Starting phenix.real_space_refine on Sun Jan 26 09:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6te0_10473/01_2025/6te0_10473_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6te0_10473/01_2025/6te0_10473.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6te0_10473/01_2025/6te0_10473.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6te0_10473/01_2025/6te0_10473.map" model { file = "/net/cci-nas-00/data/ceres_data/6te0_10473/01_2025/6te0_10473_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6te0_10473/01_2025/6te0_10473_trim.cif" } resolution = 3.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 233 5.16 5 C 25085 2.51 5 N 6559 2.21 5 O 7457 1.98 5 H 39835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 79188 Number of models: 1 Model: "" Number of chains: 29 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8317 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 506} Chain breaks: 1 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8292 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "B" Number of atoms: 8336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 8336 Classifications: {'peptide': 529} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 508} Chain breaks: 1 Chain: "F" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "D" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "E" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "L" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "M" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3778 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 14, 'TRANS': 228} Chain: "G" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4898 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 5, 'TRANS': 297} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2448 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1077 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TRT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 31.13, per 1000 atoms: 0.39 Number of scatterers: 79188 At special positions: 0 Unit cell: (165.9, 166.95, 233.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 233 16.00 P 14 15.00 Mg 5 11.99 O 7457 8.00 N 6559 7.00 C 25085 6.00 H 39835 1.00 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: 18.32 Conformation dependent library (CDL) restraints added in 5.1 seconds 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9466 Finding SS restraints... Secondary structure from input PDB file: 209 helices and 27 sheets defined 54.6% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 189 through 200 removed outlier: 3.723A pdb=" N ALA C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 208 removed outlier: 3.856A pdb=" N GLU C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.594A pdb=" N LEU C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 275 removed outlier: 3.774A pdb=" N PHE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 300 removed outlier: 3.696A pdb=" N GLN C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 310 through 311 No H-bonds generated for 'chain 'C' and resid 310 through 311' Processing helix chain 'C' and resid 312 through 322 removed outlier: 3.970A pdb=" N LEU C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 3.552A pdb=" N GLY C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 361 removed outlier: 3.645A pdb=" N SER C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 395 through 419 removed outlier: 3.540A pdb=" N LYS C 399 " --> pdb=" O ASN C 395 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LYS C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA C 404 " --> pdb=" O LYS C 400 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N GLU C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 441 removed outlier: 3.801A pdb=" N ALA C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 439 " --> pdb=" O ARG C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 460 removed outlier: 3.681A pdb=" N VAL C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 502 through 507 Processing helix chain 'C' and resid 516 through 542 removed outlier: 4.394A pdb=" N GLN C 536 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N SER C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 538 " --> pdb=" O ASN C 534 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN C 540 " --> pdb=" O GLN C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 562 removed outlier: 3.802A pdb=" N VAL C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.724A pdb=" N ILE A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 260 through 275 removed outlier: 3.760A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 300 removed outlier: 3.780A pdb=" N VAL A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.508A pdb=" N ALA A 308 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 322 removed outlier: 3.726A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 395 through 416 removed outlier: 4.088A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.595A pdb=" N ALA A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 439 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 460 removed outlier: 3.787A pdb=" N VAL A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.820A pdb=" N TYR A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 535 removed outlier: 4.648A pdb=" N GLU A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 544 through 562 removed outlier: 3.663A pdb=" N LEU A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 109 through 113 Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.748A pdb=" N ARG B 154 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.103A pdb=" N ALA B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 Processing helix chain 'B' and resid 224 through 238 removed outlier: 3.500A pdb=" N VAL B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 275 removed outlier: 3.741A pdb=" N GLN B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Proline residue: B 262 - end of helix removed outlier: 3.668A pdb=" N GLU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 300 removed outlier: 3.605A pdb=" N GLN B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 312 through 322 Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 351 through 361 removed outlier: 3.631A pdb=" N ILE B 360 " --> pdb=" O ASN B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 389 through 393 removed outlier: 4.150A pdb=" N SER B 392 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 416 removed outlier: 4.231A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B 404 " --> pdb=" O LYS B 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 441 removed outlier: 3.854A pdb=" N ALA B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 460 removed outlier: 3.741A pdb=" N VAL B 453 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 481 Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 516 through 540 removed outlier: 5.460A pdb=" N ILE B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 538 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 562 removed outlier: 3.529A pdb=" N GLN B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 188 removed outlier: 3.814A pdb=" N MET F 178 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 214 removed outlier: 3.702A pdb=" N GLY F 204 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 241 removed outlier: 3.843A pdb=" N ARG F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 256 removed outlier: 3.876A pdb=" N TYR F 252 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE F 253 " --> pdb=" O MET F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 283 removed outlier: 3.737A pdb=" N PHE F 271 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN F 275 " --> pdb=" O PHE F 271 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL F 278 " --> pdb=" O ALA F 274 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 322 through 326 Processing helix chain 'F' and resid 329 through 336 removed outlier: 3.626A pdb=" N THR F 335 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.759A pdb=" N ALA F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 399 removed outlier: 3.849A pdb=" N GLU F 393 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.551A pdb=" N GLU F 405 " --> pdb=" O GLY F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 424 removed outlier: 3.606A pdb=" N ILE F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 444 through 448 Processing helix chain 'F' and resid 450 through 456 Processing helix chain 'F' and resid 472 through 501 removed outlier: 3.511A pdb=" N LYS F 482 " --> pdb=" O GLU F 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 removed outlier: 4.462A pdb=" N THR D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.682A pdb=" N ILE D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 214 removed outlier: 3.559A pdb=" N THR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU D 210 " --> pdb=" O ASP