Starting phenix.real_space_refine on Wed Sep 25 01:19:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdo_4825/09_2024/6rdo_4825.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdo_4825/09_2024/6rdo_4825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdo_4825/09_2024/6rdo_4825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdo_4825/09_2024/6rdo_4825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdo_4825/09_2024/6rdo_4825.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdo_4825/09_2024/6rdo_4825.cif" } resolution = 3.1 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= 1.038 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 390 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: "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: 22.16, per 1000 atoms: 0.41 Number of scatterers: 53748 At special positions: 0 Unit cell: (209.547, 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: 10.88 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 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: 309 helices and 0 sheets defined 58.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.38 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.902A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.582A 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 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.575A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 77 through 81 removed outlier: 3.624A pdb=" N LYS 1 80 " --> pdb=" O PRO 1 77 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN 1 81 " --> pdb=" O LEU 1 78 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 77 through 81' Processing helix chain '1' and resid 96 through 100 removed outlier: 3.550A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.807A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 4.432A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 3.521A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 208 No H-bonds generated for 'chain '1' and resid 206 through 208' Processing helix chain '1' and resid 209 through 224 removed outlier: 4.030A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 Processing helix chain '1' and resid 272 through 277 removed outlier: 3.788A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 278 through 282 removed outlier: 3.717A pdb=" N PHE 1 282 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 removed outlier: 3.683A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.580A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 4.116A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.769A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.796A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.928A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.658A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 removed outlier: 3.620A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.980A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.672A 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 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 587 Processing helix chain '1' and resid 588 through 591 Processing helix chain '1' and resid 592 through 606 Processing helix chain '1' and resid 610 through 614 Processing helix chain '2' and resid 7 through 17 removed outlier: 3.547A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 40 Processing helix chain '2' and resid 44 through 58 removed outlier: 4.133A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 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 Processing helix chain '2' and resid 117 through 131 removed outlier: 3.885A 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 154 through 168 removed outlier: 3.658A 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: 4.289A 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 206 through 220 Processing helix chain '2' and resid 228 through 235 Processing helix chain '2' and resid 240 through 253 removed outlier: 3.819A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.733A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.600A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 4.109A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.688A 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 354 Processing helix chain '2' and resid 396 through 408 removed outlier: 3.937A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 102 through 113 removed outlier: 3.605A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 128 removed outlier: 3.534A pdb=" N PHE 3 121 " --> pdb=" O SER 3 117 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (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: 3.755A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 187 removed outlier: 4.205A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 205 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.512A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.585A 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 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.644A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 287 removed outlier: 4.029A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 311 removed outlier: 3.677A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 13 removed outlier: 3.674A pdb=" N LEU 4 12 " --> pdb=" O LYS 4 8 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 13' Processing helix chain '4' and resid 19 through 35 removed outlier: 3.531A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 4.187A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.697A 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 removed outlier: 3.502A pdb=" N VAL 4 122 " --> pdb=" O THR 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 150 removed outlier: 3.988A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.981A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 187 removed outlier: 3.735A pdb=" N ILE 4 183 " --> pdb=" O PRO 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 3.759A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 258 removed outlier: 3.612A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.561A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 3.500A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.640A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 removed outlier: 3.579A pdb=" N PHE 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 106 removed outlier: 4.040A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 removed outlier: 3.828A pdb=" N ILE 6 54 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.521A 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 117 removed outlier: 3.811A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.090A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 102 removed outlier: 3.733A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 113 removed outlier: 3.790A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 121 removed outlier: 3.623A pdb=" N TYR 7 120 " --> pdb=" O LYS 7 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG 7 121 " --> pdb=" O ASP 7 117 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 removed outlier: 3.590A 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 Processing helix chain '7' and resid 174 through 188 removed outlier: 3.567A pdb=" N SER 7 188 " --> pdb=" O ASN 7 184 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.532A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.578A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 3.755A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 17 Processing helix chain '9' and resid 32 through 55 removed outlier: 4.020A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 3.619A pdb=" N GLU 9 92 " --> pdb=" O GLU 9 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 4.684A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.867A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.588A 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 126 removed outlier: 3.570A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 