Starting phenix.real_space_refine on Tue Aug 26 16:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6von_21270/08_2025/6von_21270.cif Found real_map, /net/cci-nas-00/data/ceres_data/6von_21270/08_2025/6von_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_21270/08_2025/6von_21270.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6von_21270/08_2025/6von_21270.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6von_21270/08_2025/6von_21270.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6von_21270/08_2025/6von_21270.map" } 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-2.0-5787/lib/python3.9/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: 9.63, per 1000 atoms: 0.25 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.79 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: 8.12 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 22864 26.17 - 52.34: 1177 52.34 - 78.51: 133 78.51 - 104.68: 26 104.68 - 130.85: 1 Dihedral angle restraints: 24201 sinusoidal: 9491 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 24198 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: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 34.760 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 15.353 130.850 14779 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 aren 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 covalent geometry : bond 0.00549 (39715) covalent geometry : angle 0.90771 (53861) hydrogen bonds : bond 0.12290 ( 2489) hydrogen bonds : angle 6.18608 ( 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 : 1.447 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: 0.7796 (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: 0.4434 (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: 0.2461 time to fit residues: 287.2083 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 : 1.306 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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: 48 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.144227 restraints weight = 54585.867| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.54 r_work: 0.3280 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1379 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 : 0.676 10.488 53861 Z= 0.347 Chirality : 0.045 0.215 6436 Planarity : 0.006 0.087 6946 Dihedral : 7.271 114.990 5722 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.80 % Favored : 94.12 % Rotamer: Outliers : 1.69 % Allowed : 12.86 % Favored : 85.45 % 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 aren not related in a simple way. whole: -1.61 (0.11), residues: 5134 helix: -0.09 (0.09), residues: 2830 sheet: -2.04 (0.18), residues: 648 loop : -2.22 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 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 covalent geometry : bond 0.00408 (39715) covalent geometry : angle 0.67631 (53861) hydrogen bonds : bond 0.05236 ( 2489) hydrogen bonds : angle 5.08823 ( 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 665 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 596 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8412 (p0) cc_final: 0.8186 (p0) REVERT: A 413 ARG cc_start: 0.7275 (ttm170) cc_final: 0.6347 (ttp80) REVERT: A 498 MET cc_start: 0.8490 (tpt) cc_final: 0.8101 (tpp) REVERT: B 41 ARG cc_start: 0.7972 (mmm160) cc_final: 0.7685 (mmm160) REVERT: B 90 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7830 (mmtm) REVERT: B 216 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7565 (mmm160) REVERT: B 285 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8206 (mt-10) REVERT: C 362 ILE cc_start: 0.8580 (tp) cc_final: 0.8252 (tt) REVERT: D 32 ASP cc_start: 0.8655 (p0) cc_final: 0.8453 (p0) REVERT: D 120 ASN cc_start: 0.7866 (m-40) cc_final: 0.7647 (m-40) REVERT: D 127 ARG cc_start: 0.6373 (mtm110) cc_final: 0.6100 (mtm110) REVERT: D 225 GLN cc_start: 0.6927 (mm110) cc_final: 0.6666 (mp10) REVERT: E 47 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8692 (pp) REVERT: E 141 GLN cc_start: 0.8099 (tt0) cc_final: 0.7873 (tt0) REVERT: E 280 GLN cc_start: 0.7480 (tm-30) cc_final: 0.6977 (tt0) REVERT: E 453 GLU cc_start: 0.7294 (mp0) cc_final: 0.7083 (mt-10) REVERT: F 53 ASP cc_start: 0.6963 (t0) cc_final: 0.6501 (t0) REVERT: F 73 ARG cc_start: 0.8379 (mtt90) cc_final: 0.7854 (mtt90) REVERT: F 143 ASP cc_start: 0.7560 (t0) cc_final: 0.7110 (t0) REVERT: F 369 ASP cc_start: 0.7804 (t70) cc_final: 0.7498 (t70) REVERT: d 171 LYS cc_start: 0.6893 (mmtm) cc_final: 0.6327 (tppt) REVERT: g 84 PRO cc_start: 0.7585 (Cg_exo) cc_final: 0.7301 (Cg_endo) REVERT: g 121 MET cc_start: 0.7690 (ttm) cc_final: 0.7437 (ttm) REVERT: g 192 GLN cc_start: 0.7613 (mt0) cc_final: 0.6955 (tp40) REVERT: g 353 ILE cc_start: 0.8809 (mt) cc_final: 0.8505 (pt) REVERT: I 122 GLU cc_start: 0.4017 (mm-30) cc_final: 0.3665 (tp30) REVERT: J 116 MET cc_start: -0.3561 (ptt) cc_final: -0.3845 (ptt) REVERT: a 191 PHE cc_start: 0.4645 (m-80) cc_final: 0.4279 (m-80) REVERT: N 34 GLN cc_start: 0.5642 (mt0) cc_final: 0.5233 (mt0) REVERT: O 24 PRO cc_start: 0.4428 (Cg_exo) cc_final: 0.4173 (Cg_endo) REVERT: O 50 ARG cc_start: 0.5412 (mtm180) cc_final: 0.4212 (ptm160) REVERT: V 37 GLU cc_start: 0.6361 (tt0) cc_final: 0.6095 (mt-10) REVERT: V 75 LEU cc_start: 0.0424 (tt) cc_final: 0.0159 (tt) REVERT: W 59 PHE cc_start: 0.5071 (m-80) cc_final: 0.4355 (m-80) outliers start: 69 outliers final: 38 residues processed: 641 average time/residue: 0.2385 time to fit residues: 243.6710 Evaluate side-chains 568 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 529 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 233 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 378 optimal weight: 0.9990 chunk 470 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 476 optimal weight: 10.0000 chunk 380 optimal weight: 0.7980 chunk 461 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 367 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 359 ASN B 208 GLN C 43 HIS C 214 GLN C 273 GLN D 72 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN F 389 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.185278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.146415 restraints weight = 54735.257| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.46 r_work: 0.3315 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 39715 Z= 0.171 Angle : 0.651 11.880 53861 Z= 0.332 Chirality : 0.044 0.244 6436 Planarity : 0.005 0.069 6946 Dihedral : 7.016 105.754 5722 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 2.42 % Allowed : 14.96 % Favored : 82.62 % 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 aren not related in a simple way. whole: -0.98 (0.11), residues: 5134 helix: 0.46 (0.09), residues: 2827 sheet: -1.82 (0.19), residues: 659 loop : -1.98 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.027 0.001 TYR O 66 PHE 0.040 0.001 PHE V 59 TRP 0.008 0.001 TRP a 28 HIS 0.008 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00380 (39715) covalent geometry : angle 0.65104 (53861) hydrogen bonds : bond 0.05001 ( 2489) hydrogen bonds : angle 4.89072 ( 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 654 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 555 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6276 (mm-30) cc_final: 0.5950 (mm-30) REVERT: A 408 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7430 (mt0) REVERT: A 413 ARG cc_start: 0.7356 (ttm170) cc_final: 0.6508 (ttp80) REVERT: A 498 MET cc_start: 0.8393 (tpt) cc_final: 0.8170 (tpp) REVERT: B 79 ASP cc_start: 0.6658 (OUTLIER) cc_final: 0.6421 (p0) REVERT: B 90 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7861 (mmtm) REVERT: B 109 ILE cc_start: 0.8511 (mm) cc_final: 0.8093 (mt) REVERT: B 216 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7542 (mmm160) REVERT: C 94 ARG cc_start: 0.7436 (mtm180) cc_final: 0.7200 (mtp-110) REVERT: C 362 ILE cc_start: 0.8579 (tp) cc_final: 0.8246 (tt) REVERT: D 32 ASP cc_start: 0.8696 (p0) cc_final: 0.8483 (p0) REVERT: D 120 ASN cc_start: 0.7893 (m-40) cc_final: 0.7645 (m-40) REVERT: D 216 MET cc_start: 0.8219 (mmt) cc_final: 0.7970 (mtt) REVERT: E 120 ASN cc_start: 0.8108 (t0) cc_final: 0.7899 (t0) REVERT: E 248 ARG cc_start: 0.7570 (mmt180) cc_final: 0.7319 (mmt180) REVERT: E 280 GLN cc_start: 0.7586 (tm-30) cc_final: 0.6995 (tt0) REVERT: E 383 GLU cc_start: 0.6433 (tp30) cc_final: 0.6055 (tp30) REVERT: E 385 TYR cc_start: 0.8062 (t80) cc_final: 0.7787 (t80) REVERT: E 387 ILE cc_start: 0.8368 (tt) cc_final: 0.7871 (mm) REVERT: E 488 MET cc_start: 0.6178 (mtm) cc_final: 0.5785 (ptp) REVERT: F 53 