D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 3.610A pdb=" N ARG D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 256 removed outlier: 3.761A pdb=" N PHE D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 removed outlier: 3.820A pdb=" N PHE D 271 " --> pdb=" O ASN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.564A pdb=" N LEU D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 326 Processing helix chain 'D' and resid 329 through 339 removed outlier: 4.145A pdb=" N HIS D 338 " --> pdb=" O THR D 334 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.538A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 399 removed outlier: 3.719A pdb=" N TYR D 378 " --> pdb=" O ASP D 374 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA D 399 " --> pdb=" O GLN D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 407 through 425 removed outlier: 3.666A pdb=" N LYS D 422 " --> pdb=" O ARG D 418 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 436 Processing helix chain 'D' and resid 443 through 457 removed outlier: 3.664A pdb=" N CYS D 447 " --> pdb=" O GLN D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 501 removed outlier: 3.931A pdb=" N LYS D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 479 " --> pdb=" O SER D 475 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 148 through 154 Processing helix chain 'E' and resid 172 through 185 Processing helix chain 'E' and resid 200 through 214 removed outlier: 3.526A pdb=" N SER E 214 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.613A pdb=" N ARG E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 256 removed outlier: 3.769A pdb=" N THR E 245 " --> pdb=" O ARG E 241 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE E 253 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 removed outlier: 3.993A pdb=" N PHE E 271 " --> pdb=" O ASN E 267 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 removed outlier: 3.747A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 326 Processing helix chain 'E' and resid 329 through 336 Processing helix chain 'E' and resid 346 through 352 removed outlier: 4.044A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 399 removed outlier: 3.579A pdb=" N TYR E 378 " --> pdb=" O ASP E 374 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 383 " --> pdb=" O ASN E 379 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP E 396 " --> pdb=" O LYS E 392 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 406 removed outlier: 3.659A pdb=" N GLU E 405 " --> pdb=" O GLY E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 424 removed outlier: 3.624A pdb=" N LYS E 419 " --> pdb=" O ASP E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 436 Processing helix chain 'E' and resid 443 through 456 Processing helix chain 'E' and resid 464 through 468 Processing helix chain 'E' and resid 472 through 501 Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.545A pdb=" N LYS L 48 " --> pdb=" O GLU L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 65 removed outlier: 3.935A pdb=" N VAL L 60 " --> pdb=" O GLY L 56 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 84 Processing helix chain 'L' and resid 96 through 110 Processing helix chain 'L' and resid 117 through 132 removed outlier: 4.141A pdb=" N TYR L 123 " --> pdb=" O GLU L 119 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL L 124 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 148 Processing helix chain 'L' and resid 152 through 169 removed outlier: 3.548A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA L 169 " --> pdb=" O LYS L 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 49 removed outlier: 3.730A pdb=" N ALA J 49 " --> pdb=" O GLU J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 64 removed outlier: 4.005A pdb=" N ALA J 55 " --> pdb=" O PHE J 51 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY J 56 " --> pdb=" O TYR J 52 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU J 64 " --> pdb=" O VAL J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 96 through 110 removed outlier: 3.885A pdb=" N ILE J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 132 removed outlier: 3.512A pdb=" N VAL J 124 " --> pdb=" O SER J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 147 removed outlier: 3.545A pdb=" N VAL J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU J 147 " --> pdb=" O GLY J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 169 removed outlier: 3.630A pdb=" N VAL J 156 " --> pdb=" O ASP J 152 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 179 removed outlier: 4.176A pdb=" N LYS J 178 " --> pdb=" O PRO J 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 48 removed outlier: 3.521A pdb=" N GLU K 45 " --> pdb=" O PRO K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 65 removed outlier: 3.534A pdb=" N GLU K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 96 through 110 removed outlier: 3.994A pdb=" N ALA K 100 " --> pdb=" O ASN K 96 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET K 101 " --> pdb=" O LYS K 97 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU K 105 " --> pdb=" O MET K 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU K 106 " --> pdb=" O MET K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 132 removed outlier: 3.524A pdb=" N LYS K 126 " --> pdb=" O GLY K 122 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU K 127 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 147 Processing helix chain 'K' and resid 152 through 169 removed outlier: 3.627A pdb=" N ALA K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 33 Processing helix chain 'M' and resid 48 through 63 removed outlier: 4.099A pdb=" N PHE M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA M 53 " --> pdb=" O HIS M 49 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 84 removed outlier: 3.552A pdb=" N VAL M 72 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER M 80 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA M 83 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 103 removed outlier: 4.174A pdb=" N GLY M 102 " --> pdb=" O THR M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 119 through 122 Processing helix chain 'M' and resid 123 through 138 removed outlier: 3.886A pdb=" N ALA M 129 " --> pdb=" O ASN M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 159 Processing helix chain 'M' and resid 159 through 170 removed outlier: 3.654A pdb=" N GLU M 165 " --> pdb=" O LYS M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 222 removed outlier: 3.541A pdb=" N ALA M 209 " --> pdb=" O ALA M 205 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR M 211 " --> pdb=" O ALA M 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL M 222 " --> pdb=" O SER M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 239 through 246 removed outlier: 3.586A pdb=" N ILE M 243 " --> pdb=" O PRO M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 263 removed outlier: 3.972A pdb=" N ASP M 252 " --> pdb=" O SER M 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 39 removed outlier: 3.793A pdb=" N ARG G 8 " --> pdb=" O GLY G 4 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS G 34 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.562A pdb=" N ARG G 43 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 57 Processing helix chain 'G' and resid 62 through 70 removed outlier: 3.892A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE G 67 " --> pdb=" O ASP G 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 99 removed outlier: 3.517A pdb=" N LEU G 96 " --> pdb=" O MET G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 121 removed outlier: 3.855A pdb=" N ASP G 115 " --> pdb=" O LYS G 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 179 through 193 removed outlier: 3.737A pdb=" N ALA G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 216 through 247 Processing helix chain 'G' and resid 248 through 295 removed outlier: 4.380A pdb=" N GLN G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY G 260 " --> pdb=" O GLY G 256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 132 through 134 No H-bonds generated for 'chain 'H' and resid 132 through 134' Processing helix chain 'H' and resid 135 through 152 removed outlier: 3.739A pdb=" N LYS H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 176 removed outlier: 3.992A pdb=" N ILE H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLN H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Proline residue: H 170 - end of helix Processing helix chain 'I' and resid 9 through 25 removed outlier: 3.871A pdb=" N GLU I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL I 24 " --> pdb=" O CYS I 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN I 25 " --> pdb=" O ILE I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 35 Processing helix chain 'I' and resid 36 through 38 No H-bonds generated for 'chain 'I' and resid 36 through 38' Processing helix chain 