Starting phenix.real_space_refine on Wed Sep 25 04:21:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/09_2024/6rdw_4833.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/09_2024/6rdw_4833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/09_2024/6rdw_4833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/09_2024/6rdw_4833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/09_2024/6rdw_4833.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdw_4833/09_2024/6rdw_4833.cif" } resolution = 3.8 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= -0.000 sd= 1.005 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 Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 421 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain breaks: 1 Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" 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: "U" 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: "V" 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: "X" 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: "Y" 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} Time building chain proxies: 22.31, per 1000 atoms: 0.42 Number of scatterers: 53748 At special positions: 0 Unit cell: (211.653, 134.784, 260.091, 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) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.43 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... Secondary structure from input PDB file: 308 helices and 32 sheets defined 57.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.35 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.968A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 3 through 8' Processing helix chain '0' and resid 17 through 31 removed outlier: 3.649A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 78 through 83 removed outlier: 4.613A pdb=" N HIS 1 82 " --> pdb=" O LEU 1 78 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 88 Processing helix chain '1' and resid 96 through 100 removed outlier: 3.983A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 141 removed outlier: 3.916A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.787A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 203 removed outlier: 3.730A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 223 Processing helix chain '1' and resid 241 through 271 removed outlier: 3.527A pdb=" N SER 1 271 " --> pdb=" O ARG 1 267 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 4.035A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 279 through 286 removed outlier: 3.771A pdb=" N PHE 1 282 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP 1 283 " --> pdb=" O ASN 1 280 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA 1 284 " --> pdb=" O GLU 1 281 " (cutoff:3.500A) Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 316 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.840A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 removed outlier: 3.596A pdb=" N SER 1 333 " --> pdb=" O LYS 1 330 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 removed outlier: 3.546A pdb=" N LEU 1 342 " --> pdb=" O SER 1 338 " (cutoff:3.500A) Processing helix chain '1' and resid 353 through 362 removed outlier: 3.571A pdb=" N ALA 1 357 " --> pdb=" O ASP 1 353 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.741A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 Processing helix chain '1' and resid 435 through 445 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.838A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.623A pdb=" N SER 1 494 " --> pdb=" O TYR 1 490 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.779A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 removed outlier: 3.585A pdb=" N ILE 1 553 " --> pdb=" O ASP 1 549 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '2' and resid 7 through 17 removed outlier: 3.532A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.512A pdb=" N VAL 2 29 " --> pdb=" O SER 2 25 " (cutoff:3.500A) Processing helix chain '2' and resid 45 through 58 Processing helix chain '2' and resid 62 through 77 removed outlier: 3.751A pdb=" N LEU 2 66 " --> pdb=" O ASP 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.542A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 4.184A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 155 through 168 removed outlier: 3.648A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 197 removed outlier: 4.794A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 200 No H-bonds generated for 'chain '2' and resid 198 through 200' Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 227 through 234 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.778A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.839A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 295 removed outlier: 3.539A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 4.062A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 Processing helix chain '2' and resid 345 through 356 Processing helix chain '2' and resid 396 through 408 removed outlier: 3.919A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 removed outlier: 3.688A pdb=" N GLU 2 422 " --> pdb=" O ALA 2 418 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 418 through 422' Processing helix chain '2' and resid 426 through 442 removed outlier: 3.912A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 88 Processing helix chain '3' and resid 102 through 113 removed outlier: 3.910A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 128 removed outlier: 3.961A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 3 128 " --> pdb=" O PHE 3 124 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 removed outlier: 4.279A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 187 removed outlier: 3.751A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 Processing helix chain '3' and resid 211 through 214 removed outlier: 3.833A pdb=" N ALA 3 214 " --> pdb=" O PRO 3 211 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 211 through 214' Processing helix chain '3' and resid 215 through 230 removed outlier: 3.892A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 245 through 250 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.539A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 284 removed outlier: 4.388A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 removed outlier: 3.917A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.699A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 3.596A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.991A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 Processing helix chain '4' and resid 131 through 150 removed outlier: 4.011A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.629A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 removed outlier: 3.618A pdb=" N ILE 4 183 " --> pdb=" O PRO 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 4.739A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 4.015A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.572A pdb=" N GLU 4 266 " --> pdb=" O ALA 4 262 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 3.528A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.841A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN 5 59 " --> pdb=" O LEU 5 55 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 removed outlier: 3.673A pdb=" N SER 5 67 " --> pdb=" O ASP 5 63 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 80 Processing helix chain '5' and resid 88 through 106 removed outlier: 3.736A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 removed outlier: 3.733A pdb=" N LYS 5 119 " --> pdb=" O ILE 5 115 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 removed outlier: 3.918A pdb=" N ILE 6 54 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA 6 58 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 94 Processing helix chain '6' and resid 98 through 118 removed outlier: 4.403A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '7' and resid 63 through 67 removed outlier: 3.669A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 67' Processing helix chain '7' and resid 83 through 104 removed outlier: 3.731A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 114 Processing helix chain '7' and resid 116 through 121 removed outlier: 3.715A pdb=" N ARG 7 121 " --> pdb=" O ASP 7 117 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 removed outlier: 3.629A pdb=" N THR 7 145 " --> pdb=" O TYR 7 141 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 166 removed outlier: 3.778A pdb=" N TYR 7 161 " --> pdb=" O VAL 7 157 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 187 Processing helix chain '8' and resid 26 through 31 removed outlier: 3.615A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.962A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 78 removed outlier: 3.712A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 17 Processing helix chain '9' and resid 19 through 24 removed outlier: 3.657A pdb=" N GLN 9 23 " --> pdb=" O SER 9 19 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE 9 24 " --> pdb=" O ALA 9 20 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 19 through 24' Processing helix chain '9' and resid 36 through 55 removed outlier: 4.256A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 80 removed outlier: 3.655A pdb=" N CYS 9 79 " --> pdb=" O THR 9 76 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN 9 80 " --> pdb=" O TRP 9 77 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 76 through 80' Processing helix chain '9' and resid 82 through 95 removed outlier: 3.887A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.500A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.692A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.634A pdb=" N PHE A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.766A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.926A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.789A pdb=" N LEU B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.096A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 90 removed outlier: 4.448A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.698A pdb=" N VAL C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 66 removed outlier: 3.532A pdb=" N SER D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.081A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.840A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 66 removed outlier: 3.742A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.646A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.561A pdb=" N ILE E 95 " --> pdb=" O ASN E 92 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA E 96 " --> pdb=" O PRO E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 97 through 126 removed outlier: 4.249A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.971A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.015A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 127 removed outlier: 4.036A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.585A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.734A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.398A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.543A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 67 removed outlier: 3.974A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.797A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 97 through 126 removed outlier: 3.615A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE I 126 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.367A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 90 removed outlier: 3.781A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 95 through 127 removed outlier: 3.876A pdb=" N VAL J 100 " --> pdb=" O ALA J 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER J 112 