4.386A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.716A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 124 removed outlier: 4.374A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.786A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.969A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.883A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 4.206A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.943A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.921A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.751A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 90 removed outlier: 4.138A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 110 through 126 removed outlier: 3.880A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.985A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 124 removed outlier: 3.914A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 4.442A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.818A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 4.311A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.855A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 4.072A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.665A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 4.221A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.829A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.726A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 removed outlier: 3.526A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'I' and resid 97 through 127 removed outlier: 3.698A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.209A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 90 removed outlier: 3.975A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.583A pdb=" N ILE J 95 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 96' Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.646A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 removed outlier: 3.601A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 143 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.962A 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: 3.526A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 258 removed outlier: 4.512A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.699A pdb=" N PHE M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.820A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 60 removed outlier: 3.704A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.506A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.533A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 105 removed outlier: 3.849A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 125 removed outlier: 3.748A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.544A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.559A pdb=" N ALA P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 Processing helix chain 'P' and resid 210 through 226 Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.561A pdb=" N TYR Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.211A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 44 removed outlier: 3.865A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 removed outlier: 4.364A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.726A 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: 4.125A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 Processing helix chain 'S' and resid 40 through 70 removed outlier: 3.842A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 3.575A pdb=" N SER S 78 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 90 removed outlier: 4.342A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.617A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 3.644A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 148' Processing helix chain 'S' and resid 171 through 182 Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.730A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.650A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 76 removed outlier: 3.665A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 3.522A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.101A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.708A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.536A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 3.610A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 removed outlier: 3.525A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.734A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.525A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 434 removed outlier: 3.865A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.774A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 460 removed outlier: 3.824A pdb=" N GLN T 452 " --> pdb=" O LEU T 448 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.950A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 506 removed outlier: 3.562A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 527 removed outlier: 4.929A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 540 removed outlier: 3.807A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 554 removed outlier: 3.921A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 47 removed outlier: 3.726A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 removed outlier: 3.573A pdb=" N VAL U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 72 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.874A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.826A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.621A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.011A 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 284 Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.603A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.797A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 400 removed outlier: 3.524A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.839A pdb=" N LYS U 415 " --> pdb=" O GLU U 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.001A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.786A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.570A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.664A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.809A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.972A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (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: 3.944A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.733A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.583A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.598A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.997A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.050A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.632A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 4.030A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.681A 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 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 526 removed outlier: 4.228A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.609A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 4.169A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.528A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 4.679A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.733A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 275 removed outlier: 3.528A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 removed outlier: 3.846A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU X 300 " --> pdb=" O GLU X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.548A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 421 removed outlier: 4.548A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 491 through 505 Processing helix chain 'X' and resid 526 through 533 removed outlier: 4.052A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) 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: 