'O' and resid 33 through 45 removed outlier: 4.643A pdb=" N GLY O 38 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA O 39 " --> pdb=" O ASN O 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY O 45 " --> pdb=" O MET O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 67 removed outlier: 3.917A pdb=" N ILE O 51 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY O 52 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 101 Proline residue: O 76 - end of helix removed outlier: 3.707A pdb=" N PHE O 82 " --> pdb=" O CYS O 78 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU O 88 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 33 through 67 removed outlier: 4.245A pdb=" N GLY P 38 " --> pdb=" O ALA P 34 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA P 39 " --> pdb=" O ASN P 35 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER P 44 " --> pdb=" O GLY P 40 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY P 45 " --> pdb=" O MET P 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY P 47 " --> pdb=" O ALA P 43 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) Proline residue: P 49 - end of helix removed outlier: 3.910A pdb=" N GLY P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 101 Proline residue: P 76 - end of helix removed outlier: 3.634A pdb=" N ALA P 83 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU P 88 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA P 89 " --> pdb=" O SER P 85 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA P 96 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU P 100 " --> pdb=" O ALA P 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 47 removed outlier: 3.952A pdb=" N GLY Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY Q 45 " --> pdb=" O MET Q 41 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 67 removed outlier: 4.121A pdb=" N ILE Q 51 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY Q 52 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET Q 55 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER Q 59 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR Q 60 " --> pdb=" O CYS Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 71 Processing helix chain 'Q' and resid 74 through 102 removed outlier: 3.828A pdb=" N PHE Q 82 " --> pdb=" O CYS Q 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 89 " --> pdb=" O SER Q 85 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 45 removed outlier: 3.940A pdb=" N GLY R 38 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 67 Processing helix chain 'R' and resid 70 through 99 Proline residue: R 76 - end of helix removed outlier: 3.944A pdb=" N LEU R 88 " --> pdb=" O LEU R 84 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA R 96 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 97 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 33 through 43 removed outlier: 3.573A pdb=" N ILE S 37 " --> pdb=" O GLY S 33 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY S 38 " --> pdb=" O ALA S 34 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA S 39 " --> pdb=" O ASN S 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 46 No H-bonds generated for 'chain 'S' and resid 44 through 46' Processing helix chain 'S' and resid 47 through 67 removed outlier: 4.223A pdb=" N ILE S 51 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY S 52 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE S 57 " --> pdb=" O VAL S 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU S 62 " --> pdb=" O SER S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 Processing helix chain 'S' and resid 75 through 99 removed outlier: 3.762A pdb=" N LEU S 80 " --> pdb=" O PRO S 76 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY S 81 " --> pdb=" O TYR S 77 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU S 88 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA S 89 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE S 95 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 33 through 45 removed outlier: 3.668A pdb=" N ILE T 37 " --> pdb=" O GLY T 33 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY T 38 " --> pdb=" O ALA T 34 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA T 39 " --> pdb=" O ASN T 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET T 41 " --> pdb=" O ILE T 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY T 45 " --> pdb=" O MET T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 46 through 48 No H-bonds generated for 'chain 'T' and resid 46 through 48' Processing helix chain 'T' and resid 49 through 67 removed outlier: 3.546A pdb=" N ALA T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET T 55 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR T 60 " --> pdb=" O CYS T 56 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 102 removed outlier: 3.625A pdb=" N LEU T 75 " --> pdb=" O SER T 71 " (cutoff:3.500A) Proline residue: T 76 - end of helix removed outlier: 4.804A pdb=" N LEU T 88 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA T 89 " --> pdb=" O SER T 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL T 102 " --> pdb=" O LEU T 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 35 No H-bonds generated for 'chain 'U' and resid 33 through 35' Processing helix chain 'U' and resid 36 through 44 removed outlier: 4.547A pdb=" N GLY U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 67 removed outlier: 4.030A pdb=" N ILE U 51 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY U 52 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR U 60 " --> pdb=" O CYS U 56 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 101 Proline residue: U 76 - end of helix removed outlier: 3.505A pdb=" N LEU U 84 " --> pdb=" O LEU U 80 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER U 85 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA U 96 " --> pdb=" O THR U 92 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU U 100 " --> pdb=" O ALA U 96 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE U 101 " --> pdb=" O LEU U 97 " (cutoff:3.500A) Processing helix chain 'V' and resid 33 through 43 removed outlier: 4.259A pdb=" N GLY V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA V 39 " --> pdb=" O ASN V 35 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 47 through 67 removed outlier: 4.033A pdb=" N ILE V 51 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY V 52 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER V 59 " --> pdb=" O MET V 55 " (cutoff:3.500A) Processing helix chain 'V' and resid 70 through 101 Proline residue: V 76 - end of helix removed outlier: 3.768A pdb=" N ILE V 79 " --> pdb=" O LEU V 75 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER V 85 " --> pdb=" O GLY V 81 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU V 88 " --> pdb=" O LEU V 84 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA V 96 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU V 100 " --> pdb=" O ALA V 96 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 45 removed outlier: 4.577A pdb=" N GLY W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA W 39 " --> pdb=" O ASN W 35 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET W 41 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 48 through 67 removed outlier: 3.995A pdb=" N GLY W 52 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER W 59 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 102 removed outlier: 4.465A pdb=" N ALA W 72 " --> pdb=" O PRO W 68 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LYS W 73 " --> pdb=" O ASN W 69 " (cutoff:3.500A) Proline residue: W 76 - end of helix removed outlier: 3.544A pdb=" N LEU W 80 " --> pdb=" O PRO W 76 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY W 81 " --> pdb=" O TYR W 77 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA W 96 " --> pdb=" O THR W 92 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU W 100 " --> pdb=" O ALA W 96 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE W 101 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL W 102 " --> pdb=" O LEU W 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 45 removed outlier: 4.041A pdb=" N GLY X 38 " --> pdb=" O ALA X 34 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA X 39 " --> pdb=" O ASN X 35 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET X 41 " --> pdb=" O ILE X 37 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY X 45 " --> pdb=" O MET X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 67 removed outlier: 4.201A pdb=" N GLY X 52 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 101 removed outlier: 3.510A pdb=" N LEU X 74 " --> pdb=" O MET X 70 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU X 75 " --> pdb=" O SER X 71 " (cutoff:3.500A) Proline residue: X 76 - end of helix removed outlier: 3.861A pdb=" N GLY X 81 " --> pdb=" O TYR X 77 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE X 82 " --> pdb=" O CYS X 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU X 88 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA X 96 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU X 100 " --> pdb=" O ALA X 96 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.770A pdb=" N GLY C 81 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'C' and resid 105 through 107 Processing sheet with id=C, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.519A pdb=" N LEU C 215 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N SER C 335 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 281 " --> pdb=" O SER C 335 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR C 337 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N TYR C 283 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU C 339 " --> pdb=" O TYR C 283 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.767A pdb=" N THR C 41 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.721A pdb=" N THR A 41 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ILE A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN A 73 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE A 83 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL A 71 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=G, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=H, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.464A pdb=" N ILE A 246 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 218 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA A 249 " --> pdb=" O TYR A 218 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N SER A 220 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE A 221 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASP A 284 " --> pdb=" O ILE A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=H Processing sheet with id=I, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.950A pdb=" N GLY B 30 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA B 99 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B 28 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR B 41 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 80 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 83 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 71 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.499A pdb=" N ILE B 246 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain 'F' and resid 21 through 26 removed outlier: 3.509A pdb=" N TYR F 21 " --> pdb=" O THR F 33 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP F 31 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE F 25 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 62 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE F 72 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ILE F 60 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'F' and resid 163 through 166 removed outlier: 6.689A pdb=" N ALA F 341 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N PHE F 166 " --> pdb=" O ALA F 341 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR F 343 " --> pdb=" O PHE F 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=L Processing sheet with id=M, first strand: chain 'F' and resid 226 through 230 removed outlier: 8.105A pdb=" N VAL F 193 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU F 262 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ALA F 195 " --> pdb=" O LEU F 262 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE F 264 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL F 197 " --> pdb=" O PHE F 264 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASP F 266 " --> pdb=" O VAL F 197 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER F 313 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU F 263 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR F 315 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL F 265 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 317 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'D' and resid 85 through 87 removed outlier: 6.829A pdb=" N ASP D 31 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE D 25 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL D 29 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE D 72 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N ILE D 60 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 56 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'D' and resid 94 through 96 Processing sheet with id=P, first strand: chain 'D' and resid 316 through 319 removed outlier: 6.508A pdb=" N ALA D 341 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE D 166 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N THR D 343 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'D' and resid 262 through 265 Processing sheet with id=R, first strand: chain 'E' and resid 19 through 21 Processing sheet with id=S, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.589A pdb=" N GLN E 62 " --> pdb=" O ARG E 70 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 72 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE E 60 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU E 56 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'E' and resid 94 through 96 Processing sheet with id=U, first strand: chain 'E' and resid 342 through 344 removed outlier: 8.352A pdb=" N THR E 343 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY E 164 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE E 163 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER E 316 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N LEU E 165 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLN E 318 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 261 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL E 317 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU E 263 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA E 319 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL E 265 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'M' and resid 140 through 146 removed outlier: 5.694A pdb=" N LYS M 176 " --> pdb=" O THR M 141 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ALA M 143 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL M 178 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL M 145 " --> pdb=" O VAL M 178 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU M 180 " --> pdb=" O VAL M 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=V Processing sheet with id=W, first strand: chain 'M' and resid 190 through 194 Processing sheet with id=X, first strand: chain 'G' and resid 74 through 77 removed outlier: 6.322A pdb=" N SER G 169 " --> pdb=" O HIS G 165 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'G' and resid 106 through 109 removed outlier: 7.701A pdb=" N SER G 108 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR G 128 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain 'H' and resid 85 through 88 removed outlier: 7.200A pdb=" N LEU H 51 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS H 60 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'H' and resid 75 through 78 removed outlier: 4.231A pdb=" N ARG H 70 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE H 93 " --> pdb=" O ARG H 70 " (cutoff:3.500A) 1808 hydrogen bonds defined for protein. 5244 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: 29.66 Time building geometry restraints manager: 21.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 39771 1.02 - 1.22: 66 1.22 - 1.42: 16072 1.42 - 1.62: 23546 1.62 - 1.82: 402 Bond restraints: 79857 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 6.18e+01 bond pdb=" C4 ATP E 601 " pdb=" C5 ATP E 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.46e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.45e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.38e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.27e+01 ... (remaining 79852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 144617 4.78 - 9.56: 163 9.56 - 14.35: 2 14.35 - 19.13: 4 19.13 - 23.91: 4 Bond angle restraints: 144790 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 139.87 115.96 23.91 1.00e+00 1.00e+00 5.72e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 117.31 22.56 1.00e+00 1.00e+00 5.09e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.57 22.30 1.00e+00 1.00e+00 4.97e+02 angle pdb=" PB ATP E 601 " pdb=" O3B ATP E 601 " pdb=" PG ATP E 601 " ideal model delta sigma weight residual 139.87 118.09 21.78 1.00e+00 1.00e+00 4.74e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 118.93 17.90 1.00e+00 1.00e+00 3.20e+02 ... (remaining 144785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 34367 17.78 - 35.56: 2394 35.56 - 53.35: 585 53.35 - 71.13: 166 71.13 - 88.91: 8 Dihedral angle restraints: 37520 sinusoidal: 20701 harmonic: 16819 Sorted by residual: dihedral pdb=" CA ILE A 117 " pdb=" C ILE A 117 " pdb=" N ASN A 118 " pdb=" CA