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.793A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.747A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 259 removed outlier: 4.315A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.586A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 65 removed outlier: 3.648A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.691A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN P 76 " --> pdb=" O ASP P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'P' and resid 103 through 108 removed outlier: 5.160A pdb=" N SER P 106 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL P 108 " --> pdb=" O ILE P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 129 removed outlier: 3.645A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA P 126 " --> pdb=" O PHE P 122 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP P 127 " --> pdb=" O GLU P 123 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 144 removed outlier: 3.947A pdb=" N GLU P 143 " --> pdb=" O VAL P 139 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.629A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 210 through 227 removed outlier: 3.512A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 4.006A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.868A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 41 removed outlier: 4.269A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.782A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 168 removed outlier: 3.798A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 Processing helix chain 'S' and resid 41 through 69 removed outlier: 3.620A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.575A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.662A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 212 through 222 removed outlier: 6.304A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 241 Processing helix chain 'S' and resid 242 through 312 removed outlier: 4.129A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 65 Processing helix chain 'T' and resid 66 through 75 removed outlier: 4.207A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.895A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 removed outlier: 3.654A pdb=" N THR T 159 " --> pdb=" O GLY T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 211 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.809A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.549A pdb=" N GLN T 278 " --> pdb=" O LYS T 274 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 285 Processing helix chain 'T' and resid 295 through 311 Proline residue: T 303 - end of helix Processing helix chain 'T' and resid 311 through 316 removed outlier: 3.539A pdb=" N THR T 316 " --> pdb=" O TYR T 312 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.701A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.618A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU T 362 " --> pdb=" O HIS T 358 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 removed outlier: 3.513A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.753A pdb=" N PHE T 413 " --> pdb=" O GLU T 409 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.889A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 441 removed outlier: 4.212A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 450 Processing helix chain 'T' and resid 450 through 460 removed outlier: 4.185A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.724A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR T 481 " --> pdb=" O GLY T 477 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 499 removed outlier: 3.601A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 494 through 499' Processing helix chain 'T' and resid 501 through 506 Processing helix chain 'T' and resid 517 through 527 removed outlier: 4.452A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.818A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA T 538 " --> pdb=" O LYS T 534 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 552 removed outlier: 4.360A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 47 removed outlier: 3.800A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 50 No H-bonds generated for 'chain 'U' and resid 48 through 50' Processing helix chain 'U' and resid 58 through 71 removed outlier: 5.375A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.837A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.704A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU U 160 " --> pdb=" O PRO U 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 156 through 160' Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.589A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 Processing helix chain 'U' and resid 295 through 315 Proline residue: U 303 - end of helix removed outlier: 3.998A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 340 Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.536A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 400 Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.055A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 removed outlier: 4.262A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 496 Processing helix chain 'U' and resid 497 through 506 removed outlier: 4.233A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.594A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.125A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.628A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 4.214A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.224A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.815A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.703A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 removed outlier: 3.547A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.610A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.609A pdb=" N LEU V 372 " --> pdb=" O SER V 369 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 369 through 373' Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.686A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.797A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.847A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 517 removed outlier: 3.880A pdb=" N ASP V 516 " --> pdb=" O ARG V 513 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE V 517 " --> pdb=" O VAL V 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 513 through 517' Processing helix chain 'V' and resid 521 through 526 Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.563A pdb=" N ILE V 535 " --> pdb=" O ALA V 531 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 4.028A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.590A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 153 removed outlier: 3.597A pdb=" N GLN X 153 " --> pdb=" O PHE X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 4.839A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 removed outlier: 3.625A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 242 removed outlier: 3.501A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 removed outlier: 3.658A pdb=" N ARG X 258 " --> pdb=" O PRO X 254 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA X 259 " --> pdb=" O PRO X 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 254 through 260' Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.786A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 298 removed outlier: 3.948A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 353 Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.675A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 421 removed outlier: 7.663A pdb=" N ALA X 394 " --> pdb=" O ASN X 390 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N GLU X 395 " --> pdb=" O VAL X 391 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS X 396 " --> pdb=" O ILE X 392 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 425 Processing helix chain 'X' and resid 426 through 442 removed outlier: 3.543A pdb=" N THR X 432 " --> pdb=" O GLU X 428 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 removed outlier: 3.682A pdb=" N THR X 454 " --> pdb=" O ALA X 450 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY X 455 " --> pdb=" O GLU X 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 450 through 455' Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 483 through 487 Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.847A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 removed outlier: 3.545A pdb=" N LEU X 530 " --> pdb=" O SER X 526 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 526 through 533' Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.997A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 removed outlier: 3.556A pdb=" N ALA Y 259 " --> pdb=" O PRO Y 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.639A pdb=" N THR Y 264 " --> pdb=" O ARG Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.790A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 353 Processing helix chain 'Y' and resid 354 through 358 removed outlier: 3.971A pdb=" N LEU Y 358 " --> pdb=" O PHE Y 355 " (cutoff:3.500A) Processing helix chain 'Y' and resid 366 through 371 Processing helix chain 'Y' and resid 393 through 421 removed outlier: 3.726A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA Y 418 " --> pdb=" O GLN Y 414 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 removed outlier: 3.826A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) Processing helix chain 'Y' and resid 448 through 452 removed outlier: 4.134A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 474 removed outlier: 3.600A pdb=" N GLY Y 472 " --> pdb=" O SER Y 468 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 508 removed outlier: 3.708A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 532 Processing helix chain 'Y' and resid 544 through 555 removed outlier: 4.220A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 removed outlier: 3.642A pdb=" N THR Z 117 " --> pdb=" O GLY Z 114 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU Z 118 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 114 through 118' Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 188 through 204 removed outlier: 3.532A pdb=" N LEU Z 192 " --> pdb=" O GLY Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.615A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 removed outlier: 3.646A pdb=" N ARG Z 258 " --> pdb=" O PRO Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.501A pdb=" N THR Z 264 " --> pdb=" O ARG Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.509A pdb=" N LEU Z 301 " --> pdb=" O VAL Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.417A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 367 through 372 Processing helix chain 'Z' and resid 388 through 393 removed outlier: 3.613A pdb=" N ILE Z 392 " --> pdb=" O ASN Z 388 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY Z 393 " --> pdb=" O PRO Z 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 388 through 393' Processing helix chain 'Z' and resid 393 through 412 Processing helix chain 'Z' and resid 426 through 440 removed outlier: 3.576A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.906A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 491 through 502 removed outlier: 3.737A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 185 removed outlier: 4.338A pdb=" N VAL 1 226 " --> pdb=" O ALA 1 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 368 through 372 removed outlier: 4.361A pdb=" N ILE 2 368 " --> pdb=" O VAL 2 379 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA 2 375 " --> pdb=" O LYS 2 372 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA5, first strand: chain 'P' and resid 188 through 190 Processing sheet with id=AA6, first strand: chain 'Q' and resid 62 through 63 removed outlier: 7.096A pdb=" N GLN S 159 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL S 139 " --> pdb=" O GLN S 159 