ASP cc_start: 0.6902 (t0) cc_final: 0.6517 (t0) REVERT: F 73 ARG cc_start: 0.8328 (mtt90) cc_final: 0.7852 (mtt90) REVERT: F 143 ASP cc_start: 0.7288 (t0) cc_final: 0.6925 (t0) REVERT: F 369 ASP cc_start: 0.7834 (t70) cc_final: 0.7429 (t70) REVERT: F 399 LYS cc_start: 0.8339 (ttpp) cc_final: 0.8136 (ttpt) REVERT: d 171 LYS cc_start: 0.6982 (mmtm) cc_final: 0.6399 (tppt) REVERT: g 84 PRO cc_start: 0.7492 (Cg_exo) cc_final: 0.7167 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7682 (mt0) cc_final: 0.6993 (tp40) REVERT: g 353 ILE cc_start: 0.8803 (mt) cc_final: 0.8592 (pt) REVERT: e 45 ASP cc_start: 0.7182 (p0) cc_final: 0.6977 (p0) REVERT: I 122 GLU cc_start: 0.3928 (mm-30) cc_final: 0.3571 (tp30) REVERT: I 181 GLU cc_start: 0.5304 (OUTLIER) cc_final: 0.5023 (mp0) REVERT: J 116 MET cc_start: -0.3183 (ptt) cc_final: -0.3475 (ptt) REVERT: a 191 PHE cc_start: 0.4703 (m-80) cc_final: 0.4375 (m-80) REVERT: N 60 MET cc_start: 0.3376 (mtp) cc_final: 0.3007 (mmm) REVERT: O 50 ARG cc_start: 0.5609 (mtm180) cc_final: 0.4437 (ptm160) REVERT: S 60 MET cc_start: 0.2984 (OUTLIER) cc_final: 0.2610 (tpp) REVERT: V 75 LEU cc_start: 0.0874 (tt) cc_final: 0.0589 (tt) REVERT: W 59 PHE cc_start: 0.5034 (m-80) cc_final: 0.4259 (m-80) REVERT: Y 60 MET cc_start: 0.2809 (ppp) cc_final: 0.2401 (mpp) outliers start: 99 outliers final: 52 residues processed: 626 average time/residue: 0.2368 time to fit residues: 237.2262 Evaluate side-chains 570 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 515 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 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 393 LEU 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 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 420 THR Chi-restraints excluded: chain d residue 177 VAL Chi-restraints excluded: chain d residue 181 THR Chi-restraints excluded: chain d residue 237 VAL 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 I residue 156 LEU Chi-restraints excluded: chain I residue 181 GLU 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 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 Y residue 4 LEU 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: 0.0570 chunk 384 optimal weight: 0.6980 chunk 296 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 436 optimal weight: 0.9980 chunk 370 optimal weight: 2.9990 chunk 354 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 287 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 359 ASN A 398 GLN A 468 ASN C 398 GLN 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 389 GLN ** e 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.185970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.146383 restraints weight = 54575.376| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.51 r_work: 0.3323 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39715 Z= 0.152 Angle : 0.627 11.740 53861 Z= 0.319 Chirality : 0.043 0.204 6436 Planarity : 0.005 0.068 6946 Dihedral : 6.749 102.230 5722 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.35 % Rotamer: Outliers : 2.62 % Allowed : 16.31 % 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 aren not related in a simple way. whole: -0.61 (0.11), residues: 5134 helix: 0.77 (0.09), residues: 2832 sheet: -1.73 (0.19), residues: 667 loop : -1.81 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.029 0.001 TYR O 66 PHE 0.013 0.001 PHE D 278 TRP 0.008 0.001 TRP a 28 HIS 0.016 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00332 (39715) covalent geometry : angle 0.62749 (53861) hydrogen bonds : bond 0.04760 ( 2489) hydrogen bonds : angle 4.75777 ( 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 652 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 545 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6334 (mm-30) cc_final: 0.5831 (mm-30) REVERT: A 408 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7399 (mt0) REVERT: A 413 ARG cc_start: 0.7333 (ttm170) cc_final: 0.6502 (ttp80) REVERT: B 79 ASP cc_start: 0.6670 (OUTLIER) cc_final: 0.6412 (p0) REVERT: B 90 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7860 (mmtm) REVERT: B 109 ILE cc_start: 0.8486 (mm) cc_final: 0.8090 (mt) REVERT: B 216 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7533 (mmm160) REVERT: C 362 ILE cc_start: 0.8564 (tp) cc_final: 0.8233 (tt) REVERT: D 120 ASN cc_start: 0.7896 (m-40) cc_final: 0.7633 (m-40) REVERT: D 216 MET cc_start: 0.8224 (mmt) cc_final: 0.8015 (mtt) REVERT: E 47 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8606 (pp) REVERT: E 120 ASN cc_start: 0.8086 (t0) cc_final: 0.7816 (t0) REVERT: E 184 GLU cc_start: 0.7806 (tp30) cc_final: 0.7577 (tp30) REVERT: E 280 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6955 (tt0) REVERT: E 385 TYR cc_start: 0.8043 (t80) cc_final: 0.7748 (t80) REVERT: E 488 MET cc_start: 0.6214 (mtm) cc_final: 0.5867 (ptp) REVERT: F 53 ASP cc_start: 0.6874 (t0) cc_final: 0.6444 (t0) REVERT: F 73 ARG cc_start: 0.8317 (mtt90) cc_final: 0.7790 (mtt90) REVERT: F 143 ASP cc_start: 0.7288 (t0) cc_final: 0.6916 (t0) REVERT: F 204 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6657 (pp20) REVERT: F 214 MET cc_start: 0.7631 (mmt) cc_final: 0.7241 (mtt) REVERT: F 369 ASP cc_start: 0.7805 (t70) cc_final: 0.7390 (t70) REVERT: d 82 LEU cc_start: 0.7686 (tp) cc_final: 0.7401 (tp) REVERT: d 171 LYS cc_start: 0.6951 (mmtm) cc_final: 0.6353 (tppt) REVERT: g 84 PRO cc_start: 0.7469 (Cg_exo) cc_final: 0.7141 (Cg_endo) REVERT: g 292 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7856 (mt) REVERT: e 45 ASP cc_start: 0.7182 (p0) cc_final: 0.6954 (p0) REVERT: I 181 GLU cc_start: 0.5262 (OUTLIER) cc_final: 0.5056 (mp0) REVERT: J 116 MET cc_start: -0.3323 (ptt) cc_final: -0.3603 (ptt) REVERT: a 191 PHE cc_start: 0.4651 (m-80) cc_final: 0.4381 (m-80) REVERT: N 60 MET cc_start: 0.3586 (mtp) cc_final: 0.3204 (mmm) REVERT: O 50 ARG cc_start: 0.5609 (mtm180) cc_final: 0.4523 (ptm160) REVERT: S 60 MET cc_start: 0.2864 (OUTLIER) cc_final: 0.2049 (tpp) REVERT: V 37 GLU cc_start: 0.6080 (tt0) cc_final: 0.5728 (mt-10) REVERT: V 75 LEU cc_start: 0.0501 (tt) cc_final: 0.0283 (tt) REVERT: W 59 PHE cc_start: 0.4942 (m-80) cc_final: 0.4065 (m-80) REVERT: Y 60 MET cc_start: 0.2857 (ppp) cc_final: 0.2482 (mpp) outliers start: 107 outliers final: 67 residues processed: 621 average time/residue: 0.2187 time to fit residues: 218.1663 Evaluate side-chains 584 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 511 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 393 LEU 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 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 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 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 238 GLN 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 292 MET Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 359 LYS 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 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 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 I residue 156 LEU Chi-restraints excluded: chain I residue 181 GLU 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 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 Y residue 52 THR 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: 0.8980 chunk 124 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 235 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 448 optimal weight: 7.9990 chunk 364 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN A 497 GLN C 43 HIS D 72 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN g 325 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.184339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.148204 restraints weight = 53554.346| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.43 r_work: 0.3307 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39715 Z= 0.162 Angle : 0.631 13.128 53861 Z= 0.319 Chirality : 0.044 0.312 6436 Planarity : 0.005 0.068 6946 Dihedral : 6.666 100.651 5722 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 3.03 % Allowed : 17.41 % 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 aren not related in a simple way. whole: -0.43 (0.12), residues: 5134 helix: 0.89 (0.09), residues: 2831 sheet: -1.62 (0.19), residues: 664 loop : -1.72 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 279 TYR 0.030 0.001 TYR O 66 PHE 0.028 0.001 PHE V 59 TRP 0.006 0.001 TRP a 28 HIS 0.006 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00358 (39715) covalent geometry : angle 0.63105 (53861) hydrogen bonds : bond 0.04746 ( 2489) hydrogen bonds : angle 4.70706 ( 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 