Starting phenix.real_space_refine on Wed Sep 25 03:01:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re5_4842/09_2024/6re5_4842.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re5_4842/09_2024/6re5_4842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re5_4842/09_2024/6re5_4842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re5_4842/09_2024/6re5_4842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re5_4842/09_2024/6re5_4842.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re5_4842/09_2024/6re5_4842.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.037 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 34282 2.51 5 N 9107 2.21 5 O 10163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 450 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: 53720 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: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" 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: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} 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: "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} Chain: "Z" 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: 23.18, per 1000 atoms: 0.43 Number of scatterers: 53720 At special positions: 0 Unit cell: (212.706, 130.572, 259.038, 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 10163 8.00 N 9107 7.00 C 34282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.63 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13076 Finding SS restraints... Secondary structure from input PDB file: 314 helices and 35 sheets defined 58.8% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.663A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.688A 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 30 removed outlier: 3.610A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '1' and resid 45 through 73 Processing helix chain '1' and resid 106 through 139 Processing helix chain '1' and resid 163 through 176 removed outlier: 4.243A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 3.830A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 224 removed outlier: 3.718A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.918A 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: 3.630A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL 1 277 " --> pdb=" O LEU 1 274 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.562A pdb=" N ALA 1 305 " --> pdb=" O LEU 1 301 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 317 removed outlier: 3.734A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.717A 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: 3.903A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.616A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.579A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.877A 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: 3.586A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 515 removed outlier: 3.917A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.703A 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 577 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '2' and resid 7 through 19 removed outlier: 3.904A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.648A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.580A pdb=" N LEU 2 66 " --> pdb=" O ASP 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 87 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.995A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.596A 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: 3.627A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.651A 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 198 removed outlier: 4.196A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 221 removed outlier: 3.909A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 228 through 234 Processing helix chain '2' and resid 240 through 253 removed outlier: 3.667A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.684A pdb=" N PHE 2 262 " --> pdb=" O ASP 2 258 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) Proline residue: 2 271 - end of helix removed outlier: 3.693A pdb=" N ALA 2 276 " --> pdb=" O ALA 2 272 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 296 Processing helix chain '2' and resid 300 through 321 removed outlier: 4.344A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS 2 321 " --> pdb=" O ALA 2 317 " (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 407 removed outlier: 3.907A 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 442 removed outlier: 3.779A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 89 removed outlier: 3.744A pdb=" N LYS 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 99 removed outlier: 3.583A pdb=" N VAL 3 98 " --> pdb=" O ASN 3 94 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.750A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 129 removed outlier: 4.290A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS 3 129 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 removed outlier: 3.687A pdb=" N PHE 3 158 " --> pdb=" O ASP 3 154 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.650A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 169 through 172' Processing helix chain '3' and resid 173 through 187 removed outlier: 3.822A 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: 3.552A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 4.013A 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 removed outlier: 3.689A pdb=" N LYS 3 251 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 272 removed outlier: 3.823A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 removed outlier: 3.953A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.848A pdb=" N LEU 4 12 " --> pdb=" O LYS 4 8 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.753A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 3.609A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.823A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 Processing helix chain '4' and resid 131 through 150 removed outlier: 3.867A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.527A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 188 removed outlier: 3.516A pdb=" N ILE 4 183 " --> pdb=" O PRO 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 3.798A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.811A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.642A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 3.624A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.602A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.237A 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 Processing helix chain '5' and resid 87 through 106 removed outlier: 4.215A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.045A 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: 3.856A pdb=" N ILE 6 54 " --> pdb=" O SER 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 94 Processing helix chain '6' and resid 98 through 120 removed outlier: 4.083A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '7' and resid 68 through 72 removed outlier: 3.638A pdb=" N GLY 7 71 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER 7 72 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 68 through 72' Processing helix chain '7' and resid 83 through 106 removed outlier: 3.740A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN 7 106 " --> pdb=" O GLN 7 102 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 114 removed outlier: 3.780A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 165 Processing helix chain '7' and resid 174 through 187 Processing helix chain '8' and resid 26 through 31 removed outlier: 3.713A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.702A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 3.628A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 33 through 55 removed outlier: 3.619A pdb=" N VAL 9 37 " --> pdb=" O LYS 9 33 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 3.577A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.521A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.029A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.731A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.640A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 114 through 126 removed outlier: 3.944A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.871A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.542A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.555A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.044A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 3.989A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.572A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 4.148A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 64 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.222A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 124 removed outlier: 4.251A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.782A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 92 removed outlier: 3.891A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 127 removed outlier: 