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA S 161 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N SER S 141 " --> pdb=" O ALA S 161 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ALA S 163 " --> pdb=" O SER S 141 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER S 189 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 85 through 86 removed outlier: 3.551A pdb=" N LYS R 86 " --> pdb=" O PHE R 70 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY R 132 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE R 108 " --> pdb=" O GLU S 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.751A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU R 125 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.716A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS T 116 " --> pdb=" O PHE T 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 107 through 111 removed outlier: 6.894A pdb=" N LEU T 108 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR T 147 " --> pdb=" O LEU T 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 121 through 122 removed outlier: 4.664A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG Y 51 " --> pdb=" O VAL Y 40 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AB4, first strand: chain 'T' and resid 163 through 164 removed outlier: 6.274A pdb=" N THR T 164 " --> pdb=" O SER T 289 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR T 378 " --> pdb=" O GLY T 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 382 through 384 removed outlier: 7.966A pdb=" N ILE T 383 " --> pdb=" O GLU T 221 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ILE T 223 " --> pdb=" O ILE T 383 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.732A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 62 through 65 removed outlier: 4.732A pdb=" N LEU X 72 " --> pdb=" O VAL X 65 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL X 76 " --> pdb=" O ILE X 88 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 37 through 44 current: chain 'U' and resid 94 through 99 removed outlier: 6.660A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AB9, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.448A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR U 256 " --> pdb=" O LEU U 321 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE U 323 " --> pdb=" O TYR U 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL U 258 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP U 325 " --> pdb=" O VAL U 258 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL U 260 " --> pdb=" O ASP U 325 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR U 378 " --> pdb=" O GLY U 320 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU U 222 " --> pdb=" O GLY U 404 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 116 through 122 removed outlier: 3.816A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'V' and resid 163 through 164 Processing sheet with id=AC4, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AC5, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.089A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.677A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 279 through 282 removed outlier: 6.220A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL X 339 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU X 181 " --> pdb=" O VAL X 339 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AC9, first strand: chain 'Y' and resid 110 through 113 removed outlier: 4.501A pdb=" N VAL Y 113 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASP Y 139 " --> pdb=" O VAL Y 113 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.809A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N TYR Y 340 " --> pdb=" O VAL Y 284 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL Y 339 " --> pdb=" O ILE Y 179 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU Y 181 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA Y 360 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR Y 383 " --> pdb=" O THR Y 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.314A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AD4, first strand: chain 'Z' and resid 178 through 181 removed outlier: 5.768A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 559 through 561 2783 hydrogen bonds defined for protein. 8109 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: 22.19 Time building geometry restraints manager: 11.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15806 1.33 - 1.46: 11117 1.46 - 1.58: 27487 1.58 - 1.70: 21 1.70 - 1.83: 254 Bond restraints: 54685 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.07e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.37e+01 bond pdb=" C4 ATP T1001 " pdb=" N9 ATP T1001 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.77e+01 bond pdb=" C5 ATP U1001 " pdb=" N7 ATP U1001 " ideal model delta sigma weight residual 1.387 1.326 0.061 1.00e-02 1.00e+04 3.75e+01 ... (remaining 54680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 73658 4.35 - 8.69: 449 8.69 - 13.04: 44 13.04 - 17.39: 3 17.39 - 21.73: 3 Bond angle restraints: 74157 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.14 21.73 1.00e+00 1.00e+00 4.72e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 118.49 21.38 1.00e+00 1.00e+00 4.57e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 118.96 20.91 1.00e+00 1.00e+00 4.37e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 119.81 17.02 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.47 14.36 1.00e+00 1.00e+00 2.06e+02 ... (remaining 74152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 31393 26.67 - 53.35: 1469 53.35 - 80.02: 133 80.02 - 106.69: 28 106.69 - 133.37: 1 Dihedral angle restraints: 33024 sinusoidal: 12667 harmonic: 20357 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -125.01 -54.99 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual 180.00 -126.64 -53.36 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -126.85 -53.15 0 5.00e+00 4.00e-02 1.13e+02 ... (remaining 33021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 7023 0.075 - 0.150: 1497 0.150 - 0.225: 151 0.225 - 0.301: 14 0.301 - 0.376: 4 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL 2 357 " pdb=" CA VAL 2 357 " pdb=" CG1 VAL 2 357 " pdb=" CG2 VAL 2 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 8686 not shown) Planarity restraints: 9508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.92e-02 3.50e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA X 350 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N PRO X 351 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO X 351 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO X 351 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 203 " 0.026 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE U 203 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE U 203 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE U 203 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE U 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE U 203 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE U 203 " 0.003 2.00e-02 2.50e+03 ... (remaining 9505 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 734 2.62 - 3.19: 46614 3.19 - 3.76: 85484 3.76 - 4.33: 117664 4.33 - 4.90: 193983 Nonbonded interactions: 444479 Sorted by model distance: nonbonded pdb=" OE1 GLU Y 215 " pdb="MG MG Y 602 " model vdw 2.050 2.170 nonbonded pdb=" OE2 GLU X 215 " pdb="MG MG X 602 " model vdw 2.060 2.170 nonbonded pdb=" O2B ATP T1001 " pdb="MG MG T1002 " model vdw 2.138 2.170 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.205 3.040 nonbonded pdb=" O SER 1 29 " pdb=" OG SER 1 29 " model vdw 2.230 3.040 ... (remaining 444474 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.510 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 100.570 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.350 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.010 0.130 54685 Z= 0.673 Angle : 1.050 21.732 74157 Z= 0.593 Chirality : 0.061 0.376 8689 Planarity : 0.008 0.091 9508 Dihedral : 15.095 133.367 19938 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.77 % Favored : 94.02 % Rotamer: Outliers : 0.55 % Allowed : 11.37 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.13 % 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: -4.32 (0.08), residues: 7036 helix: -3.08 (0.06), residues: 3747 sheet: -2.12 (0.19), residues: 618 loop : -2.43 (0.10), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP X 141 HIS 0.010 0.002 HIS 0 75 PHE 0.059 0.003 PHE U 203 TYR 0.028 0.003 TYR 4 211 ARG 0.012 0.001 ARG 3 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1135 time to evaluate : 4.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 173 LYS cc_start: 0.8869 (mttt) cc_final: 0.8589 (tptp) REVERT: 1 391 ASP cc_start: 0.7758 (p0) cc_final: 0.7498 (p0) REVERT: 1 519 GLU cc_start: 0.7850 (pt0) cc_final: 0.7605 (pt0) REVERT: 4 61 GLN cc_start: 0.8630 (mt0) cc_final: 0.8407 (mt0) REVERT: 4 64 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7901 (mm-30) REVERT: 4 134 TYR cc_start: 0.7846 (t80) cc_final: 0.7432 (t80) REVERT: 4 232 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8407 (mtp85) REVERT: 4 244 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7944 (tm-30) REVERT: 4 249 TYR cc_start: 0.8642 (t80) cc_final: 0.8391 (t80) REVERT: 5 35 MET cc_start: 0.8235 (mmt) cc_final: 0.7883 (mmt) REVERT: 5 63 ASP cc_start: 0.8002 (p0) cc_final: 0.7800 (p0) REVERT: 5 104 ASP cc_start: 0.8078 (m-30) cc_final: 0.7849 (m-30) REVERT: 6 52 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8612 (mtmm) REVERT: 6 54 ILE cc_start: 0.9452 (mt) cc_final: 0.9217 (mt) REVERT: 6 99 TRP cc_start: 0.8455 (p-90) cc_final: 0.7754 (p-90) REVERT: 7 135 ASP cc_start: 0.7931 (t0) cc_final: 0.7599 (t0) REVERT: 8 70 LYS cc_start: 0.7883 (mtpp) cc_final: 0.6948 (mmtt) REVERT: 9 13 LYS cc_start: 0.7465 (mtmt) cc_final: 0.7237 (tptt) REVERT: 9 26 LEU cc_start: 0.8493 (tp) cc_final: 0.8207 (tp) REVERT: 9 46 MET cc_start: 0.6876 (mtm) cc_final: 0.6480 (ttt) REVERT: A 81 MET cc_start: 0.9062 (ttp) cc_final: 0.8831 (ttp) REVERT: B 81 MET cc_start: 0.8799 (ttp) cc_final: 0.8433 (ttp) REVERT: C 97 LYS cc_start: 0.8464 (mmtm) cc_final: 0.7821 (mtpt) REVERT: E 78 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7960 (mp) REVERT: E 109 LEU cc_start: 0.8497 (tp) cc_final: 0.8289 (tp) REVERT: G 82 PHE cc_start: 0.8670 (m-80) cc_final: 0.8202 (m-80) REVERT: G 94 ASN cc_start: 0.8842 (t0) cc_final: 0.8635 (t0) REVERT: H 81 MET cc_start: 0.8162 (tmm) cc_final: 0.7888 (tmm) REVERT: H 82 PHE cc_start: 0.8871 (m-80) cc_final: 0.8660 (m-80) REVERT: H 97 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8153 (mttt) REVERT: H 109 LEU cc_start: 0.8931 (tp) cc_final: 0.8723 (tt) REVERT: I 69 ILE cc_start: 0.8702 (mm) cc_final: 0.8491 (mm) REVERT: J 124 ILE cc_start: 0.8715 (mt) cc_final: 0.8360 (mt) REVERT: M 133 ARG cc_start: 0.8491 (tpt90) cc_final: 0.8205 (tpt170) REVERT: M 160 ILE cc_start: 0.9450 (tt) cc_final: 0.9184 (tt) REVERT: M 281 LEU cc_start: 0.9358 (mt) cc_final: 0.9105 (mt) REVERT: P 76 GLN cc_start: 0.8171 (mt0) cc_final: 0.7888 (mt0) REVERT: P 141 TYR cc_start: 0.9187 (t80) cc_final: 0.8537 (t80) REVERT: P 143 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8015 (mm-30) REVERT: P 183 LYS cc_start: 0.7338 (ptpt) cc_final: 0.7027 (mmmt) REVERT: P 186 MET cc_start: 0.8142 (mtt) cc_final: 0.7763 (mmm) REVERT: P 216 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8102 (tm-30) REVERT: Q 42 ARG cc_start: 0.8401 (ptp90) cc_final: 0.7735 (mtm-85) REVERT: R 62 GLU cc_start: 0.7923 (pp20) cc_final: 0.7695 (pp20) REVERT: R 146 VAL cc_start: 0.9303 (m) cc_final: 0.9079 (p) REVERT: S 68 MET cc_start: 0.8593 (ttp) cc_final: 0.8031 (ttp) REVERT: S 79 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7487 (ttm110) REVERT: T 134 ASN cc_start: 0.8313 (t0) cc_final: 0.8049 (t0) REVERT: T 271 