ASN A 118 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA ALA D 287 " pdb=" C ALA D 287 " pdb=" N ALA D 288 " pdb=" CA ALA D 288 " ideal model delta harmonic sigma weight residual 180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP B 284 " pdb=" C ASP B 284 " pdb=" N ASP B 285 " pdb=" CA ASP B 285 " ideal model delta harmonic sigma weight residual 180.00 -160.12 -19.88 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 37517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 6030 0.098 - 0.197: 275 0.197 - 0.295: 2 0.295 - 0.394: 0 0.394 - 0.492: 1 Chirality restraints: 6308 Sorted by residual: chirality pdb=" CG LEU F 82 " pdb=" CB LEU F 82 " pdb=" CD1 LEU F 82 " pdb=" CD2 LEU F 82 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA ARG F 83 " pdb=" N ARG F 83 " pdb=" C ARG F 83 " pdb=" CB ARG F 83 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ILE M 146 " pdb=" N ILE M 146 " pdb=" C ILE M 146 " pdb=" CB ILE M 146 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 6305 not shown) Planarity restraints: 11833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 385 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C VAL F 385 " 0.072 2.00e-02 2.50e+03 pdb=" O VAL F 385 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU F 386 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 318 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C SER A 318 " 0.069 2.00e-02 2.50e+03 pdb=" O SER A 318 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG A 319 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 315 " -0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C TYR A 315 " 0.068 2.00e-02 2.50e+03 pdb=" O TYR A 315 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU A 316 " -0.023 2.00e-02 2.50e+03 ... (remaining 11830 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.07: 755 2.07 - 2.70: 133859 2.70 - 3.33: 232095 3.33 - 3.97: 294433 3.97 - 4.60: 476976 Nonbonded interactions: 1138118 Sorted by model distance: nonbonded pdb=" PB ATP A 601 " pdb="MG MG A 602 " model vdw 1.432 2.450 nonbonded pdb=" O2B ATP A 601 " pdb="MG MG A 602 " model vdw 1.443 2.050 nonbonded pdb="HG21 THR F 174 " pdb="MG MG F 602 " model vdw 1.496 1.870 nonbonded pdb=" O ASP F 450 " pdb=" HG SER F 453 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU B 207 " pdb=" HH TYR B 504 " model vdw 1.663 2.450 ... (remaining 1138113 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' selection = (chain 'B' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) selection = (chain 'E' and resid 15 through 501) selection = (chain 'F' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.130 Extract box with map and model: 2.540 Check model and map are aligned: 0.480 Set scattering table: 0.580 Process input model: 135.430 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.007 0.086 40022 Z= 0.468 Angle : 0.811 23.911 54248 Z= 0.493 Chirality : 0.046 0.492 6308 Planarity : 0.006 0.070 6928 Dihedral : 11.704 88.912 14811 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.03 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.10), residues: 5084 helix: -2.58 (0.07), residues: 2437 sheet: -3.22 (0.17), residues: 572 loop : -1.89 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 113 HIS 0.009 0.002 HIS E 377 PHE 0.023 0.002 PHE E 336 TYR 0.025 0.002 TYR F 391 ARG 0.017 0.001 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 904 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 904 time to evaluate : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 297 SER cc_start: 0.9523 (m) cc_final: 0.9255 (p) REVERT: C 430 MET cc_start: 0.7601 (mmm) cc_final: 0.7303 (tpt) REVERT: A 263 TYR cc_start: 0.8949 (m-10) cc_final: 0.8712 (m-80) REVERT: A 281 LEU cc_start: 0.9109 (tp) cc_final: 0.8820 (tp) REVERT: B 64 THR cc_start: 0.8164 (p) cc_final: 0.7930 (t) REVERT: B 350 THR cc_start: 0.8255 (p) cc_final: 0.8035 (m) REVERT: F 145 VAL cc_start: 0.8736 (t) cc_final: 0.8507 (p) REVERT: F 261 VAL cc_start: 0.8867 (t) cc_final: 0.8666 (m) REVERT: F 315 THR cc_start: 0.8354 (m) cc_final: 0.8082 (p) REVERT: F 325 ASP cc_start: 0.8082 (m-30) cc_final: 0.6963 (t70) REVERT: E 179 GLU cc_start: 0.6453 (tp30) cc_final: 0.6114 (tp30) REVERT: E 491 ARG cc_start: 0.8384 (mtt180) cc_final: 0.8168 (mtm180) REVERT: L 153 GLN cc_start: 0.8342 (mm-40) cc_final: 0.8126 (mm-40) REVERT: K 53 ASP cc_start: 0.7435 (t70) cc_final: 0.6770 (t0) REVERT: K 141 ILE cc_start: 0.8714 (mm) cc_final: 0.8386 (mm) REVERT: M 48 SER cc_start: 0.7875 (m) cc_final: 0.7477 (t) REVERT: G 300 LYS cc_start: 0.7655 (tttt) cc_final: 0.7375 (mmtm) REVERT: H 172 GLU cc_start: 0.9047 (tt0) cc_final: 0.8562 (tp30) REVERT: O 41 MET cc_start: 0.8063 (mtp) cc_final: 0.7759 (mtp) REVERT: O 95 ILE cc_start: 0.8999 (mt) cc_final: 0.8654 (tt) REVERT: P 56 CYS cc_start: 0.8919 (t) cc_final: 0.8613 (p) REVERT: Q 82 PHE cc_start: 0.8190 (t80) cc_final: 0.7714 (t80) REVERT: R 86 GLU cc_start: 0.8821 (tp30) cc_final: 0.8435 (tp30) REVERT: T 56 CYS cc_start: 0.8644 (t) cc_final: 0.8421 (t) REVERT: U 37 ILE cc_start: 0.8916 (mt) cc_final: 0.8598 (tt) REVERT: U 51 ILE cc_start: 0.9352 (mt) cc_final: 0.9143 (tp) REVERT: U 56 CYS cc_start: 0.9038 (t) cc_final: 0.8780 (t) REVERT: U 61 MET cc_start: 0.9300 (mtt) cc_final: 0.8986 (mtp) REVERT: U 92 THR cc_start: 0.9016 (m) cc_final: 0.8811 (p) REVERT: W 29 VAL cc_start: 0.9462 (m) cc_final: 0.9091 (p) REVERT: W 55 MET cc_start: 0.8863 (ttm) cc_final: 0.8312 (ttm) REVERT: X 55 MET cc_start: 0.8614 (ttm) cc_final: 0.8042 (tpp) REVERT: X 90 LEU cc_start: 0.9014 (tt) cc_final: 0.8803 (tt) outliers start: 0 outliers final: 0 residues processed: 904 average time/residue: 1.1309 time to fit residues: 1625.2286 Evaluate side-chains 533 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 533 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 259 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 397 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 295 optimal weight: 4.9990 chunk 460 optimal weight: 0.0670 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN C 178 GLN C 395 ASN C 460 ASN C 529 ASN A 200 ASN A 460 ASN B 200 ASN B 356 ASN B 460 ASN B 469 GLN B 550 GLN F 18 GLN D 62 GLN D 115 GLN D 128 HIS D 231 GLN L 162 ASN H 124 ASN U 69 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.099493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073184 restraints weight = 323348.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.074564 restraints weight = 151341.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.075282 restraints weight = 92813.701| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40022 Z= 0.210 Angle : 0.574 6.759 54248 Z= 0.307 Chirality : 0.041 0.166 6308 Planarity : 0.005 0.069 6928 Dihedral : 6.029 68.941 5686 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 0.93 % Allowed : 8.65 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.11), residues: 5084 helix: -0.81 (0.10), residues: 2489 sheet: -2.85 (0.18), residues: 579 loop : -1.45 (0.14), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 224 HIS 0.004 0.001 HIS A 317 PHE 0.028 0.001 PHE P 82 TYR 0.016 0.001 TYR G 267 ARG 0.010 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 639 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 600 time to evaluate : 5.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 281 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.8836 (mp) REVERT: C 297 SER cc_start: 0.9545 (m) cc_final: 0.9256 (p) REVERT: A 263 TYR cc_start: 0.9059 (m-10) cc_final: 0.8789 (m-80) REVERT: A 281 LEU cc_start: 0.9005 (tp) cc_final: 0.8668 (tp) REVERT: A 449 MET cc_start: 0.8125 (ttp) cc_final: 0.7896 (ttp) REVERT: A 497 MET cc_start: 0.8738 (mmm) cc_final: 0.8469 (mmt) REVERT: B 64 THR cc_start: 0.8314 (p) cc_final: 0.8053 (t) REVERT: B 350 THR cc_start: 0.8446 (p) cc_final: 0.8228 (t) REVERT: F 74 MET cc_start: 0.7204 (mtm) cc_final: 0.6949 (mtm) REVERT: F 206 ASP cc_start: 0.8053 (m-30) cc_final: 0.7829 (t0) REVERT: F 266 ASP cc_start: 0.7628 (t0) cc_final: 0.7395 (m-30) REVERT: F 325 ASP cc_start: 0.8095 (m-30) cc_final: 0.7277 (t70) REVERT: F 368 MET cc_start: 0.8137 (tpp) cc_final: 0.7927 (ttm) REVERT: D 410 ASP cc_start: 0.8192 (m-30) cc_final: 0.7940 (m-30) REVERT: D 424 MET cc_start: 0.8416 (mmt) cc_final: 0.8177 (mmt) REVERT: D 469 MET cc_start: 0.7581 (tpp) cc_final: 0.7267 (tpp) REVERT: E 179 GLU cc_start: 0.6397 (tp30) cc_final: 0.6181 (tp30) REVERT: J 70 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7251 (t70) REVERT: K 102 MET cc_start: 0.7776 (tpt) cc_final: 0.7449 (tpt) REVERT: M 48 SER cc_start: 0.7913 (m) cc_final: 0.7540 (t) REVERT: M 136 GLU cc_start: 0.7717 (tt0) cc_final: 0.7460 (tp30) REVERT: G 300 LYS cc_start: 0.7639 (tttt) cc_final: 0.7380 (mmtm) REVERT: H 138 LYS cc_start: 0.8329 (tttt) cc_final: 0.8040 (ttmt) REVERT: H 172 GLU cc_start: 0.9137 (tt0) cc_final: 0.8623 (tp30) REVERT: O 37 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (tt) REVERT: O 61 MET