3.746A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.019A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.199A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 4.078A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.799A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 90 removed outlier: 4.099A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.571A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.801A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 90 removed outlier: 4.209A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 94 No H-bonds generated for 'chain 'I' and resid 92 through 94' Processing helix chain 'I' and resid 95 through 126 removed outlier: 4.004A pdb=" N GLY I 101 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.409A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 3.801A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.554A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 142 Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 200 removed outlier: 3.593A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 265 removed outlier: 4.313A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.813A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.661A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.531A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.910A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.773A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 149 removed outlier: 4.140A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 removed outlier: 3.888A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 213 through 227 removed outlier: 3.693A pdb=" N ASN P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 3.700A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.847A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 39 removed outlier: 3.533A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.611A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR R 55 " --> pdb=" O SER R 52 " (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 169 removed outlier: 3.942A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.942A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 79 removed outlier: 3.746A pdb=" N ARG S 48 " --> pdb=" O LYS S 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.472A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 131 removed outlier: 3.503A pdb=" N ALA S 128 " --> pdb=" O ARG S 124 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU S 131 " --> pdb=" O LEU S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 Processing helix chain 'S' and resid 149 through 154 removed outlier: 4.084A pdb=" N ILE S 153 " --> pdb=" O GLN S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 Processing helix chain 'S' and resid 212 through 222 removed outlier: 5.375A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.650A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 313 Processing helix chain 'T' and resid 57 through 64 Processing helix chain 'T' and resid 66 through 76 removed outlier: 4.028A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.919A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.531A 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 removed outlier: 3.596A pdb=" N LEU T 160 " --> pdb=" O PRO T 157 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 213 Processing helix chain 'T' and resid 230 through 246 Processing helix chain 'T' and resid 265 through 279 Processing helix chain 'T' and resid 280 through 284 removed outlier: 3.707A pdb=" N ARG T 283 " --> pdb=" O GLY T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.265A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.715A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' 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: 3.756A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 400 removed outlier: 3.564A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 431 through 435 Processing helix chain 'T' and resid 436 through 443 removed outlier: 3.530A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 443 through 458 Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.652A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.563A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.362A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 4.379A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 545 through 556 removed outlier: 3.685A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.834A pdb=" N ARG U 49 " --> pdb=" O ASP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 72 removed outlier: 4.275A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.110A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.687A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.523A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 Processing helix chain 'U' and resid 281 through 283 No H-bonds generated for 'chain 'U' and resid 281 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.880A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.537A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.017A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 467 through 485 removed outlier: 3.607A pdb=" N GLN U 471 " --> pdb=" O ASP U 467 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.621A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.890A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 43 through 49 removed outlier: 3.741A pdb=" N ASP V 46 " --> pdb=" O LYS V 43 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.810A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (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: 3.936A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.507A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 212 removed outlier: 3.525A pdb=" N LEU V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.697A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS V 243 " --> pdb=" O ILE V 239 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 285 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.818A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.628A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 430 through 435 removed outlier: 3.589A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 430 through 435' Processing helix chain 'V' and resid 438 through 457 removed outlier: 3.572A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA V 457 " --> pdb=" O TYR V 453 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 484 removed outlier: 3.616A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.644A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) 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 528 removed outlier: 3.748A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 531 through 540 removed outlier: 3.871A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 554 removed outlier: 3.519A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.529A 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 203 Processing helix chain 'X' and resid 216 through 231 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.962A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.608A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 301 Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.557A pdb=" N ASP X 344 " --> pdb=" O VAL X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 413 Processing helix chain 'X' and resid 414 through 420 Processing helix chain 'X' and resid 421 through 425 removed outlier: 3.733A pdb=" N GLU X 424 " --> pdb=" O GLY X 421 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU X 425 " --> pdb=" O MET X 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 421 through 425' Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.564A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 453 removed outlier: 4.299A pdb=" N VAL X 452 " --> pdb=" O VAL X 449 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.934A pdb=" N PHE X 486 " --> pdb=" O PRO X 482 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR X 487 " --> pdb=" O GLU X 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 482 through 487' Processing helix chain 'X' and resid 491 through 504 removed outlier: 3.537A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 505 through 507 No H-bonds generated for 'chain 'X' and resid 505 through 507' Processing helix chain 'X' and resid 526 through 532 Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.738A pdb=" N THR Y 117 " --> pdb=" O GLY Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 190 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 237 through 242 removed outlier: 4.607A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.600A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 299 removed outlier: 3.759A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Y 299 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.592A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 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 370 Processing helix chain 'Y' and resid 388 through 393 removed outlier: 3.566A pdb=" N GLY Y 393 " --> pdb=" O PRO Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 393 through 412 Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 421 through 425 removed outlier: 3.705A