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7889 (mt0) REVERT: T 304 TYR cc_start: 0.8463 (m-80) cc_final: 0.8187 (m-80) REVERT: T 360 ARG cc_start: 0.8736 (ttp-110) cc_final: 0.8520 (ptm160) REVERT: T 453 TYR cc_start: 0.7507 (t80) cc_final: 0.6666 (t80) REVERT: T 479 ARG cc_start: 0.7936 (mmt180) cc_final: 0.7651 (mtt90) REVERT: T 502 TYR cc_start: 0.7591 (t80) cc_final: 0.7211 (t80) REVERT: T 506 LYS cc_start: 0.6701 (mmtp) cc_final: 0.6436 (mptt) REVERT: U 112 ASP cc_start: 0.7841 (t0) cc_final: 0.7460 (t0) REVERT: U 215 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8762 (mp) REVERT: U 411 GLU cc_start: 0.7608 (tp30) cc_final: 0.7382 (tp30) REVERT: U 511 LYS cc_start: 0.8120 (tttt) cc_final: 0.7351 (mmtp) REVERT: V 485 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8723 (mtpt) REVERT: V 492 ILE cc_start: 0.8738 (mt) cc_final: 0.8271 (tt) REVERT: V 536 LEU cc_start: 0.8438 (tp) cc_final: 0.7910 (tt) REVERT: X 251 MET cc_start: 0.8457 (ptp) cc_final: 0.8144 (ptp) REVERT: X 359 ASP cc_start: 0.8658 (m-30) cc_final: 0.8372 (m-30) REVERT: X 386 MET cc_start: 0.8197 (mmm) cc_final: 0.7919 (tpp) REVERT: Y 195 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6656 (mm-30) REVERT: Y 401 ARG cc_start: 0.7589 (mmm160) cc_final: 0.6732 (mmm-85) REVERT: Y 411 LYS cc_start: 0.8385 (ttmt) cc_final: 0.8141 (mtpp) REVERT: Y 467 ILE cc_start: 0.8496 (mt) cc_final: 0.8155 (pt) REVERT: Y 550 LYS cc_start: 0.6142 (mmtt) cc_final: 0.5922 (pptt) REVERT: Z 404 GLN cc_start: 0.8423 (mt0) cc_final: 0.7869 (mt0) REVERT: Z 441 ARG cc_start: 0.8805 (mmt-90) cc_final: 0.8564 (mmt90) REVERT: Z 484 MET cc_start: 0.7819 (mmm) cc_final: 0.7409 (mmm) outliers start: 31 outliers final: 19 residues processed: 1163 average time/residue: 0.5509 time to fit residues: 1046.4715 Evaluate side-chains 802 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 781 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 113 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 215 ILE Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 10.0000 chunk 529 optimal weight: 0.0870 chunk 293 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 356 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 chunk 547 optimal weight: 0.4980 chunk 211 optimal weight: 0.9980 chunk 332 optimal weight: 0.9990 chunk 407 optimal weight: 7.9990 chunk 633 optimal weight: 0.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 81 ASN 1 285 GLN 1 527 GLN 1 590 HIS 1 606 ASN 2 122 ASN 2 153 ASN 2 243 GLN 2 289 HIS 2 380 GLN 2 427 GLN 3 80 ASN 3 188 ASN 3 189 HIS 3 206 ASN 4 61 GLN 5 38 HIS 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 60 GLN 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 60 ASN G 94 ASN G 98 GLN I 98 GLN M 108 ASN M 163 ASN P 65 ASN P 223 ASN ** Q 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 ASN R 38 ASN R 119 HIS R 137 HIS S 195 ASN S 250 HIS S 267 HIS S 297 GLN T 61 HIS T 126 HIS T 169 GLN T 241 HIS T 264 GLN T 386 GLN T 405 GLN T 497 GLN U 134 ASN U 241 HIS U 246 ASN U 319 HIS U 386 GLN U 441 GLN U 497 GLN U 529 ASN V 196 GLN V 242 GLN V 244 ASN V 271 GLN V 486 GLN V 497 GLN V 539 ASN X 199 ASN X 337 GLN X 408 GLN X 412 ASN Y 174 GLN ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Y 390 ASN Y 514 ASN Z 199 ASN Z 252 ASN Z 278 GLN Z 404 GLN Z 414 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 54685 Z= 0.173 Angle : 0.613 11.724 74157 Z= 0.318 Chirality : 0.042 0.169 8689 Planarity : 0.005 0.064 9508 Dihedral : 6.676 113.473 7697 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.77 % Favored : 96.06 % Rotamer: Outliers : 2.11 % Allowed : 15.27 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.12 % 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: -2.44 (0.09), residues: 7036 helix: -1.30 (0.08), residues: 3811 sheet: -1.75 (0.20), residues: 594 loop : -1.84 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 5 21 HIS 0.005 0.001 HIS M 252 PHE 0.025 0.001 PHE V 459 TYR 0.023 0.001 TYR 4 211 ARG 0.011 0.001 ARG U 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 997 time to evaluate : 4.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 143 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7818 (ptpp) REVERT: 1 173 LYS cc_start: 0.8878 (mttt) cc_final: 0.8662 (tmtt) REVERT: 1 391 ASP cc_start: 0.7645 (p0) cc_final: 0.7415 (p0) REVERT: 2 439 LYS cc_start: 0.6634 (mmtp) cc_final: 0.6430 (mmmt) REVERT: 3 209 LEU cc_start: 0.9236 (mt) cc_final: 0.8954 (mt) REVERT: 3 278 ILE cc_start: 0.9174 (tp) cc_final: 0.8891 (tp) REVERT: 4 134 TYR cc_start: 0.7928 (t80) cc_final: 0.7215 (t80) REVERT: 4 207 PHE cc_start: 0.8894 (t80) cc_final: 0.8675 (t80) REVERT: 5 39 LYS cc_start: 0.9069 (mttt) cc_final: 0.8448 (mttp) REVERT: 5 43 CYS cc_start: 0.7591 (m) cc_final: 0.7235 (m) REVERT: 6 28 GLU cc_start: 0.6919 (tt0) cc_final: 0.6626 (tp30) REVERT: 6 52 LYS cc_start: 0.9084 (mtpt) cc_final: 0.8637 (mtmm) REVERT: 6 54 ILE cc_start: 0.9395 (mt) cc_final: 0.9177 (mt) REVERT: 6 99 TRP cc_start: 0.8064 (p-90) cc_final: 0.7624 (p-90) REVERT: 7 24 GLN cc_start: 0.7400 (pt0) cc_final: 0.7101 (pt0) REVERT: 7 135 ASP cc_start: 0.7883 (t0) cc_final: 0.7577 (t0) REVERT: 7 179 ASP cc_start: 0.8442 (t0) cc_final: 0.8216 (t0) REVERT: 7 185 PHE cc_start: 0.8528 (t80) cc_final: 0.8258 (t80) REVERT: 8 69 LYS cc_start: 0.8576 (mttt) cc_final: 0.7708 (tmtt) REVERT: 9 46 MET cc_start: 0.6726 (mtm) cc_final: 0.6421 (ttt) REVERT: A 107 PHE cc_start: 0.9103 (t80) cc_final: 0.8802 (t80) REVERT: B 81 MET cc_start: 0.8732 (ttp) cc_final: 0.8395 (ttp) REVERT: C 97 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7998 (tptm) REVERT: G 82 PHE cc_start: 0.8713 (m-80) cc_final: 0.8327 (m-80) REVERT: H 81 MET cc_start: 0.8058 (tmm) cc_final: 0.7717 (tmm) REVERT: H 97 LYS cc_start: 0.8684 (mmtt) cc_final: 0.7979 (mttt) REVERT: H 109 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8598 (tt) REVERT: I 69 ILE cc_start: 0.8494 (mm) cc_final: 0.8279 (mm) REVERT: I 100 VAL cc_start: 0.9076 (t) cc_final: 0.8826 (p) REVERT: M 160 ILE cc_start: 0.9260 (tt) cc_final: 0.8970 (tt) REVERT: P 45 GLN cc_start: 0.6790 (pm20) cc_final: 0.6588 (pm20) REVERT: P 66 GLN cc_start: 0.8267 (mt0) cc_final: 0.7927 (mt0) REVERT: P 140 ASN cc_start: 0.8431 (m-40) cc_final: 0.8184 (m110) REVERT: P 141 TYR cc_start: 0.9030 (t80) cc_final: 0.8578 (t80) REVERT: P 182 PHE cc_start: 0.7883 (m-10) cc_final: 0.7556 (m-10) REVERT: P 183 LYS cc_start: 0.7646 (ptpt) cc_final: 0.7422 (ptmm) REVERT: Q 42 ARG cc_start: 0.8313 (ptp90) cc_final: 0.8031 (ptp90) REVERT: R 100 VAL cc_start: 0.9472 (t) cc_final: 0.9159 (p) REVERT: R 126 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6536 (mtmt) REVERT: R 147 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8327 (mp) REVERT: S 68 MET cc_start: 0.8491 (ttp) cc_final: 0.8022 (ttp) REVERT: S 115 LEU cc_start: 0.8286 (tp) cc_final: 0.7900 (mt) REVERT: S 183 ILE cc_start: 0.8715 (mt) cc_final: 0.8385 (mt) REVERT: S 261 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8399 (mm-30) REVERT: S 287 LYS cc_start: 0.8908 (mttp) cc_final: 0.8450 (pttt) REVERT: T 304 TYR cc_start: 0.8431 (m-80) cc_final: 0.8176 (m-80) REVERT: T 455 GLU cc_start: 0.6623 (pm20) cc_final: 0.6371 (pt0) REVERT: T 502 TYR cc_start: 0.7397 (t80) cc_final: 0.6977 (t80) REVERT: U 112 ASP cc_start: 0.7741 (t0) cc_final: 0.7341 (t0) REVERT: U 389 ASP cc_start: 0.8107 (t0) cc_final: 0.7695 (m-30) REVERT: U 475 GLU cc_start: 0.7069 (pt0) cc_final: 0.6704 (mm-30) REVERT: U 511 LYS cc_start: 0.7818 (tttt) cc_final: 0.7193 (mmtp) REVERT: U 550 LEU cc_start: 0.8797 (mt) cc_final: 0.8407 (mt) REVERT: V 287 MET cc_start: 0.9000 (mmm) cc_final: 0.8737 (tpp) REVERT: V 492 ILE cc_start: 0.8615 (mt) cc_final: 0.8117 (tt) REVERT: X 251 MET cc_start: 0.8295 (ptp) cc_final: 0.7977 (ptp) REVERT: Y 401 ARG cc_start: 0.7429 (mmm160) cc_final: 0.6835 (mmm-85) REVERT: Y 497 GLU cc_start: 0.7996 (tp30) cc_final: 0.7436 (tp30) REVERT: Z 75 GLU cc_start: 0.7391 (tt0) cc_final: 0.7127 (tt0) REVERT: Z 404 GLN cc_start: 0.8216 (mt0) cc_final: 0.7800 (mt0) outliers start: 119 outliers final: 66 residues processed: 1075 average time/residue: 0.5788 time to fit residues: 1056.4095 Evaluate side-chains 860 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 791 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 196 ASP Chi-restraints excluded: chain 3 residue 282 ILE Chi-restraints excluded: chain 6 residue 77 ILE Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 145 THR Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 518 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 527 optimal weight: 1.9990 chunk 431 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 635 optimal weight: 0.0770 chunk 685 optimal weight: 0.8980 chunk 565 optimal weight: 4.9990 chunk 629 optimal weight: 0.7980 chunk 216 optimal weight: 9.9990 chunk 509 optimal weight: 10.0000 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 316 ASN ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 117 ASN 2 122 ASN 3 309 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 171 GLN T 61 HIS T 121 ASN T 405 GLN U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN U 529 ASN X 412 ASN Y 42 GLN Y 198 ASN Y 294 ASN ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 54685 Z= 0.189 Angle : 0.582 10.991 74157 Z= 0.298 Chirality : 0.042 0.169 8689 Planarity : 0.004 0.061 9508 Dihedral : 6.166 109.251 7680 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 2.73 % Allowed : 17.35 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % 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: -1.52 (0.10), residues: 7036 helix: -0.46 (0.08), residues: 3839 sheet: -1.51 (0.20), residues: 604 loop : -1.54 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 71 HIS 0.008 0.001 HIS 4 233 PHE 0.025 0.001 PHE F 82 TYR 0.025 0.001 TYR 4 211 ARG 0.005 0.000 ARG T 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1031 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 877 time to evaluate : 4.470 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: 1 61 MET cc_start: 0.8710 (mmm) cc_final: 0.8367 (mmm) REVERT: 1 543 SER cc_start: 0.8447 (t) cc_final: 0.7889 (m) REVERT: 2 439 LYS cc_start: 0.6748 (mmtp) cc_final: 0.6491 (mmmt) REVERT: 3 209 LEU cc_start: 0.9269 (mt) cc_final: 0.8988 (mt) REVERT: 4 134 TYR cc_start: 0.7995 (t80) cc_final: 0.7248 (t80) REVERT: 5 39 LYS cc_start: 0.9067 (mttt) cc_final: 0.8429 (mttp) REVERT: 5 43 CYS cc_start: 0.7553 (m) cc_final: 0.7201 (m) REVERT: 6 52 LYS cc_start: 0.9039 (mtpt) cc_final: 0.8587 (mtmm) REVERT: 6 54 ILE cc_start: 0.9419 (mt) cc_final: 0.9217 (mt) REVERT: 6 99 TRP cc_start: 0.7994 (p-90) cc_final: 0.7576 (p-90) REVERT: 7 135 ASP cc_start: 0.7949 (t0) cc_final: 0.7625 (t0) REVERT: 7 185 PHE cc_start: 0.8494 (t80) cc_final: 0.8247 (t80) REVERT: 8 43 ARG cc_start: 0.8726 (mmm-85) cc_final: 0.8394 (mmm160) REVERT: 8 69 LYS cc_start: 0.8397 (mttt) cc_final: 0.7680 (tmtt) REVERT: 9 11 PHE cc_start: 0.8130 (t80) cc_final: 0.7927 (t80) REVERT: 9 29 PHE cc_start: 0.6487 (m-80) cc_final: 0.5289 (m-80) REVERT: A 107 PHE cc_start: 0.9197 (t80) cc_final: 0.8854 (t80) REVERT: C 97 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7959 (tptm) REVERT: F 122 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7375 (t80) REVERT: G 82 PHE cc_start: 0.8584 (m-80) cc_final: 0.8335 (m-80) REVERT: G 95 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8367 (tp) REVERT: H 78 LEU cc_start: 0.8715 (mt) cc_final: 0.8388 (tt) REVERT: H 97 LYS cc_start: 0.8707 (mmtt) cc_final: 0.7989 (mttt) REVERT: H 109 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8494 (tt) REVERT: I 100 VAL cc_start: 0.9067 (t) cc_final: 0.8779 (p) REVERT: M 259 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8630 (mp) REVERT: M 281 LEU cc_start: 0.9213 (mt) cc_final: 0.8993 (mt) REVERT: P 182 PHE cc_start: 0.7889 (m-10) cc_final: 0.7577 (m-10) REVERT: P 183 LYS cc_start: 0.7724 (ptpt) cc_final: 0.7376 (ptmm) REVERT: Q 