659 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 535 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6298 (mm-30) cc_final: 0.5797 (mm-30) REVERT: A 182 ASP cc_start: 0.7775 (t70) cc_final: 0.7389 (t0) REVERT: A 408 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7342 (mt0) REVERT: A 413 ARG cc_start: 0.7325 (ttm170) cc_final: 0.6583 (ttp80) REVERT: B 79 ASP cc_start: 0.6646 (OUTLIER) cc_final: 0.6377 (p0) REVERT: B 90 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7854 (mmtp) REVERT: B 109 ILE cc_start: 0.8485 (mm) cc_final: 0.8151 (mt) REVERT: B 216 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7534 (mmm160) REVERT: B 355 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6637 (mmp-170) REVERT: B 466 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7590 (mmtm) REVERT: C 362 ILE cc_start: 0.8580 (tp) cc_final: 0.8254 (tt) REVERT: C 415 GLN cc_start: 0.7670 (tt0) cc_final: 0.7394 (tt0) REVERT: D 120 ASN cc_start: 0.7884 (m-40) cc_final: 0.7629 (m-40) REVERT: E 47 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8583 (pp) REVERT: E 120 ASN cc_start: 0.8039 (t0) cc_final: 0.7787 (t0) REVERT: E 280 GLN cc_start: 0.7511 (tm-30) cc_final: 0.6928 (tt0) REVERT: E 385 TYR cc_start: 0.8025 (t80) cc_final: 0.7758 (t80) REVERT: E 488 MET cc_start: 0.6118 (mtm) cc_final: 0.5780 (ptp) REVERT: F 53 ASP cc_start: 0.6684 (t0) cc_final: 0.6323 (t0) REVERT: F 73 ARG cc_start: 0.8337 (mtt90) cc_final: 0.7812 (mtt90) REVERT: F 143 ASP cc_start: 0.7218 (t0) cc_final: 0.6846 (t0) REVERT: F 204 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6575 (pp20) REVERT: F 214 MET cc_start: 0.7629 (mmt) cc_final: 0.7213 (mtt) REVERT: F 369 ASP cc_start: 0.7845 (t70) cc_final: 0.7405 (t70) REVERT: F 378 ARG cc_start: 0.7617 (mtt90) cc_final: 0.7312 (mtt90) REVERT: d 171 LYS cc_start: 0.6859 (mmtm) cc_final: 0.6288 (tppt) REVERT: g 84 PRO cc_start: 0.7217 (Cg_exo) cc_final: 0.6925 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7737 (mt0) cc_final: 0.6942 (tp40) REVERT: e 45 ASP cc_start: 0.7093 (p0) cc_final: 0.6799 (p0) REVERT: e 76 ILE cc_start: 0.7501 (mp) cc_final: 0.7082 (mt) REVERT: J 116 MET cc_start: -0.3348 (ptt) cc_final: -0.3678 (ptt) REVERT: a 191 PHE cc_start: 0.4679 (m-80) cc_final: 0.4388 (m-80) REVERT: N 60 MET cc_start: 0.3565 (mtp) cc_final: 0.3334 (mmm) REVERT: O 50 ARG cc_start: 0.5608 (mtm180) cc_final: 0.4597 (ptm160) REVERT: P 63 LEU cc_start: 0.1148 (OUTLIER) cc_final: 0.0802 (mt) REVERT: Q 60 MET cc_start: 0.1447 (ptp) cc_final: 0.0858 (tmm) REVERT: S 60 MET cc_start: 0.2978 (OUTLIER) cc_final: 0.2185 (tpp) REVERT: V 75 LEU cc_start: 0.0478 (tt) cc_final: 0.0248 (tt) REVERT: W 59 PHE cc_start: 0.5177 (m-80) cc_final: 0.4340 (m-80) outliers start: 124 outliers final: 89 residues processed: 629 average time/residue: 0.2187 time to fit residues: 222.7412 Evaluate side-chains 606 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 511 time to evaluate : 0.871 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 130 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 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 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 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 128 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 230 SER 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 359 LYS 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 122 VAL 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 260 LYS 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 156 LEU Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain J residue 207 ILE Chi-restraints excluded: chain a residue 70 ASN Chi-restraints excluded: chain a residue 146 VAL 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 63 LEU Chi-restraints excluded: chain R residue 57 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 Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR Chi-restraints excluded: chain Z residue 26 VAL 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: 0.0000 chunk 234 optimal weight: 0.2980 chunk 349 optimal weight: 3.9990 chunk 426 optimal weight: 6.9990 chunk 302 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 452 optimal weight: 0.9980 chunk 327 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 174 