pdb=" N GLU Y 424 " --> pdb=" O GLY Y 421 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 421 through 425' Processing helix chain 'Y' and resid 426 through 443 removed outlier: 3.900A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.517A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 505 removed outlier: 4.027A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 506 through 508 No H-bonds generated for 'chain 'Y' and resid 506 through 508' Processing helix chain 'Y' and resid 511 through 515 removed outlier: 4.155A pdb=" N ASN Y 514 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS Y 515 " --> pdb=" O ALA Y 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 511 through 515' Processing helix chain 'Y' and resid 526 through 532 removed outlier: 3.555A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 550 removed outlier: 4.177A pdb=" N ASP Y 548 " --> pdb=" O GLY Y 544 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE Y 549 " --> pdb=" O LEU Y 545 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 544 through 550' Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 201 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.571A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 4.874A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.965A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 342 through 345 Processing helix chain 'Z' and resid 348 through 354 removed outlier: 4.032A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.561A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 418 removed outlier: 7.601A pdb=" N ALA Z 394 " --> pdb=" O ASN Z 390 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N GLU Z 395 " --> pdb=" O VAL Z 391 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR Z 397 " --> pdb=" O GLY Z 393 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.601A pdb=" N ALA Z 434 " --> pdb=" O LYS Z 430 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 491 through 506 removed outlier: 4.011A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) Processing helix chain 'Z' and resid 507 through 509 No H-bonds generated for 'chain 'Z' and resid 507 through 509' Processing helix chain 'Z' and resid 526 through 534 removed outlier: 3.918A pdb=" N LEU Z 530 " --> pdb=" O SER Z 526 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE Z 534 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 7.577A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 removed outlier: 3.513A pdb=" N GLU 3 314 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL 3 316 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 removed outlier: 3.892A pdb=" N GLU 7 47 " --> pdb=" O ALA 7 40 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '7' and resid 36 through 41 removed outlier: 3.892A pdb=" N GLU 7 47 " --> pdb=" O ALA 7 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 151 through 153 removed outlier: 7.215A pdb=" N VAL P 152 " --> pdb=" O VAL P 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'P' and resid 188 through 190 removed outlier: 6.765A pdb=" N VAL P 156 " --> pdb=" O LYS P 189 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 198 " --> pdb=" O MET P 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 61 through 65 removed outlier: 9.916A pdb=" N VAL S 137 " --> pdb=" O TYR S 158 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N LEU S 160 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER S 100 " --> pdb=" O VAL S 138 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS S 99 " --> pdb=" O SER S 189 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLN S 191 " --> pdb=" O LYS S 99 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL S 101 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU S 193 " --> pdb=" O VAL S 101 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL S 103 " --> pdb=" O LEU S 193 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ASN S 195 " --> pdb=" O VAL S 103 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VAL S 105 " --> pdb=" O ASN S 195 " (cutoff:3.500A) removed outlier: 10.549A pdb=" N PHE S 197 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AB1, first strand: chain 'R' and resid 80 through 82 Processing sheet with id=AB2, first strand: chain 'R' and resid 96 through 100 removed outlier: 3.539A pdb=" N THR R 88 " --> pdb=" O HIS R 119 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 87 through 89 removed outlier: 5.434A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB4, first strand: chain 'T' and resid 87 through 89 removed outlier: 5.434A pdb=" N VAL T 87 " --> pdb=" O TYR T 98 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR T 98 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE T 132 " --> pdb=" O GLY T 117 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLY T 117 " --> pdb=" O PHE T 132 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 61 through 65 removed outlier: 4.474A pdb=" N SER Y 61 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG Y 86 " --> pdb=" O ALA Y 77 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N HIS Y 79 " --> pdb=" O THR Y 84 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N THR Y 84 " --> pdb=" O HIS Y 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 37 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB5, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'T' and resid 163 through 164 Processing sheet with id=AB7, first strand: chain 'T' and resid 382 through 384 removed outlier: 6.515A pdb=" N LEU T 222 " --> pdb=" O ILE T 406 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU T 408 " --> pdb=" O LEU T 222 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE T 224 " --> pdb=" O LEU T 408 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 116 through 122 removed outlier: 4.067A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN U 121 " --> pdb=" O GLY U 128 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL U 130 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA U 119 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain 'U' and resid 163 through 164 removed outlier: 6.269A pdb=" N THR U 164 " --> pdb=" O SER U 289 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.526A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 38 through 44 current: chain 'V' and resid 144 through 150 Processing sheet with id=AC3, first strand: chain 'V' and resid 85 through 89 removed outlier: 6.526A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 116 through 122 current: chain 'Z' and resid 62 through 65 removed outlier: 4.836A pdb=" N LEU Z 72 " --> pdb=" O VAL Z 65 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 38 through 44 current: chain 'V' and resid 144 through 150 Processing sheet with id=AC4, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AC5, first strand: chain 'V' and resid 163 through 164 Processing sheet with id=AC6, first strand: chain 'V' and resid 382 through 384 removed outlier: 6.715A pdb=" N LEU V 222 " --> pdb=" O ILE V 406 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU V 408 " --> pdb=" O LEU V 222 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE V 224 " --> pdb=" O LEU V 408 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'X' and resid 110 through 113 removed outlier: 3.620A pdb=" N ASP X 139 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.214A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLN X 250 " --> pdb=" O MET X 122 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL X 284 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.446A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AD2, first strand: chain 'Y' and resid 110 through 113 Processing sheet with id=AD3, first strand: chain 'Y' and resid 121 through 122 removed outlier: 6.315A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER Y 208 " --> pdb=" O THR Y 245 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL Y 247 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE Y 210 " --> pdb=" O VAL Y 247 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLY Y 249 " --> pdb=" O PHE Y 210 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY Y 212 " --> pdb=" O GLY Y 249 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE Y 207 " --> pdb=" O ASP Y 279 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL Y 280 " --> pdb=" O THR Y 334 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL Y 336 " --> pdb=" O VAL Y 280 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU Y 282 " --> pdb=" O VAL Y 336 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ALA Y 338 " --> pdb=" O LEU Y 282 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL Y 284 " --> pdb=" O ALA Y 338 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.090A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 110 through 113 Processing sheet with id=AD6, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.944A pdb=" N SER Z 208 " --> pdb=" O THR Z 245 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL Z 247 " --> pdb=" O SER Z 208 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE Z 210 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLY Z 212 " --> pdb=" O GLY Z 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.369A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 559 through 561 2910 hydrogen bonds defined for protein. 