32 LYS cc_start: 0.6096 (mmmt) cc_final: 0.5725 (mtpt) REVERT: Q 42 ARG cc_start: 0.8186 (ptp90) cc_final: 0.7920 (ptp90) REVERT: Q 48 ARG cc_start: 0.8157 (ptt90) cc_final: 0.7938 (ptt90) REVERT: R 100 VAL cc_start: 0.9443 (t) cc_final: 0.9147 (p) REVERT: R 117 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7385 (mm-30) REVERT: S 68 MET cc_start: 0.8433 (ttp) cc_final: 0.7953 (ttp) REVERT: S 115 LEU cc_start: 0.8303 (tp) cc_final: 0.7881 (mt) REVERT: S 124 ARG cc_start: 0.7732 (ptm160) cc_final: 0.6576 (ttp80) REVERT: S 183 ILE cc_start: 0.8781 (mt) cc_final: 0.8503 (mt) REVERT: S 287 LYS cc_start: 0.8953 (mttp) cc_final: 0.8539 (pttt) REVERT: T 304 TYR cc_start: 0.8580 (m-80) cc_final: 0.8241 (m-80) REVERT: T 494 ILE cc_start: 0.7112 (tp) cc_final: 0.6891 (tp) REVERT: U 112 ASP cc_start: 0.7748 (t0) cc_final: 0.7364 (t0) REVERT: U 260 VAL cc_start: 0.9312 (t) cc_final: 0.9012 (m) REVERT: U 389 ASP cc_start: 0.8269 (t0) cc_final: 0.7835 (m-30) REVERT: U 511 LYS cc_start: 0.7787 (tttt) cc_final: 0.7211 (mmtp) REVERT: U 550 LEU cc_start: 0.8695 (mt) cc_final: 0.8364 (mt) REVERT: V 287 MET cc_start: 0.8955 (mmm) cc_final: 0.8750 (tpp) REVERT: V 384 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6505 (pp20) REVERT: V 492 ILE cc_start: 0.8638 (mt) cc_final: 0.8141 (tt) REVERT: X 179 ILE cc_start: 0.9262 (mm) cc_final: 0.8558 (mt) REVERT: X 427 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: Y 401 ARG cc_start: 0.7361 (mmm160) cc_final: 0.6843 (mmm-85) REVERT: Y 497 GLU cc_start: 0.7943 (tp30) cc_final: 0.7652 (tp30) REVERT: Z 404 GLN cc_start: 0.8218 (mt0) cc_final: 0.7701 (mt0) REVERT: Z 425 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.4702 (mt) outliers start: 154 outliers final: 110 residues processed: 985 average time/residue: 0.5249 time to fit residues: 888.9631 Evaluate side-chains 897 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 780 time to evaluate : 4.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 3 residue 132 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 111 THR Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 2 VAL Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 206 VAL Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 200 VAL Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 425 LEU Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 303 optimal weight: 20.0000 chunk 426 optimal weight: 1.9990 chunk 637 optimal weight: 0.6980 chunk 674 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 603 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 65 GLN 4 68 HIS 5 38 HIS ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN P 140 ASN ** T 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN U 123 GLN U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN U 549 HIS V 488 GLN Z 144 HIS ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 54685 Z= 0.306 Angle : 0.630 12.020 74157 Z= 0.322 Chirality : 0.044 0.334 8689 Planarity : 0.005 0.055 9508 Dihedral : 6.167 104.683 7679 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.76 % Favored : 95.07 % Rotamer: Outliers : 3.84 % Allowed : 18.43 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % 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: -1.18 (0.10), residues: 7036 helix: -0.15 (0.08), residues: 3834 sheet: -1.52 (0.20), residues: 632 loop : -1.40 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 21 HIS 0.008 0.001 HIS 4 233 PHE 0.029 0.002 PHE V 459 TYR 0.029 0.002 TYR 2 180 ARG 0.013 0.000 ARG U 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 817 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 52 GLN cc_start: 0.8294 (tp-100) cc_final: 0.8022 (tp-100) REVERT: 4 134 TYR cc_start: 0.8007 (t80) cc_final: 0.7087 (t80) REVERT: 5 39 LYS cc_start: 0.9087 (mttt) cc_final: 0.8493 (mttp) REVERT: 5 43 CYS cc_start: 0.7628 (m) cc_final: 0.7246 (m) REVERT: 6 52 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8591 (mtmm) REVERT: 6 54 ILE cc_start: 0.9462 (mt) cc_final: 0.9261 (mt) REVERT: 6 99 TRP cc_start: 0.8177 (p-90) cc_final: 0.7770 (p-90) REVERT: 7 129 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8204 (mttp) REVERT: 7 135 ASP cc_start: 0.8008 (t0) cc_final: 0.7689 (t0) REVERT: 8 69 LYS cc_start: 0.8437 (mttt) cc_final: 0.7674 (tmtt) REVERT: 9 29 PHE cc_start: 0.6567 (m-80) cc_final: 0.5417 (m-80) REVERT: B 81 MET cc_start: 0.8798 (ttp) cc_final: 0.8498 (ttp) REVERT: C 97 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7934 (tptm) REVERT: F 82 PHE cc_start: 0.8329 (m-80) cc_final: 0.8127 (m-80) REVERT: F 122 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.7344 (t80) REVERT: G 82 PHE cc_start: 0.8593 (m-80) cc_final: 0.8295 (m-80) REVERT: G 95 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8562 (tt) REVERT: H 81 MET cc_start: 0.8109 (tmm) cc_final: 0.7869 (ptp) REVERT: H 97 LYS cc_start: 0.8704 (mmtt) cc_final: 0.7975 (mttt) REVERT: H 109 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8590 (tt) REVERT: I 100 VAL cc_start: 0.9148 (t) cc_final: 0.8944 (p) REVERT: M 259 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8715 (mp) REVERT: P 140 ASN cc_start: 0.8294 (m-40) cc_final: 0.8070 (m110) REVERT: P 172 LYS cc_start: 0.7731 (tppt) cc_final: 0.7159 (mtmm) REVERT: Q 42 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7769 (mtm-85) REVERT: R 31 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7541 (ttpp) REVERT: R 126 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6780 (ptpt) REVERT: S 68 MET cc_start: 0.8451 (ttp) cc_final: 0.7988 (ttp) REVERT: S 124 ARG cc_start: 0.7766 (ptm160) cc_final: 0.6600 (ttp80) REVERT: S 183 ILE cc_start: 0.8801 (mt) cc_final: 0.8477 (mt) REVERT: S 248 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: S 287 LYS cc_start: 0.8965 (mttp) cc_final: 0.8529 (pttt) REVERT: T 304 TYR cc_start: 0.8622 (m-80) cc_final: 0.8276 (m-80) REVERT: U 112 ASP cc_start: 0.7823 (t0) cc_final: 0.7370 (t0) REVERT: U 371 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: U 389 ASP cc_start: 0.8295 (t0) cc_final: 0.7865 (m-30) REVERT: U 447 LYS cc_start: 0.7613 (mttt) cc_final: 0.7409 (mttt) REVERT: U 511 LYS cc_start: 0.7760 (tttt) cc_final: 0.7167 (mmtp) REVERT: U 550 LEU cc_start: 0.8638 (mt) cc_final: 0.8292 (mt) REVERT: V 61 HIS cc_start: 0.7725 (t-170) cc_final: 0.7523 (t-170) REVERT: V 384 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6470 (pp20) REVERT: V 488 GLN cc_start: 0.7169 (tp40) cc_final: 0.6817 (tp-100) REVERT: X 427 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: X 527 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7380 (tt) REVERT: Y 401 ARG cc_start: 0.7430 (mmm160) cc_final: 0.6769 (mmm-85) REVERT: Y 497 GLU cc_start: 0.8006 (tp30) cc_final: 0.7709 (tp30) REVERT: Z 370 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6155 (mm-30) REVERT: Z 404 GLN cc_start: 0.8254 (mt0) cc_final: 0.7717 (mt0) REVERT: Z 425 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.4819 (mt) outliers start: 216 outliers final: 166 residues processed: 962 average time/residue: 0.4978 time to fit residues: 819.2963 Evaluate side-chains 935 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 758 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 57 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 561 THR Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 3 residue 132 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 279 GLU Chi-restraints excluded: chain 3 residue 282 ILE Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 9 LYS Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 16 THR Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 111 THR Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 129 LYS Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 195 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 209 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 284 MET Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 255 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 127 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 217 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 425 LEU Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 2.9990 chunk 382 optimal weight: 5.9990 chunk 9 optimal weight: 0.0040 chunk 502 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 575 optimal weight: 2.9990 chunk 466 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 605 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 427 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN ** T 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN U 529 ASN U 549 HIS ** Z 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 54685 Z= 0.221 Angle : 0.584 11.054 74157 Z= 0.298 Chirality : 0.043 0.173 8689 Planarity : 0.004 0.051 9508 Dihedral : 5.976 99.372 7679 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.42 % Favored : 95.44 % Rotamer: Outliers : 3.75 % Allowed : 19.89 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.83 (0.10), residues: 7036 helix: 0.17 (0.09), residues: 3824 sheet: -1.37 (0.20), residues: 625 loop : -1.30 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 5 21 HIS 0.007 0.001 HIS 4 233 PHE 0.028 0.001 PHE 7 185 TYR 0.035 0.001 TYR 2 180 ARG 0.011 0.000 ARG U 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 844 time to evaluate : 4.575 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: 1 391 ASP cc_start: 0.7830 (p0) cc_final: 0.7609 (p0) REVERT: 3 209 LEU cc_start: 0.9241 (mt) cc_final: 0.9005 (mt) REVERT: 4 52 GLN cc_start: 0.8293 (tp-100) cc_final: 0.7958 (tp40) REVERT: 4 134 TYR cc_start: 0.8030 (t80) cc_final: 0.7199 (t80) REVERT: 4 232 ARG cc_start: 0.8667 (ttp-110) cc_final: 0.8438 (mtp85) REVERT: 5 39 LYS cc_start: 0.9105 (mttt) cc_final: 0.8494 (mttp) REVERT: 5 43 CYS cc_start: 0.7653 (m) cc_final: 0.7240 (m) REVERT: 6 52 LYS cc_start: 0.9052 (mtpt) cc_final: 0.8565 (mtmm) REVERT: 6 99 TRP cc_start: 0.7994 (p-90) cc_final: 0.7629 (p-90) REVERT: 7 135 ASP cc_start: 0.7981 (t0) cc_final: 0.7641 (t0) REVERT: 8 69 LYS cc_start: 0.8331 (mttt) cc_final: 0.7672 (tmtt) REVERT: 9 11 PHE cc_start: 0.8131 (t80) cc_final: 0.7849 (t80) REVERT: 9 29 PHE cc_start: 0.6487 (m-80) cc_final: 0.5364 (m-80) REVERT: A 107 PHE cc_start: 0.9116 (t80) cc_final: 0.8823 (t80) REVERT: B 81 MET cc_start: 0.8769 (ttp) cc_final: 0.8524 (ttp) REVERT: B 99 LEU cc_start: 0.8781 (mt) cc_final: 0.8573 (mp) REVERT: C 97 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7894 (tptm) REVERT: F 122 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7295 (t80) REVERT: G 82 PHE cc_start: 0.8531 (m-80) cc_final: 0.8273 (m-80) REVERT: G 95 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8619 (tt) REVERT: H 78 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8472 (tt) REVERT: H 97 LYS cc_start: 0.8686 (mmtt) cc_final: 0.7895 (mttt) REVERT: H 109 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8490 (tt) REVERT: I 100 VAL cc_start: 0.9086 (t) cc_final: 0.8842 (p) REVERT: M 259 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8642 (mp) REVERT: P 140 ASN cc_start: 0.8417 (m-40) cc_final: 0.8168 (m110) REVERT: Q 48 ARG cc_start: 0.8187 (ptt90) cc_final: 0.7970 (ptt90) REVERT: R 117 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: R 126 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6424 (ptmt) REVERT: S 68 MET cc_start: 0.8386 (ttp) cc_final: 0.7958 (ttp) REVERT: S 115 LEU cc_start: 0.8283 (tp) cc_final: 0.7826 (mt) REVERT: S 186 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7376 (p0) REVERT: S 248 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: S 274 MET cc_start: 0.8550 (mmt) cc_final: 0.7800 (mmt) REVERT: S 287 LYS cc_start: 0.8980 (mttp) cc_final: 0.8503 (pttt) REVERT: T 304 TYR cc_start: 0.8603 (m-80) cc_final: 0.8293 (m-80) REVERT: U 112 ASP cc_start: 0.7790 (t0) cc_final: 0.7404 (t0) REVERT: U 260 VAL cc_start: 0.9357 (t) cc_final: 0.9046 (m) REVERT: U 389 ASP cc_start: 0.8274 (t0) cc_final: 0.7848 (m-30) REVERT: U 483 MET