cc_start: 0.8792 (mtt) cc_final: 0.8535 (mtp) REVERT: O 95 ILE cc_start: 0.8984 (mt) cc_final: 0.8563 (tt) REVERT: P 56 CYS cc_start: 0.8892 (t) cc_final: 0.8625 (p) REVERT: P 61 MET cc_start: 0.9133 (mtt) cc_final: 0.8407 (mtp) REVERT: P 73 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8448 (tmtt) REVERT: R 86 GLU cc_start: 0.8817 (tp30) cc_final: 0.8362 (tp30) REVERT: T 56 CYS cc_start: 0.8539 (t) cc_final: 0.8289 (t) REVERT: U 41 MET cc_start: 0.9115 (mtp) cc_final: 0.7765 (mtp) REVERT: U 51 ILE cc_start: 0.9239 (mt) cc_final: 0.8987 (tp) REVERT: U 61 MET cc_start: 0.9147 (mtt) cc_final: 0.8665 (mtp) REVERT: W 35 ASN cc_start: 0.8899 (p0) cc_final: 0.8636 (p0) REVERT: W 55 MET cc_start: 0.8763 (ttm) cc_final: 0.8223 (ttm) outliers start: 39 outliers final: 25 residues processed: 625 average time/residue: 1.0121 time to fit residues: 1026.8762 Evaluate side-chains 534 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 506 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain O residue 37 ILE Chi-restraints excluded: chain U residue 69 ASN Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 420 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 477 optimal weight: 4.9990 chunk 421 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 345 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 385 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 442 GLN B 501 ASN B 512 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN F 188 HIS D 231 GLN D 233 ASN ** L 96 ASN ** 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 = 0.3637 r_free = 0.3637 target = 0.094757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.068100 restraints weight = 327783.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068758 restraints weight = 155011.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068772 restraints weight = 103279.804| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 40022 Z= 0.420 Angle : 0.654 9.047 54248 Z= 0.351 Chirality : 0.043 0.202 6308 Planarity : 0.005 0.082 6928 Dihedral : 6.190 84.509 5686 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 1.61 % Allowed : 10.19 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.11), residues: 5084 helix: -0.08 (0.10), residues: 2484 sheet: -2.93 (0.18), residues: 585 loop : -1.36 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 224 HIS 0.008 0.002 HIS E 377 PHE 0.030 0.002 PHE P 82 TYR 0.018 0.002 TYR A 165 ARG 0.006 0.001 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 579 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 512 time to evaluate : 4.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ASN cc_start: 0.8383 (m110) cc_final: 0.8098 (m110) REVERT: C 281 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 263 TYR cc_start: 0.9281 (m-10) cc_final: 0.9052 (m-80) REVERT: A 449 MET cc_start: 0.8341 (ttp) cc_final: 0.8128 (ttp) REVERT: B 350 THR cc_start: 0.8512 (p) cc_final: 0.8293 (t) REVERT: F 59 GLU cc_start: 0.7436 (tt0) cc_final: 0.7156 (tt0) REVERT: E 179 GLU cc_start: 0.6933 (tp30) cc_final: 0.6468 (tp30) REVERT: J 70 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7547 (t70) REVERT: K 102 MET cc_start: 0.8147 (tpt) cc_final: 0.7835 (tpt) REVERT: G 300 LYS cc_start: 0.7673 (tttt) cc_final: 0.7335 (mmtm) REVERT: H 172 GLU cc_start: 0.9298 (tt0) cc_final: 0.8679 (tp30) REVERT: O 61 MET cc_start: 0.8971 (mtt) cc_final: 0.8704 (mtp) REVERT: O 95 ILE cc_start: 0.9016 (mt) cc_final: 0.8610 (tt) REVERT: P 41 MET cc_start: 0.6922 (tpt) cc_final: 0.6582 (tpp) REVERT: P 56 CYS cc_start: 0.9054 (t) cc_final: 0.8742 (p) REVERT: P 61 MET cc_start: 0.9227 (mtt) cc_final: 0.8933 (mtp) REVERT: P 73 LYS cc_start: 0.9252 (mtpt) cc_final: 0.8506 (tmtt) REVERT: R 55 MET cc_start: 0.9078 (ttp) cc_final: 0.8848 (ttp) REVERT: R 86 GLU cc_start: 0.8924 (tp30) cc_final: 0.8424 (tp30) REVERT: U 51 ILE cc_start: 0.9296 (mt) cc_final: 0.9095 (tp) REVERT: V 55 MET cc_start: 0.9050 (ttm) cc_final: 0.8766 (ttm) REVERT: W 35 ASN cc_start: 0.9201 (p0) cc_final: 0.8862 (p0) REVERT: W 55 MET cc_start: 0.8837 (ttm) cc_final: 0.8280 (ttm) REVERT: W 82 PHE cc_start: 0.8950 (t80) cc_final: 0.8717 (t80) outliers start: 67 outliers final: 55 residues processed: 553 average time/residue: 0.9932 time to fit residues: 900.1807 Evaluate side-chains 517 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 460 time to evaluate : 4.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 169 ASP Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 158 CYS Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain M residue 226 SER Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 61 MET Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain W residue 41 MET Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 434 optimal weight: 10.0000 chunk 252 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 429 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 466 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 428 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 501 ASN C 529 ASN B 200 ASN B 356 ASN L 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.095609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.069080 restraints weight = 324021.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.069615 restraints weight = 155779.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.069785 restraints weight = 102577.140| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40022 Z= 0.244 Angle : 0.544 8.261 54248 Z= 0.286 Chirality : 0.041 0.158 6308 Planarity : 0.004 0.071 6928 Dihedral : 5.872 86.479 5686 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Rotamer: Outliers : 1.34 % Allowed : 11.67 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 5084 helix: 0.34 (0.10), residues: 2508 sheet: -2.72 (0.19), residues: 580 loop : -1.13 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 10 HIS 0.004 0.001 HIS E 377 PHE 0.015 0.001 PHE P 82 TYR 0.015 0.001 TYR J 52 ARG 0.004 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 560 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 504 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ASN cc_start: 0.8485 (m110) cc_final: 0.8234 (m110) REVERT: C 281 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.8821 (mp) REVERT: C 297 SER cc_start: 0.9486 (m) cc_final: 0.9243 (p) REVERT: A 281 LEU cc_start: 0.9036 (tp) cc_final: 0.8650 (tp) REVERT: B 324 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8520 (p) REVERT: F 151 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7955 (mt) REVERT: F 266 ASP cc_start: 0.8090 (t0) cc_final: 0.7689 (m-30) REVERT: D 410 ASP cc_start: 0.8236 (m-30) cc_final: 0.7861 (m-30) REVERT: E 109 MET cc_start: 0.8287 (mpp) cc_final: 0.7679 (mpp) REVERT: E 148 ILE cc_start: 0.8590 (mt) cc_final: 0.8296 (mt) REVERT: E 179 GLU cc_start: 0.6945 (tp30) cc_final: 0.6415 (tp30) REVERT: J 70 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7777 (t70) REVERT: K 102 MET cc_start: 0.8173 (tpt) cc_final: 0.7771 (tpt) REVERT: M 51 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8667 (t70) REVERT: G 300 LYS cc_start: 0.7676 (tttt) cc_final: 0.7348 (mmtm) REVERT: H 172 GLU cc_start: 0.9194 (tt0) cc_final: 0.8555 (tp30) REVERT: O 61 MET cc_start: 0.8991 (mtt) cc_final: 0.8740 (mtp) REVERT: O 95 ILE cc_start: 0.8975 (mt) cc_final: 0.8568 (tt) REVERT: P 41 MET cc_start: 0.6812 (tpt) cc_final: 0.6523 (tpp) REVERT: P 56 CYS cc_start: 0.8951 (t) cc_final: 0.8702 (p) REVERT: P 61 MET cc_start: 0.9146 (mtt) cc_final: 0.8455 (mtp) REVERT: P 73 LYS cc_start: 0.9269 (mtpt) cc_final: 0.8528 (tmtt) REVERT: Q 82 PHE cc_start: 0.8338 (t80) cc_final: 0.8009 (t80) REVERT: R 55 MET cc_start: 0.8972 (ttp) cc_final: 0.8487 (tmm) REVERT: R 73 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8637 (mmmm) REVERT: R 86 GLU cc_start: 0.8804 (tp30) cc_final: 0.8307 (tp30) REVERT: V 82 PHE cc_start: 0.8694 (t80) cc_final: 0.7315 (t80) REVERT: W 35 ASN cc_start: 0.9055 (p0) cc_final: 0.8729 (p0) REVERT: W 55 MET cc_start: 0.8830 (ttm) cc_final: 0.8275 (ttm) outliers start: 56 outliers final: 39 residues processed: 545 average time/residue: 0.9920 time to fit residues: 882.9098 Evaluate side-chains 510 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 466 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain T residue 56 CYS Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 439 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 398 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN B 200 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.095416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.068951 restraints weight = 324084.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069428 restraints weight = 157131.