8490 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: 20.99 Time building geometry restraints manager: 11.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13676 1.33 - 1.45: 9766 1.45 - 1.57: 30941 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54658 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.18e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.85e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.69e+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 3.44e+01 ... (remaining 54653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 73620 3.93 - 7.87: 460 7.87 - 11.80: 32 11.80 - 15.74: 6 15.74 - 19.67: 3 Bond angle restraints: 74121 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.20 19.67 1.00e+00 1.00e+00 3.87e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 120.51 19.36 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 123.97 15.90 1.00e+00 1.00e+00 2.53e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.22 15.61 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 121.91 14.92 1.00e+00 1.00e+00 2.23e+02 ... (remaining 74116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 32349 35.83 - 71.66: 620 71.66 - 107.50: 35 107.50 - 143.33: 0 143.33 - 179.16: 1 Dihedral angle restraints: 33005 sinusoidal: 12661 harmonic: 20344 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual 180.00 -130.29 -49.71 0 5.00e+00 4.00e-02 9.88e+01 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 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" C5' ADP Z 601 " pdb=" O5' ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" O2A ADP Z 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.16 -179.16 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 33002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 7547 0.086 - 0.172: 1077 0.172 - 0.258: 53 0.258 - 0.344: 3 0.344 - 0.430: 3 Chirality restraints: 8683 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB VAL T 180 " pdb=" CA VAL T 180 " pdb=" CG1 VAL T 180 " pdb=" CG2 VAL T 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 8680 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.032 2.00e-02 2.50e+03 6.26e-02 3.92e+01 pdb=" C ALA Y 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.82e-02 3.38e+01 pdb=" C ALA Z 503 " -0.101 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.037 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU T 509 " 0.015 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LEU T 509 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU T 509 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP T 510 " 0.019 2.00e-02 2.50e+03 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2531 2.71 - 3.26: 52131 3.26 - 3.81: 90493 3.81 - 4.35: 115163 4.35 - 4.90: 195481 Nonbonded interactions: 455799 Sorted by model distance: nonbonded pdb=" O3B ADP Z 601 " pdb="MG MG Z 602 " model vdw 2.163 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.224 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.225 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.228 2.170 nonbonded pdb=" O LYS Z 515 " pdb=" N VAL Z 517 " model vdw 2.233 3.120 ... (remaining 455794 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 562 or resid 1001 through 1002)) selection = chain 'V' } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } 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: 9.000 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: 1.540 Check model and map are aligned: 0.300 Set scattering table: 0.370 Process input model: 103.410 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 54658 Z= 0.650 Angle : 0.944 19.673 74121 Z= 0.541 Chirality : 0.059 0.430 8683 Planarity : 0.007 0.078 9504 Dihedral : 14.497 179.161 19929 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.85 % Favored : 94.97 % Rotamer: Outliers : 0.27 % Allowed : 9.95 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.94 (0.08), residues: 7034 helix: -2.75 (0.06), residues: 3825 sheet: -1.65 (0.20), residues: 606 loop : -2.32 (0.10), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP Y 141 HIS 0.012 0.002 HIS 7 123 PHE 0.034 0.003 PHE S 249 TYR 0.031 0.003 TYR 7 119 ARG 0.010 0.001 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 888 time to evaluate : 4.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 313 GLN cc_start: 0.8618 (tt0) cc_final: 0.8402 (mt0) REVERT: 1 341 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7757 (mt-10) REVERT: 2 108 GLU cc_start: 0.7968 (tt0) cc_final: 0.7574 (tt0) REVERT: 5 109 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8130 (mm-40) REVERT: 7 142 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6713 (mt-10) REVERT: 8 70 LYS cc_start: 0.7206 (tttm) cc_final: 0.6084 (mmtt) REVERT: 9 13 LYS cc_start: 0.7764 (mtmt) cc_final: 0.7428 (mmmt) REVERT: C 95 ILE cc_start: 0.8260 (tt) cc_final: 0.7655 (tt) REVERT: D 92 ASN cc_start: 0.8572 (t0) cc_final: 0.8212 (t0) REVERT: D 116 PHE cc_start: 0.8309 (m-10) cc_final: 0.8078 (m-80) REVERT: F 66 CYS cc_start: 0.8105 (m) cc_final: 0.7756 (m) REVERT: H 61 MET cc_start: 0.8238 (mtt) cc_final: 0.7835 (mtt) REVERT: H 81 MET cc_start: 0.8099 (ttp) cc_final: 0.7858 (ttp) REVERT: H 92 ASN cc_start: 0.8579 (p0) cc_final: 0.7857 (p0) REVERT: I 60 LYS cc_start: 0.7768 (mttt) cc_final: 0.7423 (mttp) REVERT: I 81 MET cc_start: 0.8736 (ttp) cc_final: 0.8332 (ttp) REVERT: Q 14 MET cc_start: 0.7810 (ttm) cc_final: 0.7598 (ttp) REVERT: Q 20 SER cc_start: 0.8781 (m) cc_final: 0.8572 (t) REVERT: Q 26 LEU cc_start: 0.9172 (mt) cc_final: 0.8914 (mp) REVERT: T 282 MET cc_start: 0.8554 (tpp) cc_final: 0.7865 (tpt) REVERT: T 537 LYS cc_start: 0.8548 (tmmt) cc_final: 0.8227 (ttpt) REVERT: U 483 MET cc_start: 0.6631 (tmm) cc_final: 0.6189 (tmm) REVERT: X 90 MET cc_start: 0.9073 (mmt) cc_final: 0.8738 (mmt) REVERT: X 386 MET cc_start: 0.8247 (mmm) cc_final: 0.7642 (mmm) REVERT: Y 270 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7846 (mt-10) REVERT: Z 195 GLU cc_start: 0.7672 (tp30) cc_final: 0.7378 (tp30) REVERT: Z 248 TYR cc_start: 0.8704 (m-80) cc_final: 0.8206 (m-80) REVERT: Z 310 TYR cc_start: 0.8681 (m-80) cc_final: 0.8354 (m-80) REVERT: Z 504 LYS cc_start: 0.7050 (mttt) cc_final: 0.6717 (mttt) outliers start: 15 outliers final: 5 residues processed: 900 average time/residue: 0.5742 time to fit residues: 843.9468 Evaluate side-chains 670 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 665 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 10.0000 chunk 528 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 356 optimal weight: 4.9990 chunk 282 optimal weight: 1.9990 chunk 546 optimal weight: 0.8980 chunk 211 optimal weight: 0.8980 chunk 332 optimal weight: 0.9980 chunk 406 optimal weight: 0.7980 chunk 632 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 61 HIS 1 100 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 394 GLN ** 1 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 482 ASN 1 590 HIS 1 606 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 243 GLN 2 289 HIS 2 380 GLN 2 432 GLN 3 94 ASN 3 179 GLN 3 189 HIS 3 206 ASN 4 52 GLN 4 240 GLN 5 107 ASN 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 106 GLN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN 8 26 HIS 8 78 HIS 9 60 ASN C 87 ASN I 94 ASN J 94 ASN M 108 ASN M 163 ASN P 52 GLN P 223 ASN Q 43 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN R 83 GLN R 137 HIS S 98 ASN S 174 GLN S 188 GLN S 262 ASN ** S 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 HIS T 134 ASN ** T 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 358 HIS T 386 GLN T 405 GLN T 435 GLN T 441 GLN U 104 GLN U 149 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 248 GLN U 264 GLN U 319 HIS U 358 HIS U 386 GLN U 515 GLN U 527 GLN U 539 ASN U 549 HIS V 121 ASN V 126 HIS V 134 ASN V 139 HIS V 149 GLN V 152 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN V 244 ASN V 278 GLN V 358 HIS V 486 GLN V 497 GLN X 78 GLN X 278 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 404 GLN X 574 ASN Y 174 GLN Y 199 ASN Z 83 ASN Z 174 GLN Z 204 HIS Z 337 GLN Z 408 GLN Z 414 GLN Total number of N/Q/H flips: 91 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 54658 Z= 0.176 Angle : 0.547 10.131 74121 Z= 0.288 Chirality : 0.041 0.182 8683 Planarity : 0.005 0.057 9504 Dihedral : 6.048 168.732 7669 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 1.28 % Allowed : 12.79 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.86 (0.09), residues: 7034 helix: -0.80 (0.08), residues: 3880 sheet: -1.28 (0.21), residues: 609 loop : -1.71 (0.11), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 73 HIS 0.006 0.001 HIS 7 123 PHE 0.049 0.001 PHE 3 115 TYR 0.026 0.001 TYR 4 211 ARG 0.006 0.000 ARG X 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 794 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8017 (mptt) REVERT: 1 103 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7779 (tppt) REVERT: 1 341 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7714 (mt-10) REVERT: 1 549 ASP cc_start: 0.7533 (t0) cc_final: 0.7241 (t0) REVERT: 4 112 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7738 (mm-30) REVERT: 5 109 GLN cc_start: 0.8248 (mm-40) cc_final: 0.8019 (mm-40) REVERT: 7 142 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6646 (mt-10) REVERT: 8 70 LYS cc_start: 0.7350 (tttm) cc_final: 0.6208 (mmtt) REVERT: 9 13 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7428 (mmmt) REVERT: 9 66 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7424 (mm) REVERT: C 95 ILE cc_start: 0.8191 (tt) cc_final: 0.7825 (tt) REVERT: F 61 MET cc_start: 0.7867 (mmm) cc_final: 0.7519 (mmt) REVERT: H 81 MET cc_start: 0.7903 (ttp) cc_final: 0.7638 (ttp) REVERT: I 60 LYS cc_start: 0.7826 (mttt) cc_final: 0.7274 (mttt) REVERT: I 81 MET cc_start: 0.8558 (ttp) cc_final: 0.8345 (ttp) REVERT: P 111 ASP cc_start: 0.5471 (p0) cc_final: 0.5124 (p0) REVERT: P 209 MET cc_start: 0.8240 (mmm) cc_final: 0.8036 (tpp) REVERT: Q 26 LEU cc_start: 0.9243 (mt) cc_final: 0.9003 (mp) REVERT: Q 63 TYR cc_start: 0.8288 (m-80) cc_final: 0.8029 (m-80) REVERT: R 76 THR cc_start: 0.8731 (m) cc_final: 0.8464 (m) REVERT: R 117 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7384 (mt-10) REVERT: S 52 ASN cc_start: 0.6695 (t0) cc_final: 0.6460 (t0) REVERT: S 217 GLU cc_start: 0.7842 (tp30) cc_final: 0.7574 (tp30) REVERT: T 282 MET cc_start: 0.8551 (tpp) cc_final: 0.7999 (tpt) REVERT: V 547 ASP cc_start: 0.6986 (p0) cc_final: 0.6668 (t0) REVERT: X 51 ARG cc_start: 0.7776 (ttt90) cc_final: 0.7337 (ttt-90) REVERT: X 90 MET cc_start: 0.9036 (mmt) cc_final: 0.8573 (mmt) REVERT: X 289 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8160 (mtm-85) REVERT: X 386 MET cc_start: 0.7897 (mmm) cc_final: 0.7535 (mmm) REVERT: Y 502 MET cc_start: 0.7328 (ptp) cc_final: 0.7077 (ptp) REVERT: Z 193 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8460 (tt) REVERT: Z 195 GLU cc_start: 0.7599 (tp30) cc_final: 0.7398 (tp30) REVERT: Z 248 TYR cc_start: 0.8593 (m-80) cc_final: 0.8220 (m-80) REVERT: Z 310 TYR cc_start: 0.8307 (m-80) cc_final: 0.7987 (m-80) outliers start: 72 outliers final: 50 residues processed: 841 average time/residue: 0.5784 time to fit residues: 815.2359 Evaluate side-chains 727 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 674 time to evaluate : 4.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 6 residue 61 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain T residue 541 LYS Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 351 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 526 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 634 optimal weight: 7.9990 chunk 685 optimal weight: 0.6980 chunk 564 optimal weight: 0.6980 chunk 628 optimal weight: 5.9990 chunk 216 optimal weight: 0.3980 chunk 508 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 450 ASN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN 6 57 GLN 7 24 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** 9 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 ASN M 243 ASN P 66 GLN Q 43 GLN Q 46 HIS R 85 GLN S 174 GLN S 267 HIS T 134 ASN T 196 GLN U 169 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN Y 414 GLN Z 337 GLN Z 414 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54658 Z= 0.179 Angle : 0.520 9.452 74121 Z= 0.271 Chirality : 0.041 0.169 8683 Planarity : 0.004 0.053 9504 Dihedral : 5.630 148.230 7668 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.40 % Favored : 96.50 % Rotamer: Outliers : 1.62 % Allowed : 14.39 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.89 (0.10), residues: 7034 helix: 0.09 (0.08), residues: 3866 sheet: -1.12 (0.21), residues: 624 loop : -1.37 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.004 0.001 HIS V 83 PHE 0.035 0.001 PHE 3 115 TYR 0.024 0.001 TYR 4 211 ARG 0.007 0.000 ARG X 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 732 time to evaluate : 4.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8002 (mptt) REVERT: 1 103 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7731 (tppt) REVERT: 1 341 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7659 (mt-10) REVERT: 1 549 ASP cc_start: 0.7508 (t0) cc_final: 0.7289 (t0) REVERT: 2 68 ASN cc_start: 0.8553 (m-40) cc_final: 0.8352 (m-40) REVERT: 4 269 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8345 (mm) REVERT: 5 109 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8030 (mm-40) REVERT: 7 142 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6762 (mt-10) REVERT: 8 70 LYS cc_start: 0.7315 (tttm) cc_final: 0.6220 (mmtt) REVERT: 9 13 LYS cc_start: 0.7747 (mtmt) cc_final: 0.7398 (mmmt) REVERT: 9 66 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7472 (mm) REVERT: H 81 MET cc_start: 0.7885 (ttp) cc_final: 0.7625 (ttp) REVERT: I 60 LYS cc_start: 0.7741 (mttt) cc_final: 0.7373 (mttp) REVERT: P 49 THR cc_start: 0.8810 (t) cc_final: 0.8498 (t) REVERT: P 111 ASP cc_start: 0.5205 (p0) cc_final: 0.4937 (p0) REVERT: Q 26 LEU cc_start: 0.9212 (mt) cc_final: 0.8985 (mp) REVERT: R 76 THR cc_start: 0.8673 (m) cc_final: 0.8453 (m) REVERT: S 52 ASN cc_start: 0.6761 (t0) cc_final: 0.6504 (t0) REVERT: S 164 ASP cc_start: 0.7062 (m-30) cc_final: 0.6854 (m-30) REVERT: S 217 GLU cc_start: 0.7803 (tp30) cc_final: 0.7494 (tp30) REVERT: T 537 LYS cc_start: 0.8626 (tmmt) cc_final: 0.8338 (ttpt) REVERT: T 549 HIS cc_start: 0.7453 (m-70) cc_final: 0.6932 (m-70) REVERT: U 489 PHE cc_start: 0.7742 (m-10) cc_final: 0.7531 (m-10) REVERT: V 547 ASP cc_start: 0.6995 (p0) cc_final: 0.6768 (t0) REVERT: X 90 MET cc_start: 0.9040 (mmt) cc_final: 0.8570 (mmt) REVERT: X 289 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8181 (mtm-85) REVERT: X 386 MET cc_start: 0.7813 (mmm) cc_final: 0.7491 (mmm) REVERT: Z 195 GLU cc_start: 0.7627 (tp30) cc_final: 0.7425 (tp30) REVERT: Z 196 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8900 (mt) REVERT: Z 248 TYR cc_start: 0.8585 (m-80) cc_final: 0.8205 (m-80) REVERT: Z 310 TYR cc_start: 0.8152 (m-80) cc_final: 0.7788 (m-80) REVERT: Z 536 GLU cc_start: 0.6211 (mm-30) cc_final: 0.5576 (mm-30) outliers start: 91 outliers final: 63 residues processed: 790 average time/residue: 0.5364 time to fit residues: 713.8586 Evaluate side-chains 734 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 667 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 1 residue 103 LYS Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 49 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 196 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 626 optimal weight: 0.9980 chunk 476 optimal weight: 6.9990 chunk 329 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 425 optimal weight: 0.7980 chunk 636 optimal weight: 3.9990 chunk 673 optimal weight: 5.9990 chunk 332 optimal weight: 0.0970 chunk 603 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 285 GLN ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 229 ASN 5 10 GLN ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** 9 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN J 94 ASN ** J 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 174 GLN S 219 GLN T 134 ASN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN V 152 ASN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 408 GLN Z 337 GLN Z 414 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 54658 Z= 0.236 Angle : 0.537 10.987 74121 Z= 0.279 Chirality : 0.042 0.164 8683 Planarity : 0.004 0.048 9504 Dihedral : 5.473 125.700 7667 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 1.95 % Allowed : 15.74 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 7034 helix: 0.50 (0.09), residues: 3874 sheet: -1.00 (0.21), residues: 624 loop : -1.16 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.006 0.001 HIS 7 123 PHE 0.027 0.001 PHE 3 115 TYR 0.022 0.001 TYR 4 211 ARG 0.006 0.000 ARG S 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 713 time to evaluate : 4.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8007 (mptt) REVERT: 1 72 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6984 (p0) REVERT: 1 549 ASP cc_start: 0.7499 (t0) cc_final: 0.7294 (t0) REVERT: 3 155 LYS cc_start: 0.7851 (ttpp) cc_final: 0.7514 (tptt) REVERT: 5 109 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8077 (mm-40) REVERT: 7 36 LYS cc_start: 0.7581 (mmmt) cc_final: 0.7070 (tttm) REVERT: 7 142 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6806 (mt-10) REVERT: 8 70 LYS cc_start: 0.7335 (tttm) cc_final: 0.6228 (mmtt) REVERT: 9 13 LYS cc_start: 0.7731 (mtmt) cc_final: 0.7442 (mmmt) REVERT: 9 66 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7292 (mm) REVERT: H 81 MET cc_start: 0.7928 (ttp) cc_final: 0.7675 (ttp) REVERT: I 60 LYS cc_start: 0.7738 (mttt) cc_final: 0.7370 (mttp) REVERT: P 49 THR cc_start: 0.8756 (t) cc_final: 0.8459 (t) REVERT: P 111 ASP cc_start: 0.5316 (p0) cc_final: 0.5030 (p0) REVERT: Q 66 GLU cc_start: 0.7346 (tp30) cc_final: 0.7047 (tp30) REVERT: R 76 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8585 (m) REVERT: R 161 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8196 (mtmm) REVERT: S 52 ASN cc_start: 0.6766 (t0) cc_final: 0.6516 (t0) REVERT: S 164 ASP cc_start: 0.7064 (m-30) cc_final: 0.6862 (m-30) REVERT: T 549 HIS cc_start: 0.7560 (m-70) cc_final: 0.6923 (m-70) REVERT: U 483 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6378 (ptt) REVERT: V 283 ARG cc_start: 0.7775 (ptm-80) cc_final: 0.7433 (ttp-170) REVERT: V 547 ASP cc_start: 0.6998 (p0) cc_final: 0.6720 (t0) REVERT: X 90 MET cc_start: 0.9064 (mmt) cc_final: 0.8610 (mmt) REVERT: X 289 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8210 (mtm-85) REVERT: Y 66 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7034 (mp0) REVERT: Z 248 TYR cc_start: 0.8595 (m-80) cc_final: 0.8257 (m-80) REVERT: Z 310 TYR cc_start: 0.8232 (m-80) cc_final: 0.7777 (m-80) REVERT: Z 536 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5569 (mm-30) outliers start: 110 outliers final: 85 residues processed: 787 average time/residue: 0.5782 time to fit residues: 774.3181 Evaluate side-chains 745 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 655 time to evaluate : 4.