cc_start: 0.7592 (tpp) cc_final: 0.7384 (tpp) REVERT: U 511 LYS cc_start: 0.7749 (tttt) cc_final: 0.7209 (mmtp) REVERT: V 384 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6378 (pp20) REVERT: X 179 ILE cc_start: 0.9298 (mm) cc_final: 0.8651 (mt) REVERT: X 207 PHE cc_start: 0.8452 (m-80) cc_final: 0.8244 (m-80) REVERT: X 427 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6460 (mp0) REVERT: X 527 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7183 (tt) REVERT: Y 169 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8305 (mt) REVERT: Y 401 ARG cc_start: 0.7436 (mmm160) cc_final: 0.6799 (mmm-85) REVERT: Y 497 GLU cc_start: 0.8012 (tp30) cc_final: 0.7717 (tp30) REVERT: Z 366 ARG cc_start: 0.7358 (tpt170) cc_final: 0.6000 (tpt170) REVERT: Z 370 GLU cc_start: 0.6652 (mm-30) cc_final: 0.6287 (mm-30) REVERT: Z 404 GLN cc_start: 0.8246 (mt0) cc_final: 0.7684 (mt0) REVERT: Z 425 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5060 (mt) outliers start: 211 outliers final: 159 residues processed: 981 average time/residue: 0.5076 time to fit residues: 857.0510 Evaluate side-chains 962 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 790 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 426 VAL Chi-restraints excluded: chain 1 residue 487 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 1 residue 615 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 204 THR Chi-restraints excluded: chain 2 residue 228 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 132 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 111 THR Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 37 VAL Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 84 SER Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 288 LEU Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 101 LYS Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 217 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 527 LEU Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 169 LEU Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 87 CYS Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 425 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 4.9990 chunk 607 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 396 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 675 optimal weight: 0.0870 chunk 560 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 223 optimal weight: 0.5980 chunk 354 optimal weight: 5.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 427 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 497 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54685 Z= 0.164 Angle : 0.558 10.776 74157 Z= 0.283 Chirality : 0.041 0.166 8689 Planarity : 0.004 0.050 9508 Dihedral : 5.696 92.925 7679 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 3.21 % Allowed : 21.33 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.49 (0.10), residues: 7036 helix: 0.46 (0.09), residues: 3836 sheet: -1.20 (0.21), residues: 620 loop : -1.18 (0.12), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.009 0.001 HIS V 61 PHE 0.032 0.001 PHE 2 149 TYR 0.030 0.001 TYR 2 180 ARG 0.006 0.000 ARG U 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 888 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 209 LEU cc_start: 0.9228 (mt) cc_final: 0.8983 (mt) REVERT: 4 52 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7860 (tp40) REVERT: 4 134 TYR cc_start: 0.7974 (t80) cc_final: 0.7184 (t80) REVERT: 4 156 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6817 (t0) REVERT: 4 232 ARG cc_start: 0.8675 (ttp-110) cc_final: 0.8407 (mtp85) REVERT: 5 39 LYS cc_start: 0.9071 (mttt) cc_final: 0.8438 (mttp) REVERT: 6 52 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8640 (mtmm) REVERT: 6 99 TRP cc_start: 0.7748 (p-90) cc_final: 0.7427 (p-90) REVERT: 7 135 ASP cc_start: 0.7905 (t0) cc_final: 0.7571 (t0) REVERT: 8 20 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8886 (mm) REVERT: 8 43 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8324 (mmm160) REVERT: 8 69 LYS cc_start: 0.8314 (mttt) cc_final: 0.7679 (tmtt) REVERT: 9 1 MET cc_start: 0.2296 (mmm) cc_final: 0.1553 (mmt) REVERT: 9 11 PHE cc_start: 0.8040 (t80) cc_final: 0.7782 (t80) REVERT: 9 29 PHE cc_start: 0.6413 (m-80) cc_final: 0.5295 (m-80) REVERT: B 81 MET cc_start: 0.8736 (ttp) cc_final: 0.8507 (ttp) REVERT: B 85 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 87 ASN cc_start: 0.7741 (m110) cc_final: 0.7208 (m-40) REVERT: C 97 LYS cc_start: 0.8160 (mmtm) cc_final: 0.7848 (tptm) REVERT: F 82 PHE cc_start: 0.8230 (m-80) cc_final: 0.8009 (m-10) REVERT: G 82 PHE cc_start: 0.8674 (m-80) cc_final: 0.8415 (m-80) REVERT: H 81 MET cc_start: 0.8160 (ptp) cc_final: 0.7888 (ptm) REVERT: H 97 LYS cc_start: 0.8654 (mmtt) cc_final: 0.7869 (mttt) REVERT: H 109 LEU cc_start: 0.8839 (tp) cc_final: 0.8559 (tt) REVERT: I 100 VAL cc_start: 0.9085 (t) cc_final: 0.8833 (p) REVERT: M 99 ASP cc_start: 0.8733 (t0) cc_final: 0.8455 (m-30) REVERT: M 309 GLU cc_start: 0.7721 (tp30) cc_final: 0.7453 (tp30) REVERT: P 79 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7421 (tp30) REVERT: P 136 GLU cc_start: 0.7088 (tt0) cc_final: 0.6639 (tt0) REVERT: P 140 ASN cc_start: 0.8392 (m-40) cc_final: 0.8172 (m-40) REVERT: Q 32 LYS cc_start: 0.6241 (mmmt) cc_final: 0.5858 (mtpt) REVERT: Q 48 ARG cc_start: 0.8152 (ptt90) cc_final: 0.7759 (ptt90) REVERT: R 31 LYS cc_start: 0.7875 (tmtt) cc_final: 0.7544 (ttpp) REVERT: R 117 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: R 126 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.6529 (ptmt) REVERT: S 68 MET cc_start: 0.8362 (ttp) cc_final: 0.7940 (ttp) REVERT: S 115 LEU cc_start: 0.8280 (tp) cc_final: 0.7980 (mt) REVERT: S 183 ILE cc_start: 0.8804 (mt) cc_final: 0.8545 (mt) REVERT: S 186 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7194 (p0) REVERT: S 248 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: S 287 LYS cc_start: 0.9018 (mttp) cc_final: 0.8504 (pttt) REVERT: T 260 VAL cc_start: 0.9273 (t) cc_final: 0.8956 (p) REVERT: T 304 TYR cc_start: 0.8533 (m-80) cc_final: 0.8305 (m-80) REVERT: T 475 GLU cc_start: 0.7530 (tp30) cc_final: 0.6740 (pt0) REVERT: U 112 ASP cc_start: 0.7736 (t0) cc_final: 0.7329 (t0) REVERT: U 260 VAL cc_start: 0.9354 (t) cc_final: 0.9066 (m) REVERT: U 371 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: U 389 ASP cc_start: 0.8168 (t0) cc_final: 0.7745 (m-30) REVERT: U 511 LYS cc_start: 0.7820 (tttt) cc_final: 0.7210 (mmtp) REVERT: V 384 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6395 (pp20) REVERT: V 488 GLN cc_start: 0.6604 (tp40) cc_final: 0.6332 (tp40) REVERT: V 536 LEU cc_start: 0.8366 (tp) cc_final: 0.8017 (tt) REVERT: X 179 ILE cc_start: 0.9291 (mm) cc_final: 0.8638 (mt) REVERT: X 427 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: Y 194 MET cc_start: 0.8686 (tpp) cc_final: 0.8028 (mpp) REVERT: Y 225 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7458 (mmm160) REVERT: Y 250 GLN cc_start: 0.8312 (mm110) cc_final: 0.7722 (mm110) REVERT: Y 401 ARG cc_start: 0.7392 (mmm160) cc_final: 0.6801 (mmm-85) REVERT: Y 497 GLU cc_start: 0.7971 (tp30) cc_final: 0.7712 (tp30) REVERT: Z 152 GLU cc_start: 0.7872 (tp30) cc_final: 0.7418 (tt0) REVERT: Z 366 ARG cc_start: 0.7295 (tpt170) cc_final: 0.6073 (tpt170) REVERT: Z 404 GLN cc_start: 0.8166 (mt0) cc_final: 0.7698 (mt0) REVERT: Z 425 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5059 (mt) outliers start: 181 outliers final: 126 residues processed: 1012 average time/residue: 0.5300 time to fit residues: 922.7134 Evaluate side-chains 919 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 783 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 487 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 1 residue 615 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 118 THR Chi-restraints excluded: chain 4 residue 156 ASP Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 179 ASP Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 20 ILE Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 37 VAL Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 248 GLU Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 539 ILE Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 425 LEU Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 384 optimal weight: 4.9990 chunk 493 optimal weight: 4.9990 chunk 382 optimal weight: 7.9990 chunk 568 optimal weight: 5.9990 chunk 377 optimal weight: 4.9990 chunk 672 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 410 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 427 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN P 65 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 104 GLN U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN U 549 HIS ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 54685 Z= 0.304 Angle : 0.627 14.562 74157 Z= 0.317 Chirality : 0.044 0.214 8689 Planarity : 0.004 0.081 9508 Dihedral : 5.847 98.398 7679 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 3.89 % Allowed : 21.79 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % 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: -0.53 (0.10), residues: 7036 helix: 0.41 (0.09), residues: 3833 sheet: -1.36 (0.20), residues: 637 loop : -1.11 (0.12), residues: 2566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 21 HIS 0.007 0.001 HIS 4 233 PHE 0.036 0.002 PHE A 107 TYR 0.023 0.002 TYR Q 9 ARG 0.005 0.000 ARG V 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 780 time to evaluate : 4.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 52 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7572 (tp-100) REVERT: 4 134 TYR cc_start: 0.8039 (t80) cc_final: 0.7190 (t80) REVERT: 4 232 ARG cc_start: 0.8722 (ttp-110) cc_final: 0.8414 (mtp85) REVERT: 6 52 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8637 (mtmm) REVERT: 6 99 TRP cc_start: 0.8087 (p-90) cc_final: 0.7681 (p-90) REVERT: 7 24 GLN cc_start: 0.7607 (pt0) cc_final: 0.6798 (pp30) REVERT: 7 135 ASP cc_start: 0.7973 (t0) cc_final: 0.7646 (t0) REVERT: 8 69 LYS cc_start: 0.8305 (mttt) cc_final: 0.7680 (tmtt) REVERT: 9 11 PHE cc_start: 0.8152 (t80) cc_final: 0.7875 (t80) REVERT: 9 29 PHE cc_start: 0.6502 (m-80) cc_final: 0.5355 (m-80) REVERT: B 87 ASN cc_start: 0.7860 (m110) cc_final: 0.7346 (m-40) REVERT: C 97 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7867 (tptm) REVERT: D 71 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7695 (mm) REVERT: G 82 PHE cc_start: 0.8669 (m-80) cc_final: 0.8361 (m-80) REVERT: H 81 MET cc_start: 0.8253 (ptp) cc_final: 0.7902 (ptm) REVERT: H 97 LYS cc_start: 0.8648 (mmtt) cc_final: 0.7866 (mttt) REVERT: H 109 LEU cc_start: 0.8814 (tp) cc_final: 0.8520 (tp) REVERT: I 100 VAL cc_start: 0.9136 (t) cc_final: 0.8905 (p) REVERT: M 259 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8639 (mp) REVERT: M 302 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9062 (mm) REVERT: P 140 ASN cc_start: 0.8521 (m-40) cc_final: 0.8252 (m110) REVERT: Q 32 LYS cc_start: 0.6378 (mmmt) cc_final: 0.5959 (mtpt) REVERT: Q 42 ARG cc_start: 0.8169 (ptp90) cc_final: 0.7903 (mtm-85) REVERT: R 31 LYS cc_start: 0.8039 (tmtt) cc_final: 0.7702 (ttpp) REVERT: R 117 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7437 (mm-30) REVERT: R 126 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.6443 (ptmt) REVERT: S 68 MET cc_start: 0.8395 (ttp) cc_final: 0.7893 (ttp) REVERT: S 183 ILE cc_start: 0.8834 (mt) cc_final: 0.8611 (mt) REVERT: S 186 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7273 (p0) REVERT: S 274 MET cc_start: 0.8672 (mmt) cc_final: 0.8066 (mmp) REVERT: T 304 TYR cc_start: 0.8645 (m-80) cc_final: 0.8346 (m-80) REVERT: T 537 LYS cc_start: 0.8305 (tptt) cc_final: 0.8068 (tptp) REVERT: U 112 ASP cc_start: 0.7827 (t0) cc_final: 0.7476 (t0) REVERT: U 371 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: U 389 ASP cc_start: 0.8281 (t0) cc_final: 0.7842 (m-30) REVERT: U 511 LYS cc_start: 0.7783 (tttt) cc_final: 0.7183 (mmtp) REVERT: V 384 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6268 (pp20) REVERT: V 488 GLN cc_start: 0.6915 (tp40) cc_final: 0.6564 (tp40) REVERT: V 546 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8350 (tt) REVERT: X 427 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: Y 194 MET cc_start: 0.8721 (tpp) cc_final: 0.8030 (mpp) REVERT: Y 250 GLN cc_start: 0.8296 (mm110) cc_final: 0.7668 (mm110) REVERT: Y 401 ARG cc_start: 0.7332 (mmm160) cc_final: 0.6476 (mmm-85) REVERT: Y 497 GLU cc_start: 0.8023 (tp30) cc_final: 0.7788 (tm-30) REVERT: Z 385 ARG cc_start: 0.7613 (ttm170) cc_final: 0.7388 (ttm170) REVERT: Z 404 GLN cc_start: 0.8245 (mt0) cc_final: 0.7707 (mt0) REVERT: Z 425 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5205 (mt) outliers start: 219 outliers final: 170 residues processed: 939 average time/residue: 0.4929 time to fit residues: 796.7942 Evaluate side-chains 937 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 757 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 487 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 1 residue 615 VAL Chi-restraints excluded: chain 2 residue 39 LEU Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 228 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 427 GLN Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 132 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 279 GLU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 205 THR Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 37 VAL Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 94 ASN Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 132 ASP Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 53 ILE Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 255 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 217 THR Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 326 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 425 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 481 LEU Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 6.9990 chunk 268 optimal weight: 0.0370 chunk 401 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 458 optimal weight: 0.9980 chunk 332 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 528 optimal weight: 8.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 177 GLN 2 427 GLN 5 75 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 66 GLN ** P 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 441 GLN U 134 ASN ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 54685 Z= 0.204 Angle : 0.585 13.088 74157 Z= 0.296 Chirality : 0.043 0.491 8689 Planarity : 0.004 0.056 9508 Dihedral : 5.705 95.850 7679 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.22 % Favored : 95.69 % Rotamer: Outliers : 3.14 % Allowed : 23.03 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.34 (0.10), residues: 7036 helix: 0.58 (0.09), residues: 3826 sheet: -1.24 (0.21), residues: 621 loop : -1.05 (0.12), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 21 HIS 0.006 0.001 HIS 4 233 PHE 0.041 0.001 PHE A 107 TYR 0.023 0.001 TYR Q 9 ARG 0.004 0.000 ARG V 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 804 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 142 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8661 (ttm110) REVERT: 3 209 LEU cc_start: 0.9251 (mt) cc_final: 0.9005 (mt) REVERT: 4 52 GLN cc_start: 0.8318 (tp-100) cc_final: 0.7566 (tp-100) REVERT: 4 134 TYR cc_start: 0.7984 (t80) cc_final: 0.7196 (t80) REVERT: 4 232 ARG cc_start: 0.8700 (ttp-110) cc_final: 0.8435 (mtp85) REVERT: 6 52 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8630 (mtmm) REVERT: 6 99 TRP cc_start: 0.7860 (p-90) cc_final: 0.7454 (p-90) REVERT: 7 135 ASP cc_start: 0.7925 (t0) cc_final: 0.7606 (t0) REVERT: 8 43 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8334 (mmm160) REVERT: 8 69 LYS cc_start: 0.8272 (mttt) cc_final: 0.7678 (tmtt) REVERT: 9 11 PHE cc_start: 0.8118 (t80) cc_final: 0.7865 (t80) REVERT: 9 29 PHE cc_start: 0.6407 (m-80) cc_final: 0.5265 (m-80) REVERT: 9 68 MET cc_start: 0.7760 (ptm) cc_final: 0.7446 (ptp) REVERT: B 87 ASN cc_start: 0.7779 (m110) cc_final: 0.7324 (m-40) REVERT: C 97 LYS cc_start: 0.8041 (mmtm) cc_final: 0.7782 (tptm) REVERT: G 82 PHE cc_start: 0.8610 (m-80) cc_final: 0.8336 (m-80) REVERT: H 81 MET cc_start: 0.8301 (ptp) cc_final: 0.7932 (ptm) REVERT: H 97 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7780 (mttt) REVERT: H 109 LEU cc_start: 0.8720 (tp) cc_final: 0.8478 (tt) REVERT: I 100 VAL cc_start: 0.9034 (t) cc_final: 0.8796 (p) REVERT: M 99 ASP cc_start: 0.8736 (t0) cc_final: 0.8448 (m-30) REVERT: P 140 ASN cc_start: 0.8449 (m-40) cc_final: 0.8146 (m110) REVERT: Q 32 LYS cc_start: 0.6534 (mmmt) cc_final: 0.6268 (mtpt) REVERT: Q 48 ARG cc_start: 0.8212 (ptt90) cc_final: 0.7838 (ptt90) REVERT: R 31 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7737 (ttpp) REVERT: R 117 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7443 (mm-30) REVERT: R 126 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6427 (ptmt) REVERT: S 68 MET cc_start: 0.8347 (ttp) cc_final: 0.7860 (ttp) REVERT: S 115 LEU cc_start: 0.8416 (tp) cc_final: 0.7934 (mt) REVERT: S 186 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7208 (p0) REVERT: S 274 MET cc_start: 0.8627 (mmt) cc_final: 0.7732 (mmt) REVERT: T 304 TYR cc_start: 0.8577 (m-80) cc_final: 0.8317 (m-80) REVERT: U 112 ASP cc_start: 0.7824 (t0) cc_final: 0.7449 (t0) REVERT: U 260 VAL cc_start: 0.9364 (t) cc_final: 0.9072 (m) REVERT: U 371 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7343 (pm20) REVERT: U 389 ASP cc_start: 0.8176 (t0) cc_final: 0.7693 (m-30) REVERT: V 384 GLU cc_start: 0.7015 (tm-30) cc_final: 0.6284 (pp20) REVERT: V 488 GLN cc_start: 0.6723 (tp40) cc_final: 0.6420 (tp40) REVERT: V 536 LEU cc_start: 0.8443 (tp) cc_final: 0.8072 (tt) REVERT: V 546 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8303 (tt) REVERT: X 427 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: Y 169 LEU cc_start: 0.8716 (tt) cc_final: 0.8119 (mt) REVERT: Y 250 GLN cc_start: 0.8304 (mm110) cc_final: 0.7700 (mm110) REVERT: Y 401 ARG cc_start: 0.7380 (mmm160) cc_final: 0.6768 (mmm-85) REVERT: Y 497 GLU cc_start: 0.8014 (tp30) cc_final: 0.7806 (tm-30) REVERT: Z 404 GLN cc_start: 0.8226 (mt0) cc_final: 0.7721 (mt0) REVERT: Z 425 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5321 (mt) outliers start: 177 outliers final: 149 residues processed: 933 average time/residue: 0.5049 time to fit residues: 809.6672 Evaluate side-chains 924 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 768 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 487 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 1 residue 615 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 2 residue 427 GLN Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 205 THR Chi-restraints excluded: chain 4 residue 222 ILE Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 75 GLN Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 190 GLN Chi-restraints excluded: chain 8 residue 31 SER Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 37 VAL Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 255 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 542 ILE Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain V residue 55 SER Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 425 LEU Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.8980 chunk 644 optimal weight: 10.0000 chunk 588 optimal weight: 0.0570 chunk 626 optimal weight: 8.9990 chunk 377 optimal weight: 0.7980 chunk 273 optimal weight: 3.9990 chunk 492 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 566 optimal weight: 4.9990 chunk 592 optimal weight: 0.1980 chunk 624 optimal weight: 3.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 344 GLN 5 75 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 66 GLN P 83 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN Y 388 ASN Z 471 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54685 Z= 0.188 Angle : 0.591 12.695 74157 Z= 0.297 Chirality : 0.043 0.650 8689 Planarity : 0.004 0.048 9508 Dihedral : 5.587 93.083 7679 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.67 % Rotamer: Outliers : 3.20 % Allowed : 23.23 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.26 (0.10), residues: 7036 helix: 0.63 (0.09), residues: 3839 sheet: -1.21 (0.21), residues: 625 loop : -1.01 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 5 21 HIS 0.006 0.001 HIS 4 233 PHE 0.043 0.001 PHE V 459 TYR 0.022 0.001 TYR H 102 ARG 0.009 0.000 ARG 2 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 811 time to evaluate : 4.524 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: 2 420 GLU cc_start: 0.6788 (tp30) cc_final: 0.6586 (tp30) REVERT: 3 209 LEU cc_start: 0.9259 (mt) cc_final: 0.9019 (mt) REVERT: 4 52 GLN cc_start: 0.8347 (tp-100) cc_final: 0.7630 (tp-100) REVERT: 4 134 TYR cc_start: 0.7979 (t80) cc_final: 0.7320 (t80) REVERT: 4 232 ARG cc_start: 0.8685 (ttp-110) cc_final: 0.8444 (mtp85) REVERT: 6 52 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8641 (mtmm) REVERT: 6 99 TRP cc_start: 0.7810 (p-90) cc_final: 0.7483 (p-90) REVERT: 7 135 ASP cc_start: 0.7942 (t0) cc_final: 0.7548 (t0) REVERT: 8 69 LYS cc_start: 0.8273 (mttt) cc_final: 0.7682 (tmtt) REVERT: 9 11 PHE cc_start: 0.8105 (t80) cc_final: 0.7856 (t80) REVERT: 9 29 PHE cc_start: 0.6387 (m-80) cc_final: 0.5247 (m-10) REVERT: 9 68 MET cc_start: 0.7802 (ptm) cc_final: 0.7517 (ptp) REVERT: A 123 LEU cc_start: 0.8417 (tp) cc_final: 0.8204 (tp) REVERT: B 87 ASN cc_start: 0.7807 (m110) cc_final: 0.7388 (m-40) REVERT: C 97 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7781 (tptm) REVERT: C 105 LEU cc_start: 0.8172 (tt) cc_final: 0.7751 (tp) REVERT: F 82 PHE cc_start: 0.8335 (m-80) cc_final: 0.8116 (m-10) REVERT: G 82 PHE cc_start: 0.8489 (m-80) cc_final: 0.8194 (m-80) REVERT: H 81 MET cc_start: 0.8234 (ptp) cc_final: 0.7897 (ptm) REVERT: H 97 LYS cc_start: 0.8491 (mmtt) cc_final: 0.7724 (mttt) REVERT: H 109 LEU cc_start: 0.8730 (tp) cc_final: 0.8498 (tt) REVERT: I 100 VAL cc_start: 0.9042 (t) cc_final: 0.8815 (p) REVERT: M 99 ASP cc_start: 0.8759 (t0) cc_final: 0.8498 (m-30) REVERT: P 140 ASN cc_start: 0.8421 (m-40) cc_final: 0.8118 (m110) REVERT: P 172 LYS cc_start: 0.7523 (tppt) cc_final: 0.6974 (mtmm) REVERT: Q 32 LYS cc_start: 0.6433 (mmmt) cc_final: 0.6231 (mtpt) REVERT: Q 42 ARG cc_start: 0.8094 (ptp-170) cc_final: 0.7613 (ptp90) REVERT: Q 48 ARG cc_start: 0.8205 (ptt90) cc_final: 0.7841 (ptt90) REVERT: R 117 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7422 (mm-30) REVERT: R 126 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6497 (ptmt) REVERT: S 68 MET cc_start: 0.8368 (ttp) cc_final: 0.7897 (ttp) REVERT: S 115 LEU cc_start: 0.8455 (tp) cc_final: 0.7968 (mt) REVERT: S 186 ASN cc_start: 0.7723 (OUTLIER) cc_final: 0.7178 (p0) REVERT: S 274 MET cc_start: 0.8597 (mmt) cc_final: 0.7689 (mmt) REVERT: T 304 TYR cc_start: 0.8556 (m-80) cc_final: 0.8295 (m-80) REVERT: T 537 LYS cc_start: 0.8327 (tptt) cc_final: 0.7968 (mmmm) REVERT: U 112 ASP cc_start: 0.7825 (t0) cc_final: 0.7420 (t0) REVERT: U 203 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: U 260 VAL cc_start: 0.9356 (t) cc_final: 0.9087 (m) REVERT: U 371 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: U 389 ASP cc_start: 0.8114 (t0) cc_final: 0.7662 (m-30) REVERT: U 403 ASP cc_start: 0.8474 (m-30) cc_final: 0.8211 (m-30) REVERT: V 49 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6948 (mmm160) REVERT: V 384 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6288 (pp20) REVERT: V 488 GLN cc_start: 0.6550 (tp40) cc_final: 0.6260 (tp40) REVERT: V 536 LEU cc_start: 0.8449 (tp) cc_final: 0.8076 (tt) REVERT: V 546 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8300 (tt) REVERT: X 179 ILE cc_start: 0.9275 (mm) cc_final: 0.8682 (mt) REVERT: X 427 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6429 (mp0) REVERT: Y 169 LEU cc_start: 0.8712 (tt) cc_final: 0.8133 (mt) REVERT: Y 225 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7558 (mmm160) REVERT: Y 401 ARG cc_start: 0.7350 (mmm160) cc_final: 0.6773 (mmm-85) REVERT: Z 404 GLN cc_start: 0.8188 (mt0) cc_final: 0.7701 (mt0) outliers start: 180 outliers final: 155 residues processed: 938 average time/residue: 0.5116 time to fit residues: 826.1375 Evaluate side-chains 941 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 779 time to evaluate : 4.