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069755 restraints weight = 101908.848| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40022 Z= 0.233 Angle : 0.533 8.470 54248 Z= 0.280 Chirality : 0.040 0.201 6308 Planarity : 0.004 0.066 6928 Dihedral : 5.792 89.893 5686 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 1.41 % Allowed : 12.34 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 5084 helix: 0.55 (0.10), residues: 2548 sheet: -2.63 (0.19), residues: 583 loop : -1.09 (0.15), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 121 HIS 0.004 0.001 HIS E 377 PHE 0.029 0.001 PHE V 82 TYR 0.015 0.001 TYR V 27 ARG 0.003 0.000 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 538 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 479 time to evaluate : 5.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 87 ASN cc_start: 0.8481 (m110) cc_final: 0.8262 (m110) REVERT: C 281 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8787 (mp) REVERT: C 297 SER cc_start: 0.9476 (m) cc_final: 0.9243 (p) REVERT: A 281 LEU cc_start: 0.9046 (tp) cc_final: 0.8704 (tp) REVERT: B 324 SER cc_start: 0.8987 (OUTLIER) cc_final: 0.8572 (p) REVERT: F 151 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7961 (mt) REVERT: D 410 ASP cc_start: 0.8220 (m-30) cc_final: 0.7852 (m-30) REVERT: E 109 MET cc_start: 0.8235 (mpp) cc_final: 0.7840 (mtp) REVERT: J 70 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7743 (t70) REVERT: K 102 MET cc_start: 0.8193 (tpt) cc_final: 0.7775 (tpt) REVERT: M 51 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8714 (t70) REVERT: G 300 LYS cc_start: 0.7695 (tttt) cc_final: 0.7345 (mmtm) REVERT: H 172 GLU cc_start: 0.9207 (tt0) cc_final: 0.8575 (tp30) REVERT: O 95 ILE cc_start: 0.8980 (mt) cc_final: 0.8580 (tt) REVERT: P 41 MET cc_start: 0.6787 (tpt) cc_final: 0.6556 (tpp) REVERT: P 56 CYS cc_start: 0.9026 (t) cc_final: 0.8755 (p) REVERT: P 61 MET cc_start: 0.9168 (mtt) cc_final: 0.8464 (mtp) REVERT: P 73 LYS cc_start: 0.9263 (mtpt) cc_final: 0.8523 (tmtt) REVERT: R 55 MET cc_start: 0.8970 (ttp) cc_final: 0.8528 (tmm) REVERT: R 73 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8659 (mmmm) REVERT: R 86 GLU cc_start: 0.8812 (tp30) cc_final: 0.8295 (tp30) REVERT: U 51 ILE cc_start: 0.9215 (mp) cc_final: 0.8635 (tp) REVERT: U 70 MET cc_start: 0.9229 (mmm) cc_final: 0.8792 (mmm) REVERT: V 55 MET cc_start: 0.8993 (ttm) cc_final: 0.8714 (ttm) REVERT: W 35 ASN cc_start: 0.9135 (p0) cc_final: 0.8813 (p0) REVERT: W 55 MET cc_start: 0.8800 (ttm) cc_final: 0.8328 (ttm) outliers start: 59 outliers final: 48 residues processed: 518 average time/residue: 0.9994 time to fit residues: 853.1272 Evaluate side-chains 513 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 460 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 449 MET Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 51 ILE Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 502 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 367 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 405 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.067421 restraints weight = 325178.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.068013 restraints weight = 153387.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068504 restraints weight = 104027.293| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 40022 Z= 0.307 Angle : 0.562 7.620 54248 Z= 0.296 Chirality : 0.041 0.196 6308 Planarity : 0.004 0.065 6928 Dihedral : 5.928 81.656 5686 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.04 % Favored : 94.94 % Rotamer: Outliers : 1.80 % Allowed : 12.37 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 5084 helix: 0.68 (0.10), residues: 2546 sheet: -2.61 (0.20), residues: 585 loop : -1.04 (0.14), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 121 HIS 0.008 0.001 HIS A 111 PHE 0.032 0.001 PHE F 166 TYR 0.016 0.001 TYR B 504 ARG 0.008 0.000 ARG C 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 544 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 469 time to evaluate : 5.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 281 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 297 SER cc_start: 0.9396 (m) cc_final: 0.9152 (p) REVERT: C 301 ARG cc_start: 0.8724 (mmm-85) cc_final: 0.8509 (tpp-160) REVERT: A 281 LEU cc_start: 0.9164 (tp) cc_final: 0.8830 (tp) REVERT: B 324 SER cc_start: 0.9260 (OUTLIER) cc_final: 0.8897 (p) REVERT: F 36 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7310 (t0) REVERT: F 151 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7976 (mp) REVERT: F 266 ASP cc_start: 0.8258 (t0) cc_final: 0.8027 (t0) REVERT: E 109 MET cc_start: 0.8169 (mpp) cc_final: 0.7889 (mtp) REVERT: J 70 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7782 (t70) REVERT: K 102 MET cc_start: 0.8279 (tpt) cc_final: 0.7864 (tpt) REVERT: M 51 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8718 (t70) REVERT: G 300 LYS cc_start: 0.7729 (tttt) cc_final: 0.7348 (mmtm) REVERT: H 172 GLU cc_start: 0.9345 (tt0) cc_final: 0.8619 (tp30) REVERT: O 55 MET cc_start: 0.8285 (tpt) cc_final: 0.8070 (tpt) REVERT: O 95 ILE cc_start: 0.9036 (mt) cc_final: 0.8656 (tt) REVERT: P 41 MET cc_start: 0.6784 (tpt) cc_final: 0.6557 (tpp) REVERT: P 56 CYS cc_start: 0.9167 (t) cc_final: 0.8817 (t) REVERT: P 61 MET cc_start: 0.9247 (mtt) cc_final: 0.8580 (mtp) REVERT: P 73 LYS cc_start: 0.9276 (mtpt) cc_final: 0.8496 (tmtt) REVERT: R 55 MET cc_start: 0.9041 (ttp) cc_final: 0.8678 (tmm) REVERT: R 86 GLU cc_start: 0.8917 (tp30) cc_final: 0.8393 (tp30) REVERT: R 91 PHE cc_start: 0.8579 (m-80) cc_final: 0.8122 (m-80) REVERT: U 70 MET cc_start: 0.9323 (mmm) cc_final: 0.8831 (mmm) REVERT: V 55 MET cc_start: 0.9074 (ttm) cc_final: 0.8737 (ttm) REVERT: W 35 ASN cc_start: 0.9206 (p0) cc_final: 0.8888 (p0) REVERT: W 55 MET cc_start: 0.8850 (ttm) cc_final: 0.8397 (ttm) REVERT: X 55 MET cc_start: 0.8494 (tpp) cc_final: 0.8143 (tpt) outliers start: 75 outliers final: 58 residues processed: 521 average time/residue: 1.0197 time to fit residues: 877.9985 Evaluate side-chains 522 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 458 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 69 ASN Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 140 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 160 optimal weight: 0.8980 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 426 optimal weight: 10.0000 chunk 329 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 212 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.067443 restraints weight = 324461.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.068095 restraints weight = 153305.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.068386 restraints weight = 104057.345| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40022 Z= 0.258 Angle : 0.539 7.825 54248 Z= 0.282 Chirality : 0.040 0.173 6308 Planarity : 0.004 0.063 6928 Dihedral : 5.791 77.203 5686 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.64 % Favored : 95.34 % Rotamer: Outliers : 1.77 % Allowed : 12.94 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.12), residues: 5084 helix: 0.82 (0.10), residues: 2543 sheet: -2.52 (0.20), residues: 580 loop : -0.93 (0.15), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 121 HIS 0.004 0.001 HIS E 377 PHE 0.014 0.001 PHE F 166 TYR 0.014 0.001 TYR J 52 ARG 0.004 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 468 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 281 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8961 (mp) REVERT: C 297 SER cc_start: 0.9418 (m) cc_final: 0.9217 (p) REVERT: C 301 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8496 (tpp-160) REVERT: C 439 LEU cc_start: 0.8686 (mt) cc_final: 0.8471 (mp) REVERT: A 281 LEU cc_start: 0.9137 (tp) cc_final: 0.8811 (tp) REVERT: B 324 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.8931 (p) REVERT: F 36 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7316 (t0) REVERT: F 266 ASP cc_start: 0.8226 (t0) cc_final: 0.8012 (t0) REVERT: D 410 ASP cc_start: 0.8257 (m-30) cc_final: 0.7917 (m-30) REVERT: E 109 MET cc_start: 0.8135 (mpp) cc_final: 0.7871 (mtp) REVERT: E 212 MET cc_start: 0.8409 (mtt) cc_final: 0.8108 (mtt) REVERT: J 70 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7624 (t70) REVERT: K 102 MET cc_start: 0.8250 (tpt) cc_final: 0.7909 (tpt) REVERT: M 51 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8746 (t70) REVERT: M 216 LYS cc_start: 0.7003 (mtmt) cc_final: 0.6529 (mmmt) REVERT: G 300 LYS cc_start: 0.7756 (tttt) cc_final: 0.7355 (mmtm) REVERT: H 172 GLU cc_start: 0.9281 (tt0) cc_final: 0.8584 (tp30) REVERT: O 55 MET cc_start: 0.8239 (tpt) cc_final: 0.7984 (tpt) REVERT: O 95 ILE cc_start: 0.9002 (mt) cc_final: 0.8627 (tt) REVERT: P 41 MET cc_start: 0.6763 (tpt) cc_final: 0.6560 (tpp) REVERT: P 61 MET cc_start: 0.9172 (mtt) cc_final: 0.8499 (mtp) REVERT: P 73 LYS cc_start: 0.9256 (mtpt) cc_final: 0.8513 (tmtt) REVERT: R 55 MET cc_start: 0.8967 (ttp) cc_final: 0.8621 (tmm) REVERT: R 70 MET cc_start: 0.8413 (ttp) cc_final: 0.7277 (ttp) REVERT: R 73 LYS cc_start: 0.9025 (mtmm) cc_final: 0.8473 (ttpp) REVERT: R 86 GLU cc_start: 0.8777 (tp30) cc_final: 0.8246 (tp30) REVERT: R 91 PHE cc_start: 0.8557 (m-80) cc_final: 0.8052 (m-80) REVERT: U 61 MET cc_start: 0.9093 (mtt) cc_final: 0.8616 (mtp) REVERT: U 70 MET cc_start: 0.9243 (mmm) cc_final: 0.8795 (mmm) REVERT: V 55 MET cc_start: 0.9011 (ttm) cc_final: 0.8684 (ttm) REVERT: W 35 ASN cc_start: 0.9142 (p0) cc_final: 0.8846 (p0) REVERT: W 55 MET cc_start: 0.8848 (ttm) cc_final: 0.8374 (ttm) REVERT: X 55 MET cc_start: 0.8444 (tpp) cc_final: 0.8098 (tpt) outliers start: 74 outliers final: 61 residues processed: 520 average time/residue: 0.9826 time to fit residues: 840.3086 Evaluate side-chains 523 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 457 time to evaluate : 4.