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 572 ASP Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 318 ILE Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 561 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 501 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 574 optimal weight: 3.9990 chunk 465 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 344 optimal weight: 4.9990 chunk 604 optimal weight: 5.9990 chunk 170 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 531 HIS ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 177 GLN ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 57 GLN 7 24 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS J 94 ASN M 243 ASN P 52 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 HIS R 154 GLN S 40 ASN S 219 GLN T 134 ASN T 140 GLN ** U 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 264 GLN X 250 GLN Z 337 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 54658 Z= 0.342 Angle : 0.582 12.288 74121 Z= 0.301 Chirality : 0.044 0.174 8683 Planarity : 0.004 0.047 9504 Dihedral : 5.587 116.289 7667 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 2.42 % Allowed : 17.18 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 7034 helix: 0.56 (0.09), residues: 3867 sheet: -1.02 (0.21), residues: 629 loop : -1.11 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 73 HIS 0.008 0.001 HIS 7 123 PHE 0.024 0.002 PHE C 107 TYR 0.021 0.002 TYR 4 211 ARG 0.007 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 681 time to evaluate : 4.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8792 (ttpt) cc_final: 0.7987 (mptt) REVERT: 1 72 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.7045 (p0) REVERT: 1 549 ASP cc_start: 0.7420 (t0) cc_final: 0.7218 (t0) REVERT: 3 155 LYS cc_start: 0.7969 (ttpp) cc_final: 0.7543 (tptt) REVERT: 5 109 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8155 (mm-40) REVERT: 7 36 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7095 (tttm) REVERT: 7 142 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6801 (mt-10) REVERT: 8 70 LYS cc_start: 0.7108 (tttm) cc_final: 0.5983 (mmtt) REVERT: 9 13 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7444 (mmmt) REVERT: 9 66 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7480 (mm) REVERT: H 81 MET cc_start: 0.8016 (ttp) cc_final: 0.7729 (ttp) REVERT: I 60 LYS cc_start: 0.7787 (mttt) cc_final: 0.7404 (mttp) REVERT: P 49 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8545 (t) REVERT: P 111 ASP cc_start: 0.5534 (p0) cc_final: 0.5264 (p0) REVERT: Q 66 GLU cc_start: 0.7504 (tp30) cc_final: 0.7226 (tp30) REVERT: R 117 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7287 (mm-30) REVERT: S 52 ASN cc_start: 0.6822 (t0) cc_final: 0.6527 (t0) REVERT: S 164 ASP cc_start: 0.7138 (m-30) cc_final: 0.6914 (m-30) REVERT: T 549 HIS cc_start: 0.7601 (m-70) cc_final: 0.6999 (m-70) REVERT: V 283 ARG cc_start: 0.7800 (ptm-80) cc_final: 0.7460 (ttp-170) REVERT: V 547 ASP cc_start: 0.6867 (p0) cc_final: 0.6619 (t0) REVERT: X 90 MET cc_start: 0.9097 (mmt) cc_final: 0.8646 (mmt) REVERT: X 289 ARG cc_start: 0.8569 (mtm-85) cc_final: 0.8298 (mtm-85) REVERT: Y 66 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: Z 248 TYR cc_start: 0.8606 (m-80) cc_final: 0.8251 (m-80) REVERT: Z 536 GLU cc_start: 0.6128 (mm-30) cc_final: 0.5446 (mm-30) outliers start: 136 outliers final: 101 residues processed: 774 average time/residue: 0.5307 time to fit residues: 696.0457 Evaluate side-chains 754 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 649 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 3 residue 318 ILE Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 4 residue 269 LEU Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 114 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 61 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 501 LYS Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 226 optimal weight: 4.9990 chunk 606 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 395 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 674 optimal weight: 0.9990 chunk 559 optimal weight: 0.6980 chunk 312 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 354 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 82 HIS ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN ** 5 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS E 94 ASN J 94 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 174 GLN T 134 ASN U 241 HIS ** U 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 250 GLN Y 412 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 54658 Z= 0.153 Angle : 0.510 9.578 74121 Z= 0.263 Chirality : 0.041 0.266 8683 Planarity : 0.004 0.049 9504 Dihedral : 5.233 95.619 7667 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 1.88 % Allowed : 18.00 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.10 (0.10), residues: 7034 helix: 0.94 (0.09), residues: 3878 sheet: -0.96 (0.21), residues: 639 loop : -0.93 (0.12), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 9 73 HIS 0.003 0.001 HIS R 119 PHE 0.024 0.001 PHE R 176 TYR 0.023 0.001 TYR 4 211 ARG 0.007 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 732 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8018 (mptt) REVERT: 1 72 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6947 (p0) REVERT: 2 68 ASN cc_start: 0.8563 (m-40) cc_final: 0.8363 (m-40) REVERT: 2 222 PHE cc_start: 0.5924 (m-80) cc_final: 0.5704 (m-80) REVERT: 3 155 LYS cc_start: 0.7835 (ttpp) cc_final: 0.7538 (tptt) REVERT: 5 109 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8117 (mm-40) REVERT: 7 142 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6777 (mt-10) REVERT: 8 70 LYS cc_start: 0.7118 (tttm) cc_final: 0.6073 (mmtt) REVERT: 9 13 LYS cc_start: 0.7751 (mtmt) cc_final: 0.7443 (mmmt) REVERT: 9 66 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7268 (mm) REVERT: B 97 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8137 (mmmt) REVERT: G 61 MET cc_start: 0.6934 (mmm) cc_final: 0.6590 (mtt) REVERT: H 81 MET cc_start: 0.7928 (ttp) cc_final: 0.7687 (ttp) REVERT: I 60 LYS cc_start: 0.7709 (mttt) cc_final: 0.7336 (mttp) REVERT: P 49 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.8161 (t) REVERT: P 111 ASP cc_start: 0.5272 (p0) cc_final: 0.4889 (p0) REVERT: Q 66 GLU cc_start: 0.7462 (tp30) cc_final: 0.7178 (tp30) REVERT: S 52 ASN cc_start: 0.6769 (t0) cc_final: 0.6519 (t0) REVERT: U 348 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7735 (mt-10) REVERT: V 283 ARG cc_start: 0.7739 (ptm-80) cc_final: 0.7421 (ttp-170) REVERT: V 300 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8853 (t80) REVERT: X 289 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8168 (mtm-85) REVERT: Y 66 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: Z 193 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8389 (tt) REVERT: Z 248 TYR cc_start: 0.8559 (m-80) cc_final: 0.8224 (m-10) REVERT: Z 310 TYR cc_start: 0.7875 (m-80) cc_final: 0.7385 (m-80) REVERT: Z 536 GLU cc_start: 0.6378 (mm-30) cc_final: 0.5784 (mm-30) outliers start: 106 outliers final: 72 residues processed: 807 average time/residue: 0.5243 time to fit residues: 717.5675 Evaluate side-chains 750 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 672 time to evaluate : 4.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 300 PHE Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 161 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 650 optimal weight: 6.9990 chunk 76 optimal weight: 0.0010 chunk 384 optimal weight: 1.9990 chunk 492 optimal weight: 6.9990 chunk 381 optimal weight: 0.9990 chunk 567 optimal weight: 0.8980 chunk 376 optimal weight: 0.9990 chunk 671 optimal weight: 0.0370 chunk 420 optimal weight: 0.0870 chunk 409 optimal weight: 1.9990 chunk 310 optimal weight: 0.5980 overall best weight: 0.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 229 ASN 4 52 GLN 5 79 ASN 6 57 GLN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS 9 41 HIS J 87 ASN J 94 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN U 515 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 250 GLN ** X 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 54658 Z= 0.137 Angle : 0.500 9.559 74121 Z= 0.257 Chirality : 0.040 0.184 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.008 86.832 7667 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 1.83 % Allowed : 18.53 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.10), residues: 7034 helix: 1.17 (0.09), residues: 3905 sheet: -0.74 (0.21), residues: 613 loop : -0.76 (0.13), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.003 0.001 HIS 5 82 PHE 0.027 0.001 PHE E 107 TYR 0.023 0.001 TYR 4 211 ARG 0.008 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 757 time to evaluate : 4.