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 487 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 1 residue 615 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 237 LEU Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 205 THR Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 190 GLN Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 37 VAL Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 207 PHE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 281 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 471 GLN Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 5.9990 chunk 662 optimal weight: 9.9990 chunk 404 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 460 optimal weight: 0.9980 chunk 695 optimal weight: 10.0000 chunk 640 optimal weight: 2.9990 chunk 553 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 427 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN ** M 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN P 66 GLN P 83 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 191 GLN T 61 HIS U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 549 HIS ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 54685 Z= 0.243 Angle : 0.613 11.676 74157 Z= 0.308 Chirality : 0.044 0.573 8689 Planarity : 0.004 0.047 9508 Dihedral : 5.610 94.702 7679 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.27 % Rotamer: Outliers : 3.16 % Allowed : 23.37 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.27 (0.10), residues: 7036 helix: 0.60 (0.09), residues: 3853 sheet: -1.21 (0.21), residues: 624 loop : -0.98 (0.13), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 21 HIS 0.009 0.001 HIS U 549 PHE 0.041 0.002 PHE A 107 TYR 0.023 0.002 TYR H 102 ARG 0.006 0.000 ARG Y 435 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14072 Ramachandran restraints generated. 7036 Oldfield, 0 Emsley, 7036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 784 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 209 LEU cc_start: 0.9226 (mt) cc_final: 0.9004 (mt) REVERT: 4 52 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7612 (tp-100) REVERT: 4 134 TYR cc_start: 0.7970 (t80) cc_final: 0.7299 (t80) REVERT: 4 232 ARG cc_start: 0.8706 (ttp-110) cc_final: 0.8459 (mtp85) REVERT: 6 52 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8612 (mtmm) REVERT: 6 94 SER cc_start: 0.8635 (p) cc_final: 0.8238 (t) REVERT: 6 99 TRP cc_start: 0.7938 (p-90) cc_final: 0.7636 (p-90) REVERT: 7 135 ASP cc_start: 0.7984 (t0) cc_final: 0.7598 (t0) REVERT: 8 69 LYS cc_start: 0.8277 (mttt) cc_final: 0.7687 (tmtt) REVERT: 9 11 PHE cc_start: 0.8156 (t80) cc_final: 0.7907 (t80) REVERT: 9 29 PHE cc_start: 0.6372 (m-80) cc_final: 0.5218 (m-10) REVERT: 9 68 MET cc_start: 0.7922 (ptm) cc_final: 0.7645 (ptp) REVERT: A 123 LEU cc_start: 0.8464 (tp) cc_final: 0.8252 (tp) REVERT: B 87 ASN cc_start: 0.7792 (m110) cc_final: 0.7372 (m-40) REVERT: C 97 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7757 (tptm) REVERT: C 105 LEU cc_start: 0.8151 (tt) cc_final: 0.7731 (tp) REVERT: D 71 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7722 (mm) REVERT: D 81 MET cc_start: 0.8831 (tpp) cc_final: 0.8347 (tpp) REVERT: G 82 PHE cc_start: 0.8529 (m-80) cc_final: 0.8211 (m-80) REVERT: H 66 CYS cc_start: 0.8203 (p) cc_final: 0.7979 (p) REVERT: H 81 MET cc_start: 0.8130 (ptp) cc_final: 0.7848 (ptm) REVERT: H 97 LYS cc_start: 0.8481 (mmtt) cc_final: 0.7737 (mttt) REVERT: H 109 LEU cc_start: 0.8753 (tp) cc_final: 0.8494 (tt) REVERT: I 100 VAL cc_start: 0.9070 (t) cc_final: 0.8859 (p) REVERT: M 99 ASP cc_start: 0.8778 (t0) cc_final: 0.8499 (m-30) REVERT: M 259 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8719 (mp) REVERT: P 136 GLU cc_start: 0.7141 (tt0) cc_final: 0.6882 (tt0) REVERT: P 140 ASN cc_start: 0.8496 (m-40) cc_final: 0.8201 (m110) REVERT: P 172 LYS cc_start: 0.7523 (tppt) cc_final: 0.6995 (mtmm) REVERT: Q 42 ARG cc_start: 0.8100 (ptp-170) cc_final: 0.7599 (ptp90) REVERT: Q 48 ARG cc_start: 0.8245 (ptt90) cc_final: 0.8002 (ptt90) REVERT: R 31 LYS cc_start: 0.7922 (tmtt) cc_final: 0.7514 (ttpp) REVERT: R 117 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7402 (mm-30) REVERT: R 126 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6492 (ptmt) REVERT: S 68 MET cc_start: 0.8389 (ttp) cc_final: 0.7914 (ttp) REVERT: S 115 LEU cc_start: 0.8442 (tp) cc_final: 0.7925 (mt) REVERT: S 186 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7123 (p0) REVERT: S 274 MET cc_start: 0.8639 (mmt) cc_final: 0.7744 (mmt) REVERT: T 304 TYR cc_start: 0.8584 (m-80) cc_final: 0.8334 (m-80) REVERT: T 537 LYS cc_start: 0.8320 (tptt) cc_final: 0.7969 (mmmm) REVERT: U 112 ASP cc_start: 0.7843 (t0) cc_final: 0.7445 (t0) REVERT: U 203 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6973 (m-80) REVERT: U 260 VAL cc_start: 0.9374 (t) cc_final: 0.9082 (m) REVERT: U 371 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: U 389 ASP cc_start: 0.8207 (t0) cc_final: 0.7784 (m-30) REVERT: V 49 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6994 (mmm160) REVERT: V 384 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6267 (pp20) REVERT: V 488 GLN cc_start: 0.6592 (tp40) cc_final: 0.6300 (tp40) REVERT: V 546 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8383 (tt) REVERT: X 427 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6356 (mp0) REVERT: Y 169 LEU cc_start: 0.8717 (tt) cc_final: 0.8134 (mt) REVERT: Y 194 MET cc_start: 0.8737 (tpp) cc_final: 0.8052 (mmm) REVERT: Y 250 GLN cc_start: 0.8218 (mm110) cc_final: 0.7720 (mm110) REVERT: Y 401 ARG cc_start: 0.7389 (mmm160) cc_final: 0.6711 (mmm-85) REVERT: Y 550 LYS cc_start: 0.6132 (mmmt) cc_final: 0.5767 (pptt) REVERT: Z 404 GLN cc_start: 0.8224 (mt0) cc_final: 0.7736 (mt0) outliers start: 178 outliers final: 160 residues processed: 912 average time/residue: 0.4878 time to fit residues: 768.6404 Evaluate side-chains 927 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 758 time to evaluate : 4.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 221 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 293 ILE Chi-restraints excluded: chain 1 residue 393 LEU Chi-restraints excluded: chain 1 residue 487 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 532 ILE Chi-restraints excluded: chain 1 residue 615 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 366 LEU Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 159 THR Chi-restraints excluded: chain 3 residue 162 GLU Chi-restraints excluded: chain 3 residue 174 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 311 LEU Chi-restraints excluded: chain 3 residue 316 VAL Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 4 residue 205 THR Chi-restraints excluded: chain 4 residue 238 VAL Chi-restraints excluded: chain 4 residue 279 ASP Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 6 residue 69 THR Chi-restraints excluded: chain 6 residue 79 LEU Chi-restraints excluded: chain 6 residue 116 PHE Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 59 THR Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 7 residue 114 TYR Chi-restraints excluded: chain 7 residue 168 THR Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 7 residue 190 GLN Chi-restraints excluded: chain 8 residue 34 THR Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 37 VAL Chi-restraints excluded: chain 9 residue 42 VAL Chi-restraints excluded: chain 9 residue 49 VAL Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 168 MET Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 158 THR Chi-restraints excluded: chain P residue 170 LEU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 126 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 186 ASN Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain S residue 301 THR Chi-restraints excluded: chain T residue 72 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 183 SER Chi-restraints excluded: chain T residue 222 LEU Chi-restraints excluded: chain T residue 255 VAL Chi-restraints excluded: chain T residue 322 ILE Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain U residue 82 ILE Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 203 PHE Chi-restraints excluded: chain U residue 204 THR Chi-restraints excluded: chain U residue 224 ILE Chi-restraints excluded: chain U residue 253 GLN Chi-restraints excluded: chain U residue 371 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 429 ARG Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 485 LYS Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 204 THR Chi-restraints excluded: chain V residue 258 VAL Chi-restraints excluded: chain V residue 399 ILE Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain X residue 122 MET Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain X residue 207 PHE Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 334 THR Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 427 GLU Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 489 VAL Chi-restraints excluded: chain X residue 537 VAL Chi-restraints excluded: chain Y residue 49 ASP Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 87 CYS Chi-restraints excluded: chain Y residue 102 VAL Chi-restraints excluded: chain Y residue 135 ILE Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 247 VAL Chi-restraints excluded: chain Y residue 261 VAL Chi-restraints excluded: chain Y residue 280 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 432 THR Chi-restraints excluded: chain Y residue 449 VAL Chi-restraints excluded: chain Y residue 452 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 547 GLU Chi-restraints excluded: chain Z residue 73 VAL Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 252 ASN Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 341 VAL Chi-restraints excluded: chain Z residue 347 THR Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 500 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.9990 chunk 589 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 chunk 510 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 554 optimal weight: 7.9990 chunk 232 optimal weight: 7.9990 chunk 569 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 344 GLN 2 427 GLN 5 75 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN P 65 ASN P 66 GLN P 83 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 441 GLN U 134 ASN ** U 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 388 ASN Z 471 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.093612 restraints weight = 105334.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095218 restraints weight = 63591.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095920 restraints weight = 46281.546| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 54685 Z= 0.280 Angle : 0.628 11.213 74157 Z= 0.317 Chirality : 0.044 0.468 8689 Planarity : 0.004 0.097 9508 Dihedral : 5.694 98.074 7679 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 3.27 % Allowed : 23.48 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.30 (0.10), residues: 7036 helix: 0.56 (0.09), residues: 3852 sheet: -1.20 (0.21), residues: 616 loop : -0.98 (0.13), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 5 21 HIS 0.007 0.001 HIS 4 233 PHE 0.041 0.002 PHE A 107 TYR 0.023 0.002 TYR H 102 ARG 0.005 0.000 ARG V 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13208.90 seconds wall clock time: 228 minutes 58.33 seconds (13738.33 seconds total)