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 95 ILE Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 136 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 374 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 337 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.093629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.067295 restraints weight = 326873.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067044 restraints weight = 185560.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.067388 restraints weight = 126568.328| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 40022 Z= 0.310 Angle : 0.564 10.209 54248 Z= 0.297 Chirality : 0.041 0.168 6308 Planarity : 0.004 0.062 6928 Dihedral : 5.846 83.249 5686 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.55 % Favored : 94.43 % Rotamer: Outliers : 1.80 % Allowed : 13.45 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 5084 helix: 0.84 (0.10), residues: 2540 sheet: -2.58 (0.20), residues: 598 loop : -0.93 (0.15), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 121 HIS 0.006 0.001 HIS E 377 PHE 0.025 0.001 PHE F 166 TYR 0.016 0.001 TYR B 159 ARG 0.004 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 542 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 467 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 281 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8950 (mp) REVERT: A 281 LEU cc_start: 0.9153 (tp) cc_final: 0.8811 (tp) REVERT: B 31 PHE cc_start: 0.7960 (p90) cc_final: 0.7690 (p90) REVERT: B 324 SER cc_start: 0.9405 (OUTLIER) cc_final: 0.9076 (p) REVERT: F 36 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7374 (t0) REVERT: F 151 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7867 (mt) REVERT: J 70 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7692 (t70) REVERT: K 102 MET cc_start: 0.8326 (tpt) cc_final: 0.7973 (tpt) REVERT: M 51 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8757 (t70) REVERT: M 216 LYS cc_start: 0.7042 (mtmt) cc_final: 0.6580 (mmmt) REVERT: G 300 LYS cc_start: 0.7913 (tttt) cc_final: 0.7444 (mmtm) REVERT: H 102 LYS cc_start: 0.8558 (ptpp) cc_final: 0.8001 (pttm) REVERT: H 172 GLU cc_start: 0.9254 (tt0) cc_final: 0.8484 (tp30) REVERT: O 95 ILE cc_start: 0.9035 (mt) cc_final: 0.8656 (tt) REVERT: P 28 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7387 (tp30) REVERT: P 56 CYS cc_start: 0.8962 (t) cc_final: 0.8626 (t) REVERT: P 61 MET cc_start: 0.9146 (mtt) cc_final: 0.8484 (mtp) REVERT: P 73 LYS cc_start: 0.9287 (mtpt) cc_final: 0.8626 (tmtt) REVERT: Q 82 PHE cc_start: 0.8311 (t80) cc_final: 0.7980 (t80) REVERT: R 73 LYS cc_start: 0.9089 (mtmm) cc_final: 0.8807 (mmmt) REVERT: R 86 GLU cc_start: 0.8714 (tp30) cc_final: 0.8196 (tp30) REVERT: R 91 PHE cc_start: 0.8575 (m-80) cc_final: 0.8062 (m-80) REVERT: U 61 MET cc_start: 0.9092 (mtt) cc_final: 0.8605 (mtp) REVERT: U 70 MET cc_start: 0.9176 (mmm) cc_final: 0.8726 (mmm) REVERT: V 55 MET cc_start: 0.8959 (ttm) cc_final: 0.8632 (ttm) REVERT: W 35 ASN cc_start: 0.9094 (p0) cc_final: 0.8757 (p0) REVERT: W 55 MET cc_start: 0.8871 (ttm) cc_final: 0.8406 (ttm) outliers start: 75 outliers final: 66 residues processed: 523 average time/residue: 0.9948 time to fit residues: 860.6706 Evaluate side-chains 525 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 453 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 373 optimal weight: 0.0270 chunk 210 optimal weight: 2.9990 chunk 475 optimal weight: 20.0000 chunk 349 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 356 optimal weight: 6.9990 chunk 203 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066776 restraints weight = 324960.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.067462 restraints weight = 146629.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.067752 restraints weight = 102439.190| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40022 Z= 0.302 Angle : 0.561 8.498 54248 Z= 0.295 Chirality : 0.041 0.182 6308 Planarity : 0.004 0.061 6928 Dihedral : 5.851 85.856 5686 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.23 % Favored : 94.75 % Rotamer: Outliers : 1.82 % Allowed : 13.93 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.93 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 5084 helix: 0.86 (0.10), residues: 2548 sheet: -2.60 (0.20), residues: 598 loop : -0.92 (0.15), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 224 HIS 0.006 0.001 HIS E 377 PHE 0.022 0.001 PHE F 166 TYR 0.015 0.001 TYR B 159 ARG 0.004 0.000 ARG M 37 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 537 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 461 time to evaluate : 5.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 281 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 281 LEU cc_start: 0.9134 (tp) cc_final: 0.8813 (tp) REVERT: B 31 PHE cc_start: 0.7939 (p90) cc_final: 0.7686 (p90) REVERT: B 324 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9071 (p) REVERT: F 36 ASP cc_start: 0.7855 (OUTLIER) cc_final: 0.7395 (t0) REVERT: E 212 MET cc_start: 0.8443 (mtt) cc_final: 0.8196 (mtt) REVERT: J 70 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7744 (t70) REVERT: K 102 MET cc_start: 0.8365 (tpt) cc_final: 0.8038 (tpt) REVERT: M 51 ASP cc_start: 0.8988 (OUTLIER) cc_final: 0.8787 (t70) REVERT: M 216 LYS cc_start: 0.7091 (mtmt) cc_final: 0.6646 (mmmt) REVERT: G 300 LYS cc_start: 0.7884 (tttt) cc_final: 0.7408 (mmtm) REVERT: H 102 LYS cc_start: 0.8689 (ptpp) cc_final: 0.8150 (pttm) REVERT: H 172 GLU cc_start: 0.9297 (tt0) cc_final: 0.8527 (tp30) REVERT: O 95 ILE cc_start: 0.9064 (mt) cc_final: 0.8677 (tt) REVERT: P 28 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7421 (tp30) REVERT: P 56 CYS cc_start: 0.9056 (t) cc_final: 0.8730 (t) REVERT: P 61 MET cc_start: 0.9195 (mtt) cc_final: 0.8534 (mtp) REVERT: P 73 LYS cc_start: 0.9286 (mtpt) cc_final: 0.8631 (tmtt) REVERT: P 74 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8247 (mm) REVERT: R 70 MET cc_start: 0.8510 (ttp) cc_final: 0.8308 (ttp) REVERT: R 86 GLU cc_start: 0.8776 (tp30) cc_final: 0.8240 (tp30) REVERT: R 91 PHE cc_start: 0.8550 (m-80) cc_final: 0.8026 (m-80) REVERT: S 55 MET cc_start: 0.9032 (mmm) cc_final: 0.8726 (mmm) REVERT: U 61 MET cc_start: 0.9139 (mtt) cc_final: 0.8694 (mtp) REVERT: U 70 MET cc_start: 0.9216 (mmm) cc_final: 0.8747 (mmm) REVERT: V 55 MET cc_start: 0.8993 (ttm) cc_final: 0.8651 (ttm) REVERT: W 35 ASN cc_start: 0.9049 (p0) cc_final: 0.8685 (p0) REVERT: W 55 MET cc_start: 0.8903 (ttm) cc_final: 0.8382 (ttm) REVERT: W 101 PHE cc_start: 0.7785 (m-80) cc_final: 0.7169 (m-80) REVERT: X 35 ASN cc_start: 0.8927 (p0) cc_final: 0.8644 (p0) outliers start: 76 outliers final: 68 residues processed: 516 average time/residue: 1.0084 time to fit residues: 854.0518 Evaluate side-chains 532 residues out of total 4172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 458 time to evaluate : 4.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 541 GLU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain F residue 36 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 273 GLN Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 337 SER Chi-restraints excluded: chain E residue 394 LEU Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 70 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 109 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 39 THR Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 103 ASP Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 GLU Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain Q residue 56 CYS Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain T residue 86 GLU Chi-restraints excluded: chain T residue 98 LEU Chi-restraints excluded: chain U residue 41 MET Chi-restraints excluded: chain U residue 97 LEU Chi-restraints excluded: chain U residue 98 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 74 LEU Chi-restraints excluded: chain W residue 94 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 71 optimal weight: 0.0070 chunk 452 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 286 optimal weight: 1.9990 chunk 281 optimal weight: 0.1980 chunk 276 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 472 optimal weight: 8.9990 chunk 269 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: