start: 0.3266 (OUTLIER) cc_final: 0.2628 (tpp) REVERT: T 60 MET cc_start: 0.4050 (OUTLIER) cc_final: 0.3479 (tpp) REVERT: V 75 LEU cc_start: 0.0618 (tt) cc_final: 0.0374 (tt) REVERT: W 59 PHE cc_start: 0.5283 (m-80) cc_final: 0.4525 (m-80) REVERT: Y 60 MET cc_start: 0.2621 (ppp) cc_final: 0.2308 (mpp) outliers start: 110 outliers final: 77 residues processed: 602 average time/residue: 0.2442 time to fit residues: 237.4338 Evaluate side-chains 582 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 495 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 260 LYS Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 217 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 282 optimal weight: 0.0060 chunk 107 optimal weight: 0.8980 chunk 389 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 370 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 464 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 chunk 340 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN D 226 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 389 GLN F 67 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN e 54 ASN e 111 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.185810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146968 restraints weight = 53845.301| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.55 r_work: 0.3317 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 39715 Z= 0.143 Angle : 0.621 12.707 53861 Z= 0.314 Chirality : 0.043 0.245 6436 Planarity : 0.005 0.075 6946 Dihedral : 5.473 93.424 5582 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.47 % Favored : 94.49 % Rotamer: Outliers : 2.64 % Allowed : 19.41 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 5134 helix: 1.26 (0.10), residues: 2831 sheet: -1.34 (0.20), residues: 660 loop : -1.51 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 455 TYR 0.047 0.001 TYR O 66 PHE 0.015 0.001 PHE F 149 TRP 0.005 0.001 TRP a 28 HIS 0.005 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (39715) covalent geometry : angle 0.62137 / 0.31 (53861) hydrogen bonds : bond 0.04424 / 3.01 ( 2489) hydrogen bonds : angle 4.53475 / 3.14 ( 7362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 510 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7538 (tp30) cc_final: 0.7316 (mm-30) REVERT: A 279 ARG cc_start: 0.8211 (mmm-85) cc_final: 0.7812 (mmm160) REVERT: A 394 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: A 408 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7223 (mt0) REVERT: A 413 ARG cc_start: 0.7367 (ttm170) cc_final: 0.6572 (ttp80) REVERT: B 79 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.6281 (p0) REVERT: B 216 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7486 (mmm160) REVERT: B 466 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7663 (mmtm) REVERT: C 362 ILE cc_start: 0.8610 (tp) cc_final: 0.8240 (tt) REVERT: E 280 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: E 488 MET cc_start: 0.5978 (mtm) cc_final: 0.5678 (ptp) REVERT: F 73 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7943 (mtp85) REVERT: F 143 ASP cc_start: 0.7236 (t0) cc_final: 0.6915 (t0) REVERT: F 204 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6597 (pp20) REVERT: F 214 MET cc_start: 0.7561 (mmt) cc_final: 0.7111 (mtt) REVERT: F 369 ASP cc_start: 0.7823 (t70) cc_final: 0.7450 (t70) REVERT: d 171 LYS cc_start: 0.6733 (mmtm) cc_final: 0.6189 (tppt) REVERT: d 235 MET cc_start: 0.3933 (OUTLIER) cc_final: 0.3617 (mtt) REVERT: g 84 PRO cc_start: 0.7356 (Cg_exo) cc_final: 0.7098 (Cg_endo) REVERT: g 139 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7225 (tmtt) REVERT: g 142 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6296 (mt-10) REVERT: g 192 GLN cc_start: 0.7660 (mt0) cc_final: 0.6816 (tp40) REVERT: g 214 TYR cc_start: 0.8302 (p90) cc_final: 0.8018 (p90) REVERT: g 292 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7705 (mt) REVERT: e 36 ASN cc_start: 0.7160 (m-40) cc_final: 0.5620 (t0) REVERT: e 76 ILE cc_start: 0.7458 (mp) cc_final: 0.7192 (mt) REVERT: J 116 MET cc_start: -0.4196 (ptt) cc_final: -0.4443 (ptt) REVERT: J 162 MET cc_start: 0.1403 (tmm) cc_final: 0.1033 (tmm) REVERT: a 191 PHE cc_start: 0.4776 (m-80) cc_final: 0.4540 (m-80) REVERT: M 54 LEU cc_start: 0.5233 (OUTLIER) cc_final: 0.4659 (mt) REVERT: O 50 ARG cc_start: 0.5555 (mtm180) cc_final: 0.4700 (ptm160) REVERT: P 63 LEU cc_start: 0.0815 (OUTLIER) cc_final: 0.0555 (mt) REVERT: Q 60 MET cc_start: 0.1051 (ptp) cc_final: 0.0685 (tmm) REVERT: S 60 MET cc_start: 0.3100 (OUTLIER) cc_final: 0.2584 (tpp) REVERT: T 60 MET cc_start: 0.4201 (OUTLIER) cc_final: 0.3424 (tpp) REVERT: W 59 PHE cc_start: 0.5412 (m-80) cc_final: 0.4666 (m-80) REVERT: X 59 PHE cc_start: 0.6148 (m-80) cc_final: 0.5945 (m-80) REVERT: Y 60 MET cc_start: 0.2516 (ppp) cc_final: 0.2257 (mpp) outliers start: 108 outliers final: 87 residues processed: 587 average time/residue: 0.2467 time to fit residues: 234.5620 Evaluate side-chains 581 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 484 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 233 LEU Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 308 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain e residue 54 ASN Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 217 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 65 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 447 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 203 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 chunk 404 optimal weight: 9.9990 chunk 189 optimal weight: 0.0020 chunk 411 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 345 optimal weight: 0.5980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN B 201 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN F 67 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN e 111 GLN P 28 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.185330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.151735 restraints weight = 53315.146| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.16 r_work: 0.3369 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 39715 Z= 0.186 Angle : 0.753 59.195 53861 Z= 0.419 Chirality : 0.045 0.572 6436 Planarity : 0.005 0.112 6946 Dihedral : 5.474 93.388 5582 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 2.62 % Allowed : 19.46 % Favored : 77.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 5134 helix: 1.27 (0.10), residues: 2831 sheet: -1.34 (0.20), residues: 660 loop : -1.51 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 141 TYR 0.044 0.001 TYR O 66 PHE 0.014 0.001 PHE F 149 TRP 0.005 0.001 TRP a 28 HIS 0.005 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (39715) covalent geometry : angle 0.75276 / 0.42 (53861) hydrogen bonds : bond 0.04418 / 3.00 ( 2489) hydrogen bonds : angle 4.54072 / 3.14 ( 7362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10268 Ramachandran restraints generated. 5134 Oldfield, 0 Emsley, 5134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 488 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7454 (tp30) cc_final: 0.7221 (mm-30) REVERT: A 279 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7729 (mmm160) REVERT: A 394 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8258 (tt0) REVERT: A 408 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7308 (mt0) REVERT: A 413 ARG cc_start: 0.7361 (ttm170) cc_final: 0.6698 (ttp80) REVERT: B 79 ASP cc_start: 0.6461 (OUTLIER) cc_final: 0.6190 (p0) REVERT: B 216 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7511 (mmm160) REVERT: B 466 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7584 (mmtm) REVERT: C 362 ILE cc_start: 0.8575 (tp) cc_final: 0.8200 (tt) REVERT: E 280 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.7199 (tt0) REVERT: E 488 MET cc_start: 0.6069 (mtm) cc_final: 0.5819 (ptp) REVERT: F 73 ARG cc_start: 0.8265 (mtt90) cc_final: 0.7882 (mtp85) REVERT: F 143 ASP cc_start: 0.7118 (t0) cc_final: 0.6791 (t0) REVERT: F 204 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6603 (pp20) REVERT: F 214 MET cc_start: 0.7539 (mmt) cc_final: 0.7190 (mtt) REVERT: F 369 ASP cc_start: 0.7772 (t70) cc_final: 0.7459 (t70) REVERT: d 171 LYS cc_start: 0.6811 (mmtm) cc_final: 0.6277 (tppt) REVERT: d 235 MET cc_start: 0.4243 (OUTLIER) cc_final: 0.3912 (mtt) REVERT: g 84 PRO cc_start: 0.7348 (Cg_exo) cc_final: 0.7097 (Cg_endo) REVERT: g 139 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7344 (tmtt) REVERT: g 142 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6273 (mt-10) REVERT: g 192 GLN cc_start: 0.7652 (mt0) cc_final: 0.6882 (tp40) REVERT: g 214 TYR cc_start: 0.8363 (p90) cc_final: 0.8084 (p90) REVERT: g 292 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7805 (mt) REVERT: e 36 ASN cc_start: 0.7168 (m-40) cc_final: 0.5698 (t0) REVERT: e 76 ILE cc_start: 0.7549 (mp) cc_final: 0.7234 (mt) REVERT: J 116 MET cc_start: -0.3184 (ptt) cc_final: -0.3579 (ptt) REVERT: J 162 MET cc_start: 0.1476 (tmm) cc_final: 0.0822 (tmm) REVERT: a 191 PHE cc_start: 0.4786 (m-80) cc_final: 0.4557 (m-80) REVERT: M 54 LEU cc_start: 0.5289 (OUTLIER) cc_final: 0.4614 (mt) REVERT: O 50 ARG cc_start: 0.5803 (mtm180) cc_final: 0.4883 (ptm160) REVERT: O 60 MET cc_start: 0.1393 (OUTLIER) cc_final: 0.1183 (mpt) REVERT: P 63 LEU cc_start: 0.0912 (OUTLIER) cc_final: 0.0689 (mt) REVERT: Q 60 MET cc_start: 0.1274 (ptp) cc_final: 0.0800 (tmm) REVERT: S 60 MET cc_start: 0.3294 (OUTLIER) cc_final: 0.2673 (tpp) REVERT: T 60 MET cc_start: 0.4135 (OUTLIER) cc_final: 0.3526 (tpp) REVERT: W 59 PHE cc_start: 0.5254 (m-80) cc_final: 0.4467 (m-80) REVERT: X 59 PHE cc_start: 0.6538 (m-80) cc_final: 0.6274 (m-80) REVERT: Y 60 MET cc_start: 0.2509 (ppp) cc_final: 0.2161 (mpp) outliers start: 107 outliers final: 88 residues processed: 563 average time/residue: 0.2430 time to fit residues: 222.4424 Evaluate side-chains 584 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 485 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 489 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 130 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 226 ASN Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 279 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 GLN Chi-restraints excluded: chain E residue 230 SER Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 280 GLN Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 223 ILE Chi-restraints excluded: chain d residue 235 MET Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 123 VAL Chi-restraints excluded: chain g residue 183 THR Chi-restraints excluded: chain g residue 203 VAL Chi-restraints excluded: chain g residue 215 THR Chi-restraints excluded: chain g residue 233 LEU Chi-restraints excluded: chain g residue 292 LEU Chi-restraints excluded: chain g residue 308 LEU Chi-restraints excluded: chain e residue 3 LEU Chi-restraints excluded: chain e residue 9 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 144 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 131 THR Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 217 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain O residue 60 MET Chi-restraints excluded: chain P residue 28 GLN Chi-restraints excluded: chain P residue 63 LEU Chi-restraints excluded: chain S residue 60 MET Chi-restraints excluded: chain T residue 15 LEU Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain U residue 17 VAL Chi-restraints excluded: chain U residue 64 THR Chi-restraints excluded: chain W residue 22 ILE Chi-restraints excluded: chain W residue 63 LEU Chi-restraints excluded: chain W residue 65 ILE Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain X residue 10 VAL Chi-restraints excluded: chain X residue 63 LEU Chi-restraints excluded: chain Y residue 4 LEU Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 389 optimal weight: 0.2980 chunk 395 optimal weight: 3.9990 chunk 222 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 401 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 383 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 GLN E 389 GLN F 67 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN ** X 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150879 restraints weight = 53519.710| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.24 r_work: 0.3358 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.351 39715 Z= 0.193 Angle : 0.797 59.177 53861 Z= 0.449 Chirality : 0.045 0.620 6436 Planarity : 0.005 0.137 6946 Dihedral : 5.479 93.389 5582 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.45 % Favored : 94.51 % Rotamer: Outliers : 2.54 % Allowed : 19.51 % Favored : 77.95 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.12), residues: 5134 helix: 1.26 (0.10), residues: 2831 sheet: -1.33 (0.20), residues: 660 loop : -1.50 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 141 TYR 0.042 0.001 TYR O 66 PHE 0.014 0.001 PHE F 149 TRP 0.005 0.001 TRP a 28 HIS 0.005 0.001 HIS F 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (39715) covalent geometry : angle 0.79652 / 0.45 (53861) hydrogen bonds : bond 0.04428 / 3.01 ( 2489) hydrogen bonds : angle 4.54242 / 3.14 ( 7362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9980.51 seconds wall clock time: 171 minutes 25.72 seconds (10285.72 seconds total)