3.787A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 3.615A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.789A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.707A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 371 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 418 removed outlier: 3.903A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 482 through 487 Processing helix chain 'Y' and resid 491 through 507 removed outlier: 3.894A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Y' and resid 544 through 555 Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 170 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.510A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.080A 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 365 through 370 Processing helix chain 'Z' and resid 392 through 412 removed outlier: 4.283A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 4.079A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 426 through 443 Processing helix chain 'Z' and resid 447 through 449 No H-bonds generated for 'chain 'Z' and resid 447 through 449' Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.615A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 487 removed outlier: 3.787A pdb=" N TYR Z 487 " --> pdb=" O MET Z 484 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 508 removed outlier: 3.683A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 2562 hydrogen bonds defined for protein. 7509 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: 13.25 Time building geometry restraints manager: 12.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12615 1.33 - 1.45: 11629 1.45 - 1.58: 30167 1.58 - 1.70: 21 1.70 - 1.82: 254 Bond restraints: 54686 Sorted by residual: 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 4.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.07e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.47e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 73447 3.81 - 7.62: 641 7.62 - 11.44: 62 11.44 - 15.25: 8 15.25 - 19.06: 3 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.01 17.86 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.70 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 31080 23.29 - 46.57: 1719 46.57 - 69.86: 172 69.86 - 93.15: 52 93.15 - 116.44: 2 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: 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 -119.20 -60.80 0 5.00e+00 4.00e-02 1.48e+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 -120.33 -59.67 0 5.00e+00 4.00e-02 1.42e+02 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 -123.12 -56.88 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 7786 0.098 - 0.196: 850 0.196 - 0.294: 49 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE P 157 " pdb=" CA ILE P 157 " pdb=" CG1 ILE P 157 " pdb=" CG2 ILE P 157 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.88e-02 3.45e+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 U 296 " 0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO U 297 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 348 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO X 349 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO X 349 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 349 " 0.046 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 544 2.60 - 3.17: 44405 3.17 - 3.75: 86749 3.75 - 4.32: 125407 4.32 - 4.90: 204044 Nonbonded interactions: 461149 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.023 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.114 2.170 nonbonded pdb=" O3G ATP V1001 " pdb="MG MG V1002 " model vdw 2.120 2.170 ... (remaining 461144 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 1.470 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 90.950 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 0.011 0.123 54686 Z= 0.691 Angle : 1.021 19.062 74161 Z= 0.577 Chirality : 0.062 0.490 8689 Planarity : 0.008 0.087 9510 Dihedral : 14.485 116.437 19939 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.19 % Favored : 94.61 % Rotamer: Outliers : 0.41 % Allowed : 6.64 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.08), residues: 7038 helix: -2.91 (0.06), residues: 3828 sheet: -1.33 (0.20), residues: 647 loop : -2.04 (0.11), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP Z 141 HIS 0.013 0.002 HIS S 250 PHE 0.043 0.003 PHE E 122 TYR 0.031 0.003 TYR 4 211 ARG 0.010 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 940 time to evaluate : 4.421 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: 0 37 LYS cc_start: 0.7934 (tptp) cc_final: 0.7580 (ttpp) REVERT: 1 191 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6311 (tp30) REVERT: 4 124 ASN cc_start: 0.8217 (m-40) cc_final: 0.7973 (m-40) REVERT: 5 108 LEU cc_start: 0.8587 (mm) cc_final: 0.8357 (mt) REVERT: 6 98 GLU cc_start: 0.7476 (mp0) cc_final: 0.7263 (mp0) REVERT: 7 184 ASN cc_start: 0.8514 (t0) cc_final: 0.8229 (t0) REVERT: 8 5 GLU cc_start: 0.8164 (tt0) cc_final: 0.7931 (tt0) REVERT: 8 69 LYS cc_start: 0.8963 (mttt) cc_final: 0.7128 (tmtt) REVERT: 8 81 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8125 (mttm) REVERT: 9 9 LYS cc_start: 0.6801 (ttpt) cc_final: 0.6274 (tttm) REVERT: 9 80 GLN cc_start: 0.8167 (tp40) cc_final: 0.7929 (tp-100) REVERT: 9 89 MET cc_start: 0.8745 (mtp) cc_final: 0.8462 (mtp) REVERT: B 81 MET cc_start: 0.7124 (ttp) cc_final: 0.6764 (ttp) REVERT: B 92 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7053 (p0) REVERT: P 52 GLN cc_start: 0.8290 (tt0) cc_final: 0.7667 (tt0) REVERT: P 191 ASP cc_start: 0.8273 (t70) cc_final: 0.7894 (t0) REVERT: S 58 LYS cc_start: 0.7859 (tttt) cc_final: 0.7587 (tptm) REVERT: S 109 LYS cc_start: 0.7730 (mttt) cc_final: 0.7509 (mtmt) REVERT: S 220 LEU cc_start: 0.8069 (mm) cc_final: 0.7794 (mm) REVERT: T 79 PRO cc_start: 0.8490 (Cg_exo) cc_final: 0.7842 (Cg_endo) REVERT: T 121 ASN cc_start: 0.8737 (p0) cc_final: 0.8477 (p0) REVERT: T 471 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7709 (tp-100) REVERT: T 475 GLU cc_start: 0.7952 (tp30) cc_final: 0.7503 (tp30) REVERT: U 41 ASP cc_start: 0.7061 (m-30) cc_final: 0.6658 (m-30) REVERT: U 47 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6890 (mm-30) REVERT: U 227 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.8051 (ttp80) REVERT: U 414 TYR cc_start: 0.7506 (t80) cc_final: 0.7032 (t80) REVERT: U 481 THR cc_start: 0.8597 (p) cc_final: 0.8388 (m) REVERT: U 483 MET cc_start: 0.7320 (tpp) cc_final: 0.7094 (tmm) REVERT: V 283 ARG cc_start: 0.8242 (ttp80) cc_final: 0.7985 (ttt-90) REVERT: V 461 GLN cc_start: 0.7638 (mp10) cc_final: 0.7303 (mp10) REVERT: V 547 ASP cc_start: 0.8628 (t0) cc_final: 0.8407 (t0) REVERT: X 440 GLN cc_start: 0.8660 (mt0) cc_final: 0.8398 (mt0) REVERT: X 488 MET cc_start: 0.8818 (mmt) cc_final: 0.8566 (mmt) REVERT: Y 371 LEU cc_start: 0.8298 (mp) cc_final: 0.8014 (mt) REVERT: Y 401 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6424 (mmt-90) REVERT: Y 405 LYS cc_start: 0.8238 (tptt) cc_final: 0.7857 (ttpt) REVERT: Y 465 ASP cc_start: 0.6976 (m-30) cc_final: 0.6645 (m-30) REVERT: Z 88 ILE cc_start: 0.9095 (tp) cc_final: 0.8862 (pt) REVERT: Z 91 ASP cc_start: 0.8375 (t0) cc_final: 0.8110 (t0) REVERT: Z 227 MET cc_start: 0.9088 (mtt) cc_final: 0.8719 (mtt) outliers start: 23 outliers final: 15 residues processed: 958 average time/residue: 0.5551 time to fit residues: 868.8734 Evaluate side-chains 673 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 657 time to evaluate : 4.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 6.9990 chunk 529 optimal weight: 9.9990 chunk 293 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 356 optimal weight: 0.9990 chunk 282 optimal weight: 0.0570 chunk 547 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 407 optimal weight: 0.8980 chunk 633 optimal weight: 5.