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 HIS D 45 ASN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN E 389 GLN F 25 GLN ** F 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 139 GLN e 54 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.151877 restraints weight = 53781.937| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.29 r_work: 0.3358 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2203 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= 0.138 Angle : 0.611 10.506 53861 Z= 0.310 Chirality : 0.043 0.212 6436 Planarity : 0.005 0.069 6946 Dihedral : 6.481 98.486 5722 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.32 % Favored : 94.64 % Rotamer: Outliers : 2.69 % Allowed : 18.17 % Favored : 79.14 % 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 aren not related in a simple way. whole: -0.23 (0.12), residues: 5134 helix: 1.06 (0.10), residues: 2828 sheet: -1.54 (0.19), residues: 656 loop : -1.63 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 301 TYR 0.032 0.001 TYR O 66 PHE 0.014 0.001 PHE D 278 TRP 0.006 0.001 TRP a 28 HIS 0.010 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00294 (39715) covalent geometry : angle 0.61101 (53861) hydrogen bonds : bond 0.04564 ( 2489) hydrogen bonds : angle 4.62340 ( 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 643 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 533 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5711 (mm-30) REVERT: A 182 ASP cc_start: 0.7546 (t70) cc_final: 0.7317 (t70) REVERT: A 408 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7371 (mt0) REVERT: A 413 ARG cc_start: 0.7350 (ttm170) cc_final: 0.6671 (ttp80) REVERT: B 79 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6288 (p0) REVERT: B 90 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7931 (mmtp) REVERT: B 109 ILE cc_start: 0.8442 (mm) cc_final: 0.8117 (mt) REVERT: B 216 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7539 (mmm160) REVERT: B 466 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7585 (mmtm) REVERT: C 362 ILE cc_start: 0.8562 (tp) cc_final: 0.8221 (tt) REVERT: C 456 LYS cc_start: 0.8015 (tppt) cc_final: 0.7636 (pttt) REVERT: D 120 ASN cc_start: 0.7865 (m-40) cc_final: 0.7644 (m-40) REVERT: E 120 ASN cc_start: 0.8019 (t0) cc_final: 0.7788 (t0) REVERT: E 280 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7345 (tt0) REVERT: E 385 TYR cc_start: 0.7979 (t80) cc_final: 0.7702 (t80) REVERT: E 488 MET cc_start: 0.6144 (mtm) cc_final: 0.5841 (ptp) REVERT: F 53 ASP cc_start: 0.6677 (t0) cc_final: 0.6341 (t0) REVERT: F 73 ARG cc_start: 0.8258 (mtt90) cc_final: 0.7745 (mtt90) REVERT: F 143 ASP cc_start: 0.7139 (t0) cc_final: 0.6780 (t0) REVERT: F 204 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6552 (pp20) REVERT: F 214 MET cc_start: 0.7642 (mmt) cc_final: 0.7256 (mtt) REVERT: F 369 ASP cc_start: 0.7789 (t70) cc_final: 0.7482 (t70) REVERT: F 378 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7296 (mtt90) REVERT: d 115 PHE cc_start: 0.6697 (m-80) cc_final: 0.6307 (m-80) REVERT: d 171 LYS cc_start: 0.6881 (mmtm) cc_final: 0.6318 (tppt) REVERT: g 84 PRO cc_start: 0.7175 (Cg_exo) cc_final: 0.6884 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7705 (mt0) cc_final: 0.6960 (tp40) REVERT: g 292 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7843 (mt) REVERT: e 45 ASP cc_start: 0.7121 (p0) cc_final: 0.6840 (p0) REVERT: e 76 ILE cc_start: 0.7448 (mp) cc_final: 0.7040 (mt) REVERT: J 116 MET cc_start: -0.2810 (ptt) cc_final: -0.3146 (ptt) REVERT: M 54 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4574 (mt) REVERT: N 60 MET cc_start: 0.3495 (mtp) cc_final: 0.3289 (mmm) REVERT: O 50 ARG cc_start: 0.5830 (mtm180) cc_final: 0.4767 (ptm160) REVERT: P 63 LEU cc_start: 0.1224 (OUTLIER) cc_final: 0.0877 (mt) REVERT: Q 60 MET cc_start: 0.1300 (ptp) cc_final: 0.0852 (tmm) REVERT: S 60 MET cc_start: 0.3165 (OUTLIER) cc_final: 0.2460 (tpp) REVERT: T 60 MET cc_start: 0.4013 (OUTLIER) cc_final: 0.3389 (tpp) REVERT: V 75 LEU cc_start: 0.0779 (tt) cc_final: 0.0526 (tt) REVERT: W 59 PHE cc_start: 0.5105 (m-80) cc_final: 0.4314 (m-80) REVERT: Y 60 MET cc_start: 0.2940 (ppp) cc_final: 0.2318 (mpp) outliers start: 110 outliers final: 78 residues processed: 613 average time/residue: 0.2285 time to fit residues: 