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8052 (mptt) REVERT: 1 72 ASP cc_start: 0.7219 (OUTLIER) cc_final: 0.7007 (p0) REVERT: 2 68 ASN cc_start: 0.8521 (m-40) cc_final: 0.8309 (m-40) REVERT: 3 155 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7615 (tptt) REVERT: 5 109 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8070 (mm-40) REVERT: 7 142 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6757 (mt-10) REVERT: 8 70 LYS cc_start: 0.7273 (tttm) cc_final: 0.6032 (mmtt) REVERT: 9 13 LYS cc_start: 0.7669 (mtmt) cc_final: 0.7413 (mmmt) REVERT: 9 26 LEU cc_start: 0.8426 (mp) cc_final: 0.8218 (mp) REVERT: 9 66 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7220 (mm) REVERT: B 82 PHE cc_start: 0.8093 (m-10) cc_final: 0.7886 (m-80) REVERT: B 97 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8109 (mmmt) REVERT: H 81 MET cc_start: 0.7909 (ttp) cc_final: 0.7660 (ttp) REVERT: I 60 LYS cc_start: 0.7650 (mttt) cc_final: 0.7272 (mttp) REVERT: M 314 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7628 (ptpt) REVERT: P 49 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7855 (t) REVERT: P 111 ASP cc_start: 0.5351 (p0) cc_final: 0.5035 (p0) REVERT: Q 66 GLU cc_start: 0.7457 (tp30) cc_final: 0.7159 (tp30) REVERT: R 161 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8172 (mtmm) REVERT: S 52 ASN cc_start: 0.6724 (t0) cc_final: 0.6468 (t0) REVERT: T 511 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7499 (ptpt) REVERT: U 53 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6224 (p90) REVERT: U 348 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7714 (mt-10) REVERT: U 483 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6596 (ptt) REVERT: V 283 ARG cc_start: 0.7745 (ptm-80) cc_final: 0.7448 (ttp-170) REVERT: Y 422 MET cc_start: 0.8537 (mmm) cc_final: 0.8212 (mmm) REVERT: Z 248 TYR cc_start: 0.8498 (m-80) cc_final: 0.8209 (m-10) REVERT: Z 310 TYR cc_start: 0.7600 (m-80) cc_final: 0.7245 (m-80) REVERT: Z 536 GLU cc_start: 0.6240 (mm-30) cc_final: 0.5657 (mm-30) outliers start: 103 outliers final: 73 residues processed: 827 average time/residue: 0.6121 time to fit residues: 862.9869 Evaluate side-chains 736 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 656 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 55 LEU Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 216 LEU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 467 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 415 optimal weight: 4.9990 chunk 268 optimal weight: 0.3980 chunk 401 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 130 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 457 optimal weight: 5.9990 chunk 332 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 528 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 229 ASN 5 79 ASN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** 9 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN J 87 ASN J 94 ASN M 243 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 262 ASN T 121 ASN T 134 ASN V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN Z 414 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54658 Z= 0.216 Angle : 0.537 10.361 74121 Z= 0.276 Chirality : 0.042 0.243 8683 Planarity : 0.004 0.047 9504 Dihedral : 5.108 87.389 7666 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.29 % Rotamer: Outliers : 2.11 % Allowed : 18.76 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.48 (0.10), residues: 7034 helix: 1.20 (0.09), residues: 3887 sheet: -0.78 (0.21), residues: 620 loop : -0.69 (0.13), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP U 73 HIS 0.005 0.001 HIS 7 123 PHE 0.044 0.001 PHE D 107 TYR 0.021 0.001 TYR 4 211 ARG 0.008 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 679 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8028 (mptt) REVERT: 1 72 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.7007 (p0) REVERT: 3 155 LYS cc_start: 0.7934 (ttpp) cc_final: 0.7655 (tptt) REVERT: 5 109 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8154 (mm-40) REVERT: 7 142 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6781 (mt-10) REVERT: 8 70 LYS cc_start: 0.7172 (tttm) cc_final: 0.6062 (mmtt) REVERT: 9 13 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7481 (mmmt) REVERT: 9 66 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7246 (mm) REVERT: H 81 MET cc_start: 0.8002 (ttp) cc_final: 0.7710 (ttp) REVERT: I 60 LYS cc_start: 0.7709 (mttt) cc_final: 0.7173 (mttt) REVERT: J 98 GLN cc_start: 0.7699 (pm20) cc_final: 0.7485 (pm20) REVERT: P 49 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8118 (t) REVERT: P 111 ASP cc_start: 0.5322 (p0) cc_final: 0.5057 (p0) REVERT: Q 66 GLU cc_start: 0.7485 (tp30) cc_final: 0.7203 (tp30) REVERT: S 52 ASN cc_start: 0.6700 (t0) cc_final: 0.6409 (t0) REVERT: T 549 HIS cc_start: 0.7890 (m-70) cc_final: 0.7663 (m-70) REVERT: U 53 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.6669 (p90) REVERT: U 483 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6727 (ptt) REVERT: V 283 ARG cc_start: 0.7735 (ptm-80) cc_final: 0.7436 (ttp-170) REVERT: Y 422 MET cc_start: 0.8506 (mmm) cc_final: 0.8184 (mmm) REVERT: Y 443 LEU cc_start: 0.8692 (mt) cc_final: 0.8474 (mt) REVERT: Z 193 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8391 (tt) REVERT: Z 248 TYR cc_start: 0.8540 (m-80) cc_final: 0.8277 (m-10) REVERT: Z 310 TYR cc_start: 0.7817 (m-80) cc_final: 0.7407 (m-80) REVERT: Z 374 TYR cc_start: 0.8809 (m-80) cc_final: 0.8587 (m-80) REVERT: Z 536 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5609 (mm-30) outliers start: 119 outliers final: 99 residues processed: 755 average time/residue: 0.5297 time to fit residues: 676.2981 Evaluate side-chains 751 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 646 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 72 ASP Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 89 VAL 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 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 409 GLU Chi-restraints excluded: chain U residue 481 THR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 237 ASP Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 467 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 611 optimal weight: 1.9990 chunk 643 optimal weight: 4.9990 chunk 587 optimal weight: 8.9990 chunk 626 optimal weight: 3.9990 chunk 376 optimal weight: 0.9990 chunk 272 optimal weight: 0.9990 chunk 491 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 565 optimal weight: 1.9990 chunk 592 optimal weight: 0.0020 chunk 623 optimal weight: 0.7980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS F 98 GLN J 94 ASN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN T 121 ASN T 134 ASN V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN X 286 ASN Z 414 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54658 Z= 0.180 Angle : 0.529 11.496 74121 Z= 0.271 Chirality : 0.041 0.221 8683 Planarity : 0.004 0.052 9504 Dihedral : 5.054 88.080 7666 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.33 % Favored : 96.57 % Rotamer: Outliers : 1.90 % Allowed : 19.17 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.58 (0.10), residues: 7034 helix: 1.27 (0.09), residues: 3886 sheet: -0.73 (0.21), residues: 626 loop : -0.63 (0.13), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP U 73 HIS 0.004 0.001 HIS 7 123 PHE 0.047 0.001 PHE D 107 TYR 0.022 0.001 TYR 4 211 ARG 0.008 0.000 ARG 7 121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 671 time to evaluate : 4.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8772 (ttpt) cc_final: 0.7988 (mptt) REVERT: 3 155 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7634 (tptt) REVERT: 5 109 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8134 (mm-40) REVERT: 7 142 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6798 (mt-10) REVERT: 8 70 LYS cc_start: 0.7169 (tttm) cc_final: 0.6087 (mmtt) REVERT: 9 13 LYS cc_start: 0.7748 (mtmt) cc_final: 0.7494 (mmmt) REVERT: 9 66 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7233 (mm) REVERT: F 61 MET cc_start: 0.7266 (mmm) cc_final: 0.6815 (mmt) REVERT: H 81 MET cc_start: 0.7970 (ttp) cc_final: 0.7696 (ttp) REVERT: I 60 LYS cc_start: 0.7645 (mttt) cc_final: 0.7184 (mttt) REVERT: M 314 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7615 (ptpt) REVERT: P 49 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8235 (t) REVERT: P 111 ASP cc_start: 0.5260 (p0) cc_final: 0.5038 (p0) REVERT: Q 66 GLU cc_start: 0.7508 (tp30) cc_final: 0.7222 (tp30) REVERT: S 52 ASN cc_start: 0.6731 (t0) cc_final: 0.6426 (t0) REVERT: T 511 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7545 (ptpt) REVERT: T 549 HIS cc_start: 0.7921 (m-70) cc_final: 0.7683 (m-70) REVERT: U 282 MET cc_start: 0.9064 (mmt) cc_final: 0.8708 (mmt) REVERT: U 348 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7721 (mt-10) REVERT: U 483 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6705 (ptt) REVERT: V 283 ARG cc_start: 0.7742 (ptm-80) cc_final: 0.7443 (ttp-170) REVERT: V 511 LYS cc_start: 0.7121 (pttt) cc_final: 0.6610 (ttmt) REVERT: X 286 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7320 (m-40) REVERT: Y 422 MET cc_start: 0.8491 (mmm) cc_final: 0.8189 (mmm) REVERT: Y 443 LEU cc_start: 0.8634 (mt) cc_final: 0.8391 (mt) REVERT: Z 248 TYR cc_start: 0.8549 (m-80) cc_final: 0.8294 (m-10) REVERT: Z 310 TYR cc_start: 0.7669 (m-80) cc_final: 0.7291 (m-80) REVERT: Z 536 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5625 (mm-30) outliers start: 107 outliers final: 91 residues processed: 739 average time/residue: 0.5254 time to fit residues: 660.1364 Evaluate side-chains 730 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 633 time to evaluate : 4.