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 257 HIS 1 285 GLN 1 313 GLN 1 316 ASN 1 346 GLN 1 365 GLN 1 423 ASN 1 482 ASN 1 587 ASN 1 590 HIS 2 40 GLN 2 68 ASN 2 122 ASN 2 243 GLN 2 289 HIS ** 2 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 97 ASN 3 179 GLN 3 189 HIS 3 206 ASN 4 38 GLN 4 124 ASN 4 135 ASN 4 240 GLN 4 276 GLN 5 29 GLN 5 107 ASN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN 8 26 HIS 9 35 GLN D 94 ASN G 87 ASN H 92 ASN M 108 ASN M 163 ASN P 220 ASN P 223 ASN R 38 ASN R 73 ASN R 85 GLN S 72 GLN S 191 GLN S 293 ASN S 297 GLN T 64 GLN T 104 GLN T 134 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 497 GLN U 104 GLN U 196 GLN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 386 GLN U 405 GLN U 461 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 539 ASN U 549 HIS V 60 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 134 ASN V 139 HIS V 149 GLN V 152 ASN V 196 GLN V 241 HIS V 244 ASN V 386 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN V 527 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 549 HIS X 199 ASN X 408 GLN Y 322 GLN Y 398 ASN Z 132 GLN Z 199 ASN Z 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54686 Z= 0.187 Angle : 0.576 9.523 74161 Z= 0.303 Chirality : 0.042 0.165 8689 Planarity : 0.005 0.062 9510 Dihedral : 6.624 98.381 7692 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.94 % Favored : 95.87 % Rotamer: Outliers : 1.51 % Allowed : 10.18 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.92 (0.09), residues: 7038 helix: -1.04 (0.08), residues: 3887 sheet: -1.03 (0.21), residues: 576 loop : -1.44 (0.12), residues: 2575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 4 206 HIS 0.005 0.001 HIS 7 123 PHE 0.034 0.001 PHE E 122 TYR 0.032 0.001 TYR 4 211 ARG 0.011 0.000 ARG V 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 779 time to evaluate : 4.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.7540 (tptp) cc_final: 0.7326 (ttmm) REVERT: 1 24 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8073 (pp) REVERT: 2 319 ARG cc_start: 0.8785 (ttt-90) cc_final: 0.8475 (ttt90) REVERT: 5 112 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7825 (ptm-80) REVERT: 6 30 ASN cc_start: 0.8696 (p0) cc_final: 0.8351 (p0) REVERT: 7 184 ASN cc_start: 0.8353 (t0) cc_final: 0.7890 (t0) REVERT: 8 62 ASP cc_start: 0.7942 (m-30) cc_final: 0.7741 (m-30) REVERT: 8 69 LYS cc_start: 0.8905 (mttt) cc_final: 0.7147 (tmtt) REVERT: 9 9 LYS cc_start: 0.6743 (ttpt) cc_final: 0.6468 (ttpp) REVERT: D 98 GLN cc_start: 0.7170 (tp40) cc_final: 0.6957 (tt0) REVERT: H 119 LEU cc_start: 0.5508 (OUTLIER) cc_final: 0.5115 (pt) REVERT: I 98 GLN cc_start: 0.7510 (tm-30) cc_final: 0.7231 (tm-30) REVERT: P 49 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8132 (t) REVERT: P 151 GLU cc_start: 0.8068 (mp0) cc_final: 0.7510 (mp0) REVERT: R 118 LEU cc_start: 0.6763 (mm) cc_final: 0.6507 (mm) REVERT: S 58 LYS cc_start: 0.7468 (tttt) cc_final: 0.7223 (tptm) REVERT: S 109 LYS cc_start: 0.7630 (mttt) cc_final: 0.7428 (mtmt) REVERT: S 204 LYS cc_start: 0.7756 (ttmm) cc_final: 0.7517 (tttt) REVERT: T 75 LYS cc_start: 0.8486 (ttpt) cc_final: 0.8196 (tttt) REVERT: T 237 ASP cc_start: 0.7582 (m-30) cc_final: 0.7283 (m-30) REVERT: T 471 GLN cc_start: 0.7597 (tm-30) cc_final: 0.7128 (tp-100) REVERT: T 475 GLU cc_start: 0.7860 (tp30) cc_final: 0.7448 (tp30) REVERT: T 479 ARG cc_start: 0.7618 (mmt180) cc_final: 0.7393 (mmt180) REVERT: U 47 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7001 (mm-30) REVERT: U 227 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7961 (ttp80) REVERT: U 414 TYR cc_start: 0.7463 (t80) cc_final: 0.7005 (t80) REVERT: V 46 ASP cc_start: 0.8241 (m-30) cc_final: 0.7644 (p0) REVERT: V 47 GLU cc_start: 0.7732 (pm20) cc_final: 0.7235 (pm20) REVERT: V 61 HIS cc_start: 0.7875 (m-70) cc_final: 0.7595 (m90) REVERT: V 283 ARG cc_start: 0.8204 (ttp80) cc_final: 0.7943 (ttt-90) REVERT: V 461 GLN cc_start: 0.7700 (mp10) cc_final: 0.7399 (mp10) REVERT: V 489 PHE cc_start: 0.8064 (m-80) cc_final: 0.7795 (m-10) REVERT: V 522 GLU cc_start: 0.7071 (pp20) cc_final: 0.6671 (pp20) REVERT: X 440 GLN cc_start: 0.8513 (mt0) cc_final: 0.8242 (mt0) REVERT: X 488 MET cc_start: 0.8830 (mmt) cc_final: 0.8516 (mmt) REVERT: Y 385 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7506 (mmp-170) REVERT: Y 386 MET cc_start: 0.8449 (mmm) cc_final: 0.8242 (mmm) REVERT: Y 405 LYS cc_start: 0.8070 (tptt) cc_final: 0.7748 (ttpt) REVERT: Y 437 ARG cc_start: 0.7809 (mtm-85) cc_final: 0.7582 (mtm-85) REVERT: Z 91 ASP cc_start: 0.8341 (t0) cc_final: 0.8105 (t0) outliers start: 85 outliers final: 46 residues processed: 830 average time/residue: 0.5489 time to fit residues: 752.8173 Evaluate side-chains 697 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 648 time to evaluate : 4.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 373 ASP Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 510 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 182 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 427 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 395 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 527 optimal weight: 1.9990 chunk 431 optimal weight: 7.9990 chunk 174 optimal weight: 2.9990 chunk 635 optimal weight: 8.9990 chunk 685 optimal weight: 0.0970 chunk 565 optimal weight: 0.9990 chunk 629 optimal weight: 0.9990 chunk 216 optimal weight: 0.0770 chunk 509 optimal weight: 3.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 240 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 35 GLN P 52 GLN P 59 GLN R 85 GLN R 181 ASN T 126 HIS ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 54686 Z= 0.181 Angle : 0.544 11.523 74161 Z= 0.281 Chirality : 0.041 0.165 8689 Planarity : 0.004 0.059 9510 Dihedral : 6.145 83.171 7684 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.22 % Favored : 95.62 % Rotamer: Outliers : 1.69 % Allowed : 11.97 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.00 (0.10), residues: 7038 helix: -0.19 (0.08), residues: 3905 sheet: -0.98 (0.21), residues: 597 loop : -1.12 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 73 HIS 0.004 0.001 HIS V 549 PHE 0.020 0.001 PHE G 107 TYR 0.028 0.001 TYR 4 211 ARG 0.006 0.000 ARG Y 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 736 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: symmetry clash REVERT: 1 24 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8055 (pp) REVERT: 1 194 LYS cc_start: 0.7476 (ptmm) cc_final: 0.6980 (ttmt) REVERT: 2 197 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6764 (mm) REVERT: 5 112 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7606 (ptm-80) REVERT: 6 30 ASN cc_start: 0.8496 (p0) cc_final: 0.8250 (p0) REVERT: 7 184 ASN cc_start: 0.8396 (t0) cc_final: 0.7947 (t0) REVERT: 8 69 LYS cc_start: 0.8888 (mttt) cc_final: 0.7151 (tmtt) REVERT: 8 81 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7677 (ttmt) REVERT: 9 9 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6390 (tttm) REVERT: E 60 LYS cc_start: 0.6416 (ptpp) cc_final: 0.5818 (mtpt) REVERT: J 95 ILE cc_start: 0.7194 (mm) cc_final: 0.6835 (mp) REVERT: P 49 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.8278 (t) REVERT: P 136 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7308 (mm-30) REVERT: P 151 GLU cc_start: 0.8041 (mp0) cc_final: 0.7499 (mp0) REVERT: P 191 ASP cc_start: 0.8160 (t70) cc_final: 0.7519 (p0) REVERT: Q 18 ARG cc_start: 0.7953 (tpt-90) cc_final: 0.7740 (tpt-90) REVERT: R 118 LEU cc_start: 0.6766 (mm) cc_final: 0.6523 (mm) REVERT: S 109 LYS cc_start: 0.7583 (mttt) cc_final: 0.7350 (mtmt) REVERT: T 471 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7075 (tp-100) REVERT: T 475 GLU cc_start: 0.7791 (tp30) cc_final: 0.7374 (tp30) REVERT: T 522 GLU cc_start: 0.6689 (mp0) cc_final: 0.6154 (mp0) REVERT: U 46 ASP cc_start: 0.7838 (m-30) cc_final: 0.7583 (m-30) REVERT: U 47 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6992 (mm-30) REVERT: U 227 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7985 (ttp80) REVERT: U 414 TYR cc_start: 0.7472 (t80) cc_final: 0.7025 (t80) REVERT: V 46 ASP cc_start: 0.8202 (m-30) cc_final: 0.7628 (p0) REVERT: V 283 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7950 (ttt-90) REVERT: V 414 TYR cc_start: 0.7663 (m-80) cc_final: 0.7409 (m-80) REVERT: V 461 GLN cc_start: 0.7534 (mp10) cc_final: 0.7234 (mp10) REVERT: V 515 GLN cc_start: 0.8205 (pt0) cc_final: 0.7839 (pt0) REVERT: V 522 GLU cc_start: 0.7073 (pp20) cc_final: 0.6577 (tm-30) REVERT: X 440 GLN cc_start: 0.8488 (mt0) cc_final: 0.8201 (mt0) REVERT: X 488 MET cc_start: 0.8848 (mmt) cc_final: 0.8485 (mmt) REVERT: X 564 GLU cc_start: 0.7581 (mp0) cc_final: 0.7332 (pt0) REVERT: Y 145 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7526 (mtt-85) REVERT: Y 385 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7472 (mmp-170) REVERT: Y 401 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6392 (mmt180) REVERT: Y 405 LYS cc_start: 0.8034 (tptt) cc_final: 0.7506 (ttpt) REVERT: Y 437 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: Z 91 ASP cc_start: 0.8266 (t0) cc_final: 0.8061 (t0) REVERT: Z 521 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5106 (tt) outliers start: 95 outliers final: 56 residues processed: 797 average time/residue: 0.5476 time to fit residues: 730.0698 Evaluate side-chains 707 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 647 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 197 LEU Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 160 GLU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 182 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 4.9990 chunk 477 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 303 optimal weight: 0.0270 chunk 426 optimal weight: 5.9990 chunk 637 optimal weight: 0.1980 chunk 674 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 603 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 overall best weight: 0.5840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 94 ASN 4 276 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 441 GLN ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 54686 Z= 0.155 Angle : 0.518 9.236 74161 Z= 0.267 Chirality : 0.041 0.169 8689 Planarity : 0.004 0.054 9510 Dihedral : 5.789 84.337 7683 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Rotamer: Outliers : 2.10 % Allowed : 12.96 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.40 (0.10), residues: 7038 helix: 0.34 (0.09), residues: 3906 sheet: -0.87 (0.21), residues: 590 loop : -0.91 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP V 73 HIS 0.004 0.001 HIS V 549 PHE 0.025 0.001 PHE Y 549 TYR 0.026 0.001 TYR 4 211 ARG 0.007 0.000 ARG Z 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 706 time to evaluate : 4.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8003 (pp) REVERT: 1 194 LYS cc_start: 0.7435 (ptmm) cc_final: 0.7083 (ttmt) REVERT: 5 112 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7683 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.7860 (t80) REVERT: 7 184 ASN cc_start: 0.8387 (t0) cc_final: 0.7989 (t0) REVERT: 8 69 LYS cc_start: 0.8877 (mttt) cc_final: 0.7150 (tmtt) REVERT: 8 81 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7687 (ttmt) REVERT: 9 1 MET cc_start: 0.3878 (ptt) cc_final: -0.0937 (mpp) REVERT: 9 9 LYS cc_start: 0.6658 (ttpt) cc_final: 0.6289 (tttm) REVERT: E 56 LEU cc_start: 0.7209 (pt) cc_final: 0.6994 (mt) REVERT: H 119 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.5508 (pp) REVERT: J 95 ILE cc_start: 0.7022 (mm) cc_final: 0.6624 (tp) REVERT: P 136 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7357 (mm-30) REVERT: P 151 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7526 (mp0) REVERT: P 191 ASP cc_start: 0.7988 (t70) cc_final: 0.7494 (p0) REVERT: Q 38 LYS cc_start: 0.7225 (ptmm) cc_final: 0.7000 (ptpt) REVERT: S 52 ASN cc_start: 0.7659 (m-40) cc_final: 0.7432 (m-40) REVERT: S 109 LYS cc_start: 0.7576 (mttt) cc_final: 0.7307 (mtpp) REVERT: S 274 MET cc_start: 0.8461 (mmp) cc_final: 0.8194 (mmt) REVERT: T 237 ASP cc_start: 0.7441 (m-30) cc_final: 0.7157 (m-30) REVERT: T 471 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7064 (tp-100) REVERT: T 475 GLU cc_start: 0.7640 (tp30) cc_final: 0.7211 (tp30) REVERT: T 516 ASP cc_start: 0.7309 (p0) cc_final: 0.6941 (p0) REVERT: T 522 GLU cc_start: 0.6591 (mp0) cc_final: 0.6156 (mp0) REVERT: U 47 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7023 (mm-30) REVERT: U 56 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7276 (mtmm) REVERT: U 414 TYR cc_start: 0.7466 (t80) cc_final: 0.7030 (t80) REVERT: V 283 ARG cc_start: 0.8240 (ttp80) cc_final: 0.8008 (ttt-90) REVERT: V 414 TYR cc_start: 0.7634 (m-80) cc_final: 0.7368 (m-80) REVERT: V 515 GLN cc_start: 0.8212 (pt0) cc_final: 0.7828 (pt0) REVERT: V 522 GLU cc_start: 0.7121 (pp20) cc_final: 0.6637 (tm-30) REVERT: X 440 GLN cc_start: 0.8466 (mt0) cc_final: 0.8180 (mt0) REVERT: X 488 MET cc_start: 0.8842 (mmt) cc_final: 0.8492 (mmt) REVERT: Y 253 GLU cc_start: 0.7865 (mp0) cc_final: 0.7148 (mp0) REVERT: Y 327 THR cc_start: 0.8475 (t) cc_final: 0.8161 (m) REVERT: Y 385 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7475 (mmp-170) REVERT: Y 405 LYS cc_start: 0.8038 (tptt) cc_final: 0.7708 (ttpt) REVERT: Z 91 ASP cc_start: 0.8289 (t0) cc_final: 0.8084 (t0) REVERT: Z 195 GLU cc_start: 0.7935 (tp30) cc_final: 0.7596 (tp30) REVERT: Z 521 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.4885 (tt) outliers start: 118 outliers final: 75 residues processed: 783 average time/residue: 0.5192 time to fit residues: 683.3227 Evaluate side-chains 724 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 645 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 119 LYS Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.7980 chunk 382 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 502 optimal weight: 0.4980 chunk 278 optimal weight: 10.0000 chunk 575 optimal weight: 0.9990 chunk 466 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 344 optimal weight: 5.9990 chunk 605 optimal weight: 9.9990 chunk 170 optimal weight: 0.2980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 276 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN G 94 ASN R 85 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 54686 Z= 0.184 Angle : 0.524 9.510 74161 Z= 0.270 Chirality : 0.041 0.167 8689 Planarity : 0.004 0.057 9510 Dihedral : 5.697 84.641 7679 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.12 % Favored : 95.72 % Rotamer: Outliers : 2.10 % Allowed : 13.59 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.12 (0.10), residues: 7038 helix: 0.57 (0.09), residues: 3922 sheet: -0.78 (0.21), residues: 590 loop : -0.79 (0.13), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP V 73 HIS 0.004 0.001 HIS V 549 PHE 0.025 0.001 PHE G 107 TYR 0.025 0.001 TYR 4 211 ARG 0.008 0.000 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 670 time to evaluate : 4.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8048 (pp) REVERT: 1 194 LYS cc_start: 0.7456 (ptmm) cc_final: 0.7120 (ttmt) REVERT: 5 112 ARG cc_start: 0.8053 (mtm180) cc_final: 0.7697 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.7959 (t80) REVERT: 7 184 ASN cc_start: 0.8408 (t0) cc_final: 0.7999 (t0) REVERT: 8 69 LYS cc_start: 0.8874 (mttt) cc_final: 0.7150 (tmtt) REVERT: 8 81 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7861 (ttmm) REVERT: 9 1 MET cc_start: 0.3639 (ptt) cc_final: -0.0785 (mpp) REVERT: 9 9 LYS cc_start: 0.6874 (ttpt) cc_final: 0.6447 (tttm) REVERT: H 119 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5673 (pp) REVERT: J 95 ILE cc_start: 0.7044 (mm) cc_final: 0.6684 (tp) REVERT: P 151 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7451 (mp0) REVERT: P 191 ASP cc_start: 0.7935 (t70) cc_final: 0.7551 (p0) REVERT: S 109 LYS cc_start: 0.7541 (mttt) cc_final: 0.7276 (mtpp) REVERT: S 144 ASP cc_start: 0.7832 (m-30) cc_final: 0.7502 (m-30) REVERT: S 274 MET cc_start: 0.8517 (mmp) cc_final: 0.8307 (mmt) REVERT: T 237 ASP cc_start: 0.7498 (m-30) cc_final: 0.7253 (m-30) REVERT: T 471 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7203 (tp-100) REVERT: T 475 GLU cc_start: 0.7597 (tp30) cc_final: 0.7121 (tp30) REVERT: T 516 ASP cc_start: 0.7258 (p0) cc_final: 0.6914 (p0) REVERT: T 522 GLU cc_start: 0.6592 (mp0) cc_final: 0.6167 (mp0) REVERT: U 47 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7018 (mm-30) REVERT: U 169 GLN cc_start: 0.8385 (mp10) cc_final: 0.8139 (mm110) REVERT: U 414 TYR cc_start: 0.7452 (t80) cc_final: 0.7032 (t80) REVERT: V 283 ARG cc_start: 0.8271 (ttp80) cc_final: 0.8039 (ttt-90) REVERT: V 414 TYR cc_start: 0.7661 (m-80) cc_final: 0.7377 (m-80) REVERT: V 515 GLN cc_start: 0.8208 (pt0) cc_final: 0.7821 (pt0) REVERT: V 522 GLU cc_start: 0.7111 (pp20) cc_final: 0.6782 (tm-30) REVERT: X 440 GLN cc_start: 0.8470 (mt0) cc_final: 0.8158 (mt0) REVERT: X 488 MET cc_start: 0.8845 (mmt) cc_final: 0.8484 (mmt) REVERT: Y 327 THR cc_start: 0.8531 (t) cc_final: 0.8144 (t) REVERT: Y 401 ARG cc_start: 0.7071 (mmm160) cc_final: 0.6469 (mmt180) REVERT: Y 405 LYS cc_start: 0.8070 (tptt) cc_final: 0.7743 (ttpt) REVERT: Y 501 LYS cc_start: 0.7255 (mtpt) cc_final: 0.6993 (mtpp) REVERT: Z 195 GLU cc_start: 0.7887 (tp30) cc_final: 0.7609 (tp30) REVERT: Z 521 LEU cc_start: 0.5181 (OUTLIER) cc_final: 0.4639 (tt) outliers start: 118 outliers final: 83 residues processed: 749 average time/residue: 0.5130 time to fit residues: 645.8141 Evaluate side-chains 731 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 644 time to evaluate : 4.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 119 LYS Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 206 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 0.0980 chunk 607 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 396 optimal weight: 0.3980 chunk 166 optimal weight: 0.6980 chunk 675 optimal weight: 0.0970 chunk 560 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 354 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 4 276 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 ASN R 85 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 264 GLN U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 54686 Z= 0.141 Angle : 0.503 11.967 74161 Z= 0.258 Chirality : 0.040 0.164 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.433 86.195 7678 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Rotamer: Outliers : 2.04 % Allowed : 13.98 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.18 (0.10), residues: 7038 helix: 0.83 (0.09), residues: 3918 sheet: -0.62 (0.22), residues: 578 loop : -0.69 (0.13), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP V 73 HIS 0.004 0.001 HIS V 549 PHE 0.029 0.001 PHE G 107 TYR 0.024 0.001 TYR 4 211 ARG 0.005 0.000 ARG T 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 708 time to evaluate : 4.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7980 (pp) REVERT: 1 194 LYS cc_start: 0.7462 (ptmm) cc_final: 0.7209 (ttmt) REVERT: 5 112 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7683 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7892 (t80) REVERT: 8 69 LYS cc_start: 0.8844 (mttt) cc_final: 0.7163 (tmtt) REVERT: 8 81 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7956 (ttmm) REVERT: 9 1 MET cc_start: 0.3132 (ptt) cc_final: -0.0267 (mpp) REVERT: 9 9 LYS cc_start: 0.6545 (ttpt) cc_final: 0.6271 (tttm) REVERT: 9 13 LYS cc_start: 0.8069 (mptt) cc_final: 0.7866 (mmtt) REVERT: D 95 ILE cc_start: 0.6310 (OUTLIER) cc_final: 0.5922 (tp) REVERT: F 81 MET cc_start: 0.6792 (ttp) cc_final: 0.6569 (ttp) REVERT: H 119 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5616 (pp) REVERT: I 98 GLN cc_start: 0.7362 (tm-30) cc_final: 0.7105 (tm-30) REVERT: J 95 ILE cc_start: 0.6969 (mm) cc_final: 0.6677 (tp) REVERT: P 151 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7421 (mp0) REVERT: P 191 ASP cc_start: 0.7867 (t70) cc_final: 0.7564 (p0) REVERT: Q 18 ARG cc_start: 0.7643 (tpt-90) cc_final: 0.7403 (tpt-90) REVERT: S 109 LYS cc_start: 0.7449 (mttt) cc_final: 0.7185 (mtpp) REVERT: S 144 ASP cc_start: 0.7833 (m-30) cc_final: 0.7531 (m-30) REVERT: S 275 GLU cc_start: 0.7546 (tt0) cc_final: 0.7148 (tp30) REVERT: T 471 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7153 (tp-100) REVERT: T 475 GLU cc_start: 0.7563 (tp30) cc_final: 0.7096 (tp30) REVERT: T 516 ASP cc_start: 0.7133 (p0) cc_final: 0.6812 (p0) REVERT: T 522 GLU cc_start: 0.6640 (mp0) cc_final: 0.6282 (mp0) REVERT: U 47 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6985 (mm-30) REVERT: U 414 TYR cc_start: 0.7417 (t80) cc_final: 0.7011 (t80) REVERT: V 283 ARG cc_start: 0.8238 (ttp80) cc_final: 0.8025 (ttt-90) REVERT: V 407 PHE cc_start: 0.8430 (t80) cc_final: 0.8084 (t80) REVERT: V 414 TYR cc_start: 0.7647 (m-80) cc_final: 0.7387 (m-80) REVERT: V 502 TYR cc_start: 0.7982 (t80) cc_final: 0.7310 (t80) REVERT: V 515 GLN cc_start: 0.8152 (pt0) cc_final: 0.7763 (pt0) REVERT: V 522 GLU cc_start: 0.7121 (pp20) cc_final: 0.6812 (tm-30) REVERT: X 440 GLN cc_start: 0.8433 (mt0) cc_final: 0.8127 (mt0) REVERT: X 488 MET cc_start: 0.8845 (mmt) cc_final: 0.8446 (mmt) REVERT: Y 253 GLU cc_start: 0.7827 (mp0) cc_final: 0.7590 (mp0) REVERT: Y 327 THR cc_start: 0.8462 (t) cc_final: 0.8164 (m) REVERT: Y 405 LYS cc_start: 0.8049 (tptt) cc_final: 0.7727 (ttpt) REVERT: Y 437 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.7163 (mtt180) REVERT: Y 501 LYS cc_start: 0.7272 (mtpt) cc_final: 0.7006 (mtpp) REVERT: Z 195 GLU cc_start: 0.7821 (tp30) cc_final: 0.7532 (tp30) REVERT: Z 521 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4596 (tt) outliers start: 115 outliers final: 73 residues processed: 784 average time/residue: 0.5479 time to fit residues: 721.9903 Evaluate side-chains 727 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 649 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 564 GLU Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 441 ARG Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 384 optimal weight: 4.9990 chunk 493 optimal weight: 0.2980 chunk 382 optimal weight: 2.9990 chunk 568 optimal weight: 1.9990 chunk 377 optimal weight: 0.8980 chunk 672 optimal weight: 0.9990 chunk 421 optimal weight: 3.9990 chunk 410 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 240 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN R 85 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Z 198 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54686 Z= 0.171 Angle : 0.515 9.644 74161 Z= 0.263 Chirality : 0.041 0.175 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.391 87.664 7678 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.91 % Favored : 95.95 % Rotamer: Outliers : 2.08 % Allowed : 14.58 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.33 (0.10), residues: 7038 helix: 0.95 (0.09), residues: 3921 sheet: -0.59 (0.22), residues: 578 loop : -0.62 (0.13), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP V 73 HIS 0.004 0.001 HIS V 549 PHE 0.029 0.001 PHE G 107 TYR 0.024 0.001 TYR 4 211 ARG 0.008 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 666 time to evaluate : 4.