226.5508 Evaluate side-chains 591 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 506 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 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 79 ASP 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 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 143 ASP 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 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 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 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 359 LYS 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 122 VAL 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 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 156 LEU Chi-restraints excluded: chain J residue 167 GLN 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 503 random chunks: chunk 258 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 387 optimal weight: 0.9990 chunk 410 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 294 optimal weight: 0.0970 chunk 12 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 497 GLN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** D 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 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 ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.185515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158563 restraints weight = 53146.468| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.85 r_work: 0.3430 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39715 Z= 0.149 Angle : 0.618 12.345 53861 Z= 0.312 Chirality : 0.043 0.288 6436 Planarity : 0.005 0.071 6946 Dihedral : 6.401 97.336 5722 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.23 % Rotamer: Outliers : 2.98 % Allowed : 18.46 % Favored : 78.56 % 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 aren not related in a simple way. whole: -0.13 (0.12), residues: 5134 helix: 1.13 (0.10), residues: 2827 sheet: -1.47 (0.19), residues: 661 loop : -1.57 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 418 TYR 0.037 0.001 TYR O 66 PHE 0.025 0.001 PHE V 59 TRP 0.005 0.001 TRP a 28 HIS 0.005 0.001 HIS F 384 Details of bonding type rmsd covalent geometry : bond 0.00325 (39715) covalent geometry : angle 0.61825 (53861) hydrogen bonds : bond 0.04557 ( 2489) hydrogen bonds : angle 4.59400 ( 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 647 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 525 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6092 (mm-30) REVERT: A 182 ASP cc_start: 0.7902 (t70) cc_final: 0.7530 (t0) REVERT: A 408 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7479 (mt0) REVERT: A 413 ARG cc_start: 0.7545 (ttm170) cc_final: 0.6808 (ttp80) REVERT: B 79 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6535 (p0) REVERT: B 90 LYS cc_start: 0.8386 (mtmt) cc_final: 0.8075 (mmtp) REVERT: B 109 ILE cc_start: 0.8494 (mm) cc_final: 0.8180 (mt) REVERT: B 216 ARG cc_start: 0.8100 (mtt-85) cc_final: 0.7590 (mmm160) REVERT: B 466 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7645 (mmtm) REVERT: C 362 ILE cc_start: 0.8606 (tp) cc_final: 0.8280 (tt) REVERT: D 311 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7458 (mm-30) REVERT: E 47 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8576 (pp) REVERT: E 280 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: E 488 MET cc_start: 0.6184 (mtm) cc_final: 0.5813 (ptp) REVERT: F 53 ASP cc_start: 0.6698 (t0) cc_final: 0.6339 (t0) REVERT: F 73 ARG cc_start: 0.8424 (mtt90) cc_final: 0.7919 (mtt90) REVERT: F 143 ASP cc_start: 0.7378 (t0) cc_final: 0.7038 (t0) REVERT: F 204 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6883 (pp20) REVERT: F 214 MET cc_start: 0.7960 (mmt) cc_final: 0.7482 (mtt) REVERT: F 369 ASP cc_start: 0.8060 (t70) cc_final: 0.7760 (t70) REVERT: d 115 PHE cc_start: 0.6709 (m-80) cc_final: 0.6252 (m-80) REVERT: d 171 LYS cc_start: 0.6913 (mmtm) cc_final: 0.6355 (tppt) REVERT: g 84 PRO cc_start: 0.7343 (Cg_exo) cc_final: 0.7072 (Cg_endo) REVERT: g 192 GLN cc_start: 0.7737 (mt0) cc_final: 0.6968 (tp40) REVERT: g 292 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7911 (mt) REVERT: e 36 ASN cc_start: 0.7188 (m-40) cc_final: 0.5701 (t0) REVERT: e 45 ASP cc_start: 0.7097 (p0) cc_final: 0.6859 (p0) REVERT: e 53 LEU cc_start: 0.5844 (mp) cc_final: 0.5035 (tt) REVERT: e 76 ILE cc_start: 0.7601 (mp) cc_final: 0.7253 (mt) REVERT: J 116 MET cc_start: -0.3421 (ptt) cc_final: -0.3804 (ptt) REVERT: J 162 MET cc_start: 0.1979 (tmm) cc_final: 0.1040 (tmm) REVERT: a 191 PHE cc_start: 0.4845 (m-80) cc_final: 0.4581 (m-80) REVERT: O 50 ARG cc_start: 0.5852 (mtm180) cc_final: 0.4789 (ptm160) REVERT: P 63 LEU cc_start: 0.1089 (OUTLIER) cc_final: 0.0793 (mt) REVERT: Q 60 MET cc_start: 0.1296 (ptp) cc_final: 0.0837 (tmm) REVERT: S 60 MET cc_start: 0.3174 (OUTLIER) cc_final: 0.2459 (tpp) REVERT: T 60 MET cc_start: 0.3995 (OUTLIER) cc_final: 0.3402 (tpp) REVERT: V 75 LEU cc_start: 0.0943 (tt) cc_final: 0.0663 (tt) REVERT: W 59 PHE cc_start: 0.5303 (m-80) cc_final: 0.4421 (m-80) REVERT: Y 60 MET cc_start: 0.2955 (ppp) cc_final: 0.2351 (mpp) outliers start: 122 outliers final: 90 residues processed: 617 average time/residue: 0.2134 time to fit residues: 212.9208 Evaluate side-chains 599 residues out of total 4090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 501 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 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 364 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 240 ASN 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 404 ILE 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 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 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 359 LYS 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 122 VAL 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 260 LYS 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 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 167 GLN 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 146 VAL 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 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 Y residue 4 LEU Chi-restraints excluded: chain Y residue 52 THR 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.7109 > 50: distance: 30 - 56: 25.517 distance: 39 - 64: 34.845 distance: 46 - 75: 31.288 distance: 52 - 56: 23.403 distance: 53 - 82: 33.085 distance: 56 - 57: 38.312 distance: 57 - 58: 26.879 distance: 57 - 60: 29.747 distance: 58 - 59: 35.982 distance: 58 - 64: 52.078 distance: 59 - 94: 54.174 distance: 60 - 61: 56.937 distance: 61 - 62: 38.962 distance: 61 - 63: 54.483 distance: 65 - 66: 57.347 distance: 65 - 68: 39.695 distance: 66 - 67: 57.464 distance: 66 - 75: 40.514 distance: 67 - 101: 40.773 distance: 69 - 70: 29.205 distance: 70 - 71: 10.728 distance: 71 - 72: 39.315 distance: 72 - 74: 27.800 distance: 75 - 76: 42.102 distance: 76 - 77: 43.681 distance: 76 - 79: 39.671 distance: 77 - 78: 24.893 distance: 77 - 82: 42.513 distance: 78 - 110: 51.562 distance: 79 - 80: 55.635 distance: 79 - 81: 35.196 distance: 82 - 83: 56.294 distance: 83 - 84: 40.386 distance: 83 - 86: 53.520 distance: 84 - 85: 40.949 distance: 84 - 94: 55.349 distance: 85 - 117: 40.478 distance: 86 - 87: 39.056 distance: 87 - 88: 7.371 distance: 87 - 89: 9.579 distance: 88 - 90: 38.978 distance: 89 - 91: 38.973 distance: 92 - 93: 56.870 distance: 94 - 95: 40.641 distance: 95 - 96: 40.634 distance: 95 - 98: 38.770 distance: 96 - 97: 39.699 distance: 96 - 101: 10.854 distance: 97 - 125: 44.374 distance: 98 - 99: 55.888 distance: 98 - 100: 41.004 distance: 101 - 102: 12.198 distance: 102 - 103: 57.369 distance: 102 - 105: 39.482 distance: 103 - 110: 39.276 distance: 106 - 107: 39.208 distance: 107 - 108: 52.345 distance: 108 - 109: 56.647 distance: 111 - 114: 17.394 distance: 112 - 113: 30.758 distance: 112 - 117: 14.440 distance: 114 - 115: 58.751 distance: 114 - 116: 24.243 distance: 117 - 118: 49.275 distance: 118 - 119: 57.620 distance: 118 - 121: 53.295 distance: 119 - 120: 24.267 distance: 119 - 125: 33.523 distance: 122 - 123: 40.001 distance: 122 - 124: 56.687 distance: 125 - 126: 58.799 distance: 126 - 127: 55.741 distance: 126 - 129: 55.623 distance: 127 - 128: 57.216 distance: 127 - 134: 56.054 distance: 130 - 131: 53.914 distance: 131 - 132: 36.124 distance: 132 - 133: 65.061 distance: 134 - 135: 38.553 distance: 134 - 140: 41.637 distance: 135 - 138: 40.280 distance: 136 - 137: 41.166 distance: 136 - 141: 33.904 distance: 137 - 165: 31.617 distance: 138 - 139: 28.120 distance: 139 - 140: 45.997