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 377 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 114 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 249 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 445 THR Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 251 LYS Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 432 THR Chi-restraints excluded: chain Z residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 411 optimal weight: 3.9990 chunk 661 optimal weight: 7.9990 chunk 404 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 460 optimal weight: 1.9990 chunk 694 optimal weight: 0.3980 chunk 639 optimal weight: 0.0870 chunk 552 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 427 optimal weight: 5.9990 chunk 339 optimal weight: 0.9990 overall best weight: 0.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 79 ASN 7 38 ASN ** 7 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS ** 9 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN P 52 GLN P 83 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN T 134 ASN V 61 HIS ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 250 GLN X 286 ASN Z 414 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54658 Z= 0.176 Angle : 0.530 11.055 74121 Z= 0.272 Chirality : 0.041 0.207 8683 Planarity : 0.004 0.051 9504 Dihedral : 4.986 88.197 7666 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.90 % Allowed : 19.40 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.63 (0.10), residues: 7034 helix: 1.31 (0.09), residues: 3898 sheet: -0.73 (0.21), residues: 611 loop : -0.61 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP U 73 HIS 0.004 0.001 HIS 7 123 PHE 0.028 0.001 PHE C 107 TYR 0.022 0.001 TYR U 57 ARG 0.008 0.000 ARG 7 121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 661 time to evaluate : 4.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8766 (ttpt) cc_final: 0.7996 (mptt) REVERT: 2 165 PHE cc_start: 0.6568 (m-80) cc_final: 0.6300 (m-80) REVERT: 3 155 LYS cc_start: 0.7935 (ttpp) cc_final: 0.7647 (tptt) REVERT: 5 109 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8110 (mm-40) REVERT: 7 142 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6758 (mt-10) REVERT: 8 70 LYS cc_start: 0.7158 (tttm) cc_final: 0.6085 (mmtt) REVERT: 9 13 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7504 (mmmt) REVERT: 9 66 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7239 (mm) REVERT: F 61 MET cc_start: 0.7357 (mmm) cc_final: 0.6875 (mmt) REVERT: H 81 MET cc_start: 0.7969 (ttp) cc_final: 0.7692 (ttp) REVERT: I 60 LYS cc_start: 0.7660 (mttt) cc_final: 0.7151 (mttt) REVERT: M 314 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7633 (ptpt) REVERT: P 49 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8153 (t) REVERT: P 72 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6818 (t0) REVERT: Q 66 GLU cc_start: 0.7509 (tp30) cc_final: 0.7223 (tp30) REVERT: S 52 ASN cc_start: 0.6707 (t0) cc_final: 0.6409 (t0) REVERT: T 511 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7470 (ptpt) REVERT: T 549 HIS cc_start: 0.7920 (m-70) cc_final: 0.7677 (m-70) REVERT: U 348 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7714 (mt-10) REVERT: U 483 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6721 (ptt) REVERT: V 283 ARG cc_start: 0.7730 (ptm-80) cc_final: 0.7432 (ttp-170) REVERT: V 511 LYS cc_start: 0.7084 (pttt) cc_final: 0.6593 (ttmt) REVERT: X 286 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.7304 (m-40) REVERT: Y 422 MET cc_start: 0.8448 (mmm) cc_final: 0.8167 (mmm) REVERT: Z 193 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8331 (tt) REVERT: Z 248 TYR cc_start: 0.8555 (m-80) cc_final: 0.8305 (m-10) REVERT: Z 310 TYR cc_start: 0.7621 (m-80) cc_final: 0.7262 (m-80) REVERT: Z 536 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5628 (mm-30) outliers start: 107 outliers final: 90 residues processed: 730 average time/residue: 0.5226 time to fit residues: 653.4289 Evaluate side-chains 742 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 644 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 SER Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 215 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 144 LEU Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 391 THR Chi-restraints excluded: chain 3 residue 181 VAL Chi-restraints excluded: chain 4 residue 42 THR Chi-restraints excluded: chain 4 residue 172 VAL Chi-restraints excluded: chain 5 residue 68 LEU Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 114 ILE Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 66 ILE Chi-restraints excluded: chain 9 residue 88 GLU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 159 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 314 LYS Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain Q residue 40 GLN Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain S residue 207 VAL Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 473 VAL Chi-restraints excluded: chain T residue 511 LYS Chi-restraints excluded: chain U residue 48 LEU Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 272 LEU Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 483 MET Chi-restraints excluded: chain U residue 516 ASP Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 430 VAL Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 232 VAL Chi-restraints excluded: chain X residue 285 ASP Chi-restraints excluded: chain X residue 286 ASN Chi-restraints excluded: chain X residue 524 ILE Chi-restraints excluded: chain Y residue 122 MET Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 151 THR Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 238 GLU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 193 ILE Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 355 PHE Chi-restraints excluded: chain Z residue 422 MET Chi-restraints excluded: chain Z residue 467 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9987 > 50: distance: 94 - 121: 35.700 distance: 99 - 133: 33.021 distance: 103 - 110: 31.785 distance: 104 - 141: 33.083 distance: 110 - 111: 4.851 distance: 111 - 112: 46.592 distance: 111 - 114: 43.393 distance: 112 - 113: 21.676 distance: 112 - 121: 23.514 distance: 113 - 150: 55.027 distance: 114 - 115: 42.824 distance: 115 - 116: 50.926 distance: 116 - 117: 17.892 distance: 117 - 118: 5.853 distance: 118 - 119: 29.831 distance: 118 - 120: 19.354 distance: 121 - 122: 40.021 distance: 122 - 123: 17.927 distance: 122 - 125: 18.196 distance: 123 - 124: 27.964 distance: 123 - 133: 9.673 distance: 124 - 159: 43.217 distance: 125 - 126: 35.067 distance: 126 - 127: 11.851 distance: 126 - 128: 38.311 distance: 128 - 130: 19.888 distance: 130 - 131: 20.301 distance: 133 - 134: 11.725 distance: 134 - 135: 4.786 distance: 134 - 137: 39.755 distance: 135 - 136: 16.808 distance: 135 - 141: 35.355 distance: 136 - 167: 57.256 distance: 137 - 138: 22.101 distance: 138 - 139: 18.698 distance: 138 - 140: 22.345 distance: 141 - 142: 32.853 distance: 142 - 143: 41.077 distance: 142 - 145: 13.017 distance: 143 - 150: 52.938 distance: 144 - 178: 43.739 distance: 145 - 146: 31.175 distance: 146 - 147: 18.796 distance: 147 - 148: 10.994 distance: 147 - 149: 42.150 distance: 150 - 151: 4.463 distance: 151 - 152: 4.080 distance: 151 - 154: 55.494 distance: 152 - 153: 35.774 distance: 152 - 159: 48.239 distance: 153 - 187: 41.398 distance: 154 - 155: 47.190 distance: 155 - 156: 47.325 distance: 156 - 157: 40.522 distance: 159 - 160: 12.459 distance: 160 - 161: 41.647 distance: 160 - 163: 44.046 distance: 162 - 195: 41.414 distance: 163 - 164: 11.130 distance: 164 - 165: 3.553 distance: 164 - 166: 41.836 distance: 167 - 168: 7.609 distance: 168 - 169: 50.813 distance: 168 - 171: 32.311 distance: 169 - 178: 17.956 distance: 171 - 172: 8.638 distance: 172 - 173: 32.504 distance: 172 - 174: 33.502 distance: 173 - 175: 19.766 distance: 175 - 177: 10.294 distance: 176 - 177: 11.519 distance: 178 - 179: 37.087 distance: 179 - 180: 33.444 distance: 179 - 182: 10.856 distance: 180 - 181: 15.105 distance: 180 - 187: 31.417 distance: 182 - 183: 19.489 distance: 183 - 184: 41.328 distance: 184 - 185: 29.228 distance: 185 - 186: 6.533 distance: 187 - 188: 18.250 distance: 188 - 189: 21.861 distance: 188 - 191: 6.281 distance: 189 - 190: 39.935 distance: 191 - 192: 32.903 distance: 192 - 193: 21.597 distance: 192 - 194: 46.241 distance: 196 - 199: 40.934 distance: 197 - 198: 54.584 distance: 197 - 203: 33.832 distance: 199 - 200: 57.518 distance: 200 - 201: 39.239