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (pp) REVERT: 1 194 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7240 (ttmt) REVERT: 5 112 ARG cc_start: 0.8090 (mtm180) cc_final: 0.7703 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.7930 (t80) REVERT: 8 69 LYS cc_start: 0.8849 (mttt) cc_final: 0.7147 (tmtt) REVERT: 8 81 LYS cc_start: 0.8282 (mtpt) cc_final: 0.8008 (ttmm) REVERT: 9 1 MET cc_start: 0.3037 (ptt) cc_final: -0.0320 (mpp) REVERT: 9 9 LYS cc_start: 0.6584 (ttpt) cc_final: 0.6201 (tttm) REVERT: H 119 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5453 (pp) REVERT: I 98 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7171 (tm-30) REVERT: J 95 ILE cc_start: 0.6937 (mm) cc_final: 0.6717 (tp) REVERT: P 151 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7442 (mp0) REVERT: P 191 ASP cc_start: 0.7875 (t70) cc_final: 0.7567 (p0) REVERT: Q 18 ARG cc_start: 0.7581 (tpt-90) cc_final: 0.7241 (tpt-90) REVERT: S 109 LYS cc_start: 0.7361 (mttt) cc_final: 0.7148 (mtpp) REVERT: S 144 ASP cc_start: 0.7781 (m-30) cc_final: 0.7537 (m-30) REVERT: S 181 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: T 471 GLN cc_start: 0.7558 (tm-30) cc_final: 0.7172 (tp-100) REVERT: T 475 GLU cc_start: 0.7555 (tp30) cc_final: 0.7124 (tp30) REVERT: T 516 ASP cc_start: 0.7122 (p0) cc_final: 0.6855 (p0) REVERT: T 522 GLU cc_start: 0.6675 (mp0) cc_final: 0.6297 (mp0) REVERT: U 47 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7004 (mm-30) REVERT: U 169 GLN cc_start: 0.8352 (mp10) cc_final: 0.8102 (mm110) REVERT: U 414 TYR cc_start: 0.7409 (t80) cc_final: 0.7009 (t80) REVERT: V 407 PHE cc_start: 0.8482 (t80) cc_final: 0.8111 (t80) REVERT: V 515 GLN cc_start: 0.8164 (pt0) cc_final: 0.7773 (pt0) REVERT: V 522 GLU cc_start: 0.7163 (pp20) cc_final: 0.6874 (tm-30) REVERT: X 86 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8090 (tpt170) REVERT: X 440 GLN cc_start: 0.8463 (mt0) cc_final: 0.8157 (mt0) REVERT: X 488 MET cc_start: 0.8842 (mmt) cc_final: 0.8489 (mmt) REVERT: Y 253 GLU cc_start: 0.7939 (mp0) cc_final: 0.7692 (mp0) REVERT: Y 327 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8302 (t) REVERT: Y 405 LYS cc_start: 0.8038 (tptt) cc_final: 0.7725 (ttpt) REVERT: Y 501 LYS cc_start: 0.7285 (mtpt) cc_final: 0.7017 (mtpp) REVERT: Z 195 GLU cc_start: 0.7811 (tp30) cc_final: 0.7511 (tp30) REVERT: Z 521 LEU cc_start: 0.5064 (OUTLIER) cc_final: 0.4552 (tt) outliers start: 117 outliers final: 87 residues processed: 745 average time/residue: 0.5463 time to fit residues: 686.3656 Evaluate side-chains 732 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 639 time to evaluate : 5.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 7 residue 189 LYS Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 564 GLU Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 132 optimal weight: 0.0070 chunk 130 optimal weight: 0.9990 chunk 427 optimal weight: 0.6980 chunk 458 optimal weight: 0.9990 chunk 332 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 528 optimal weight: 4.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 276 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 98 GLN P 140 ASN R 85 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 54686 Z= 0.160 Angle : 0.513 9.674 74161 Z= 0.262 Chirality : 0.041 0.182 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.328 89.912 7677 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.88 % Favored : 95.99 % Rotamer: Outliers : 2.04 % Allowed : 14.97 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.42 (0.10), residues: 7038 helix: 1.04 (0.09), residues: 3929 sheet: -0.63 (0.22), residues: 583 loop : -0.59 (0.13), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP V 73 HIS 0.004 0.001 HIS 4 233 PHE 0.032 0.001 PHE G 107 TYR 0.024 0.001 TYR 4 211 ARG 0.006 0.000 ARG T 513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 657 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7927 (pp) REVERT: 1 194 LYS cc_start: 0.7509 (ptmm) cc_final: 0.7216 (ttmt) REVERT: 5 112 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7690 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8004 (t80) REVERT: 8 69 LYS cc_start: 0.8843 (mttt) cc_final: 0.7164 (tmtt) REVERT: 8 81 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7966 (ttmm) REVERT: 9 1 MET cc_start: 0.2841 (OUTLIER) cc_final: -0.0261 (mpp) REVERT: D 95 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5896 (tp) REVERT: E 115 LEU cc_start: 0.6166 (OUTLIER) cc_final: 0.5704 (tp) REVERT: I 98 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7226 (tm-30) REVERT: P 151 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7437 (mp0) REVERT: P 191 ASP cc_start: 0.7860 (t70) cc_final: 0.7569 (p0) REVERT: Q 18 ARG cc_start: 0.7566 (tpt-90) cc_final: 0.7208 (tpt-90) REVERT: Q 40 GLN cc_start: 0.6949 (tp40) cc_final: 0.6631 (tp40) REVERT: S 52 ASN cc_start: 0.7648 (m110) cc_final: 0.7430 (m-40) REVERT: S 181 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: T 471 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7161 (tp-100) REVERT: T 475 GLU cc_start: 0.7585 (tp30) cc_final: 0.7077 (tp30) REVERT: T 516 ASP cc_start: 0.7096 (p0) cc_final: 0.6843 (p0) REVERT: T 522 GLU cc_start: 0.6631 (mp0) cc_final: 0.6262 (mp0) REVERT: U 47 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7013 (mm-30) REVERT: U 414 TYR cc_start: 0.7391 (t80) cc_final: 0.7019 (t80) REVERT: V 407 PHE cc_start: 0.8451 (t80) cc_final: 0.8114 (t80) REVERT: V 515 GLN cc_start: 0.8158 (pt0) cc_final: 0.7770 (pt0) REVERT: V 522 GLU cc_start: 0.7155 (pp20) cc_final: 0.6880 (tm-30) REVERT: X 86 ARG cc_start: 0.8512 (tpp80) cc_final: 0.8085 (tpt170) REVERT: X 440 GLN cc_start: 0.8465 (mt0) cc_final: 0.8135 (mt0) REVERT: X 488 MET cc_start: 0.8837 (mmt) cc_final: 0.8490 (mmt) REVERT: Y 253 GLU cc_start: 0.7936 (mp0) cc_final: 0.7088 (mp0) REVERT: Y 327 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8282 (t) REVERT: Y 405 LYS cc_start: 0.8023 (tptt) cc_final: 0.7724 (ttpt) REVERT: Y 437 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.7157 (mtt180) REVERT: Y 501 LYS cc_start: 0.7304 (mtpt) cc_final: 0.7040 (mtpp) REVERT: Z 195 GLU cc_start: 0.7792 (tp30) cc_final: 0.7509 (tp30) REVERT: Z 521 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4526 (tt) outliers start: 115 outliers final: 90 residues processed: 736 average time/residue: 0.5162 time to fit residues: 641.0096 Evaluate side-chains 722 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 624 time to evaluate : 4.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 7 residue 189 LYS Chi-restraints excluded: chain 9 residue 1 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 134 ASN Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 564 GLU Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Y residue 441 ARG Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Chi-restraints excluded: chain Z residue 521 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 5.9990 chunk 644 optimal weight: 0.9990 chunk 588 optimal weight: 10.0000 chunk 626 optimal weight: 7.9990 chunk 377 optimal weight: 0.6980 chunk 273 optimal weight: 9.9990 chunk 492 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 566 optimal weight: 0.8980 chunk 592 optimal weight: 2.9990 chunk 624 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 68 HIS ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 149 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 574 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54686 Z= 0.278 Angle : 0.570 10.376 74161 Z= 0.292 Chirality : 0.043 0.191 8689 Planarity : 0.004 0.057 9510 Dihedral : 5.679 89.519 7676 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.64 % Rotamer: Outliers : 2.10 % Allowed : 15.13 % Favored : 82.77 % 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: 0.29 (0.10), residues: 7038 helix: 0.91 (0.09), residues: 3923 sheet: -0.74 (0.21), residues: 606 loop : -0.58 (0.13), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP V 73 HIS 0.005 0.001 HIS 4 233 PHE 0.029 0.001 PHE G 107 TYR 0.023 0.002 TYR 4 211 ARG 0.006 0.000 ARG T 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 653 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8104 (pp) REVERT: 1 194 LYS cc_start: 0.7529 (ptmm) cc_final: 0.7219 (ttmt) REVERT: 5 112 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7711 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8193 (t80) REVERT: 7 184 ASN cc_start: 0.8377 (t0) cc_final: 0.8047 (t0) REVERT: 8 69 LYS cc_start: 0.8863 (mttt) cc_final: 0.7141 (tmtt) REVERT: 8 81 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7948 (ttmm) REVERT: 9 1 MET cc_start: 0.3362 (ptt) cc_final: -0.0503 (mpp) REVERT: 9 13 LYS cc_start: 0.8211 (mptt) cc_final: 0.7965 (mmtt) REVERT: A 115 LEU cc_start: 0.7733 (mt) cc_final: 0.7518 (mt) REVERT: D 95 ILE cc_start: 0.6142 (OUTLIER) cc_final: 0.5792 (tp) REVERT: E 115 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5692 (tp) REVERT: I 98 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7294 (tm-30) REVERT: M 251 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8650 (mp) REVERT: P 151 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7408 (mp0) REVERT: P 191 ASP cc_start: 0.8012 (t70) cc_final: 0.7564 (p0) REVERT: Q 18 ARG cc_start: 0.7627 (tpt-90) cc_final: 0.7255 (tpt-90) REVERT: R 188 TYR cc_start: 0.6718 (m-80) cc_final: 0.6394 (m-80) REVERT: S 181 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: T 471 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7181 (tp-100) REVERT: T 475 GLU cc_start: 0.7688 (tp30) cc_final: 0.7184 (tp30) REVERT: T 516 ASP cc_start: 0.7149 (p0) cc_final: 0.6911 (p0) REVERT: T 522 GLU cc_start: 0.6689 (mp0) cc_final: 0.6393 (mp0) REVERT: U 47 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7109 (mm-30) REVERT: U 414 TYR cc_start: 0.7304 (t80) cc_final: 0.6956 (t80) REVERT: V 322 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9024 (tp) REVERT: V 407 PHE cc_start: 0.8585 (t80) cc_final: 0.8190 (t80) REVERT: V 414 TYR cc_start: 0.7728 (m-80) cc_final: 0.7482 (m-80) REVERT: V 522 GLU cc_start: 0.7205 (pp20) cc_final: 0.6869 (tm-30) REVERT: X 440 GLN cc_start: 0.8567 (mt0) cc_final: 0.8232 (mt0) REVERT: X 488 MET cc_start: 0.8825 (mmt) cc_final: 0.8572 (mmt) REVERT: Y 405 LYS cc_start: 0.8106 (tptt) cc_final: 0.7769 (ttpt) REVERT: Y 501 LYS cc_start: 0.7326 (mtpt) cc_final: 0.7056 (mtpp) REVERT: Z 195 GLU cc_start: 0.7902 (tp30) cc_final: 0.7586 (tp30) outliers start: 118 outliers final: 93 residues processed: 733 average time/residue: 0.5214 time to fit residues: 648.3759 Evaluate side-chains 729 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 629 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 154 GLN Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 201 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 410 THR Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 322 ILE Chi-restraints excluded: chain V residue 427 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 517 VAL Chi-restraints excluded: chain X residue 564 GLU Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 251 MET Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.6980 chunk 662 optimal weight: 0.6980 chunk 404 optimal weight: 0.5980 chunk 314 optimal weight: 1.9990 chunk 460 optimal weight: 0.9990 chunk 695 optimal weight: 8.9990 chunk 640 optimal weight: 6.9990 chunk 553 optimal weight: 0.0870 chunk 57 optimal weight: 0.3980 chunk 427 optimal weight: 5.9990 chunk 339 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 65 GLN 5 82 HIS ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN R 85 GLN R 137 HIS ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54686 Z= 0.147 Angle : 0.517 9.959 74161 Z= 0.265 Chirality : 0.041 0.173 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.271 85.775 7674 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.04 % Rotamer: Outliers : 1.67 % Allowed : 15.73 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.57 (0.10), residues: 7038 helix: 1.15 (0.09), residues: 3926 sheet: -0.56 (0.22), residues: 577 loop : -0.51 (0.13), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP V 73 HIS 0.004 0.001 HIS 4 233 PHE 0.029 0.001 PHE G 107 TYR 0.031 0.001 TYR Q 19 ARG 0.007 0.000 ARG Y 145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 665 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7889 (pp) REVERT: 1 194 LYS cc_start: 0.7517 (ptmm) cc_final: 0.7220 (ttmt) REVERT: 1 235 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7110 (mm-30) REVERT: 4 34 TYR cc_start: 0.7671 (t80) cc_final: 0.7367 (t80) REVERT: 5 51 TYR cc_start: 0.8958 (t80) cc_final: 0.8641 (t80) REVERT: 5 112 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7675 (ptm-80) REVERT: 6 146 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8033 (t80) REVERT: 8 69 LYS cc_start: 0.8850 (mttt) cc_final: 0.7160 (tmtt) REVERT: 8 81 LYS cc_start: 0.8241 (mtpt) cc_final: 0.8034 (ttmm) REVERT: 9 1 MET cc_start: 0.2426 (ptt) cc_final: -0.0290 (mpp) REVERT: 9 13 LYS cc_start: 0.8166 (mptt) cc_final: 0.7942 (mmtt) REVERT: D 95 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5909 (tp) REVERT: I 98 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7356 (tm-30) REVERT: P 151 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7415 (mp0) REVERT: P 191 ASP cc_start: 0.7831 (t70) cc_final: 0.7596 (p0) REVERT: Q 18 ARG cc_start: 0.7541 (tpt-90) cc_final: 0.7022 (tpp80) REVERT: S 181 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7795 (mp0) REVERT: S 231 TYR cc_start: 0.7573 (m-80) cc_final: 0.7346 (m-80) REVERT: T 471 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7150 (tp-100) REVERT: T 475 GLU cc_start: 0.7554 (tp30) cc_final: 0.7089 (tp30) REVERT: T 516 ASP cc_start: 0.7033 (p0) cc_final: 0.6781 (p0) REVERT: T 522 GLU cc_start: 0.6529 (mp0) cc_final: 0.6162 (mp0) REVERT: U 47 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7035 (mm-30) REVERT: U 414 TYR cc_start: 0.7286 (t80) cc_final: 0.6930 (t80) REVERT: V 322 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.8984 (tp) REVERT: V 407 PHE cc_start: 0.8421 (t80) cc_final: 0.8135 (t80) REVERT: V 515 GLN cc_start: 0.8145 (pt0) cc_final: 0.7749 (pt0) REVERT: V 522 GLU cc_start: 0.7148 (pp20) cc_final: 0.6825 (tm-30) REVERT: X 86 ARG cc_start: 0.8506 (tpp80) cc_final: 0.8071 (tpt170) REVERT: X 385 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7354 (ttt90) REVERT: X 440 GLN cc_start: 0.8449 (mt0) cc_final: 0.8113 (mt0) REVERT: X 488 MET cc_start: 0.8852 (mmt) cc_final: 0.8463 (mmt) REVERT: Y 405 LYS cc_start: 0.8078 (tptt) cc_final: 0.7767 (ttpt) REVERT: Y 437 ARG cc_start: 0.7493 (mmm-85) cc_final: 0.7129 (mtt180) REVERT: Y 488 MET cc_start: 0.8349 (mmt) cc_final: 0.7656 (mmt) REVERT: Y 501 LYS cc_start: 0.7329 (mtpt) cc_final: 0.7062 (mtpp) REVERT: Z 91 ASP cc_start: 0.8262 (t0) cc_final: 0.7985 (t70) REVERT: Z 195 GLU cc_start: 0.7785 (tp30) cc_final: 0.7505 (tp30) outliers start: 94 outliers final: 75 residues processed: 725 average time/residue: 0.5190 time to fit residues: 637.9621 Evaluate side-chains 714 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 634 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain T residue 82 ILE Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 287 MET Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain T residue 532 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 542 ILE Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 322 ILE Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 532 VAL Chi-restraints excluded: chain X residue 229 GLU Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 456 THR Chi-restraints excluded: chain X residue 492 ILE Chi-restraints excluded: chain X residue 513 ASP Chi-restraints excluded: chain X residue 564 GLU Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 395 GLU Chi-restraints excluded: chain Z residue 159 ILE Chi-restraints excluded: chain Z residue 358 LEU Chi-restraints excluded: chain Z residue 439 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.5980 chunk 589 optimal weight: 7.9990 chunk 169 optimal weight: 0.6980 chunk 510 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 153 optimal weight: 0.4980 chunk 554 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 569 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS 9 80 GLN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 539 ASN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109659 restraints weight = 76187.447| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.72 r_work: 0.3063 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54686 Z= 0.151 Angle : 0.519 10.173 74161 Z= 0.266 Chirality : 0.041 0.190 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.130 85.666 7671 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 1.63 % Allowed : 15.82 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.66 (0.10), residues: 7038 helix: 1.24 (0.09), residues: 3926 sheet: -0.52 (0.22), residues: 575 loop : -0.49 (0.13), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP V 73 HIS 0.003 0.001 HIS 4 233 PHE 0.029 0.001 PHE G 107 TYR 0.030 0.001 TYR Q 19 ARG 0.008 0.000 ARG Y 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12829.82 seconds wall clock time: 223 minutes 23.33 seconds (13403.33 seconds total)