Starting phenix.real_space_refine on Wed Sep 25 01:01:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/09_2024/6ref_4852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/09_2024/6ref_4852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/09_2024/6ref_4852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/09_2024/6ref_4852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/09_2024/6ref_4852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ref_4852/09_2024/6ref_4852.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 34301 2.51 5 N 9113 2.21 5 O 10174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 390 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53756 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 23.19, per 1000 atoms: 0.43 Number of scatterers: 53756 At special positions: 0 Unit cell: (211.653, 134.784, 263.25, 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 10174 8.00 N 9113 7.00 C 34301 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: 9.85 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 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13088 Finding SS restraints... Secondary structure from input PDB file: 323 helices and 0 sheets defined 59.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.873A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 3 through 8' Processing helix chain '0' and resid 17 through 30 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 106 through 142 removed outlier: 3.823A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.999A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 205 removed outlier: 3.540A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 208 No H-bonds generated for 'chain '1' and resid 206 through 208' Processing helix chain '1' and resid 209 through 224 removed outlier: 3.767A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.509A pdb=" N SER 1 271 " --> pdb=" O ARG 1 267 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.755A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 removed outlier: 3.747A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.659A 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: 3.931A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.505A pdb=" N TYR 1 388 " --> pdb=" O THR 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 417 removed outlier: 3.604A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.756A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 446 removed outlier: 3.759A pdb=" N LYS 1 445 " --> pdb=" O PHE 1 441 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN 1 446 " --> pdb=" O ASP 1 442 " (cutoff:3.500A) Processing helix chain '1' and resid 446 through 460 Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 removed outlier: 3.513A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.690A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.740A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 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: 3.577A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.681A pdb=" N VAL 2 29 " --> pdb=" O SER 2 25 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 57 removed outlier: 4.003A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.518A pdb=" N LEU 2 66 " --> pdb=" O ASP 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.563A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.843A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS 2 131 " --> pdb=" O VAL 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 removed outlier: 3.631A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 removed outlier: 3.582A pdb=" N ALA 2 175 " --> pdb=" O ASP 2 171 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 197 removed outlier: 3.691A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 221 removed outlier: 3.928A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 235 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.628A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.738A pdb=" N PHE 2 262 " --> pdb=" O ASP 2 258 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 277 through 280 removed outlier: 4.094A pdb=" N LEU 2 280 " --> pdb=" O PRO 2 277 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 277 through 280' Processing helix chain '2' and resid 281 through 296 Processing helix chain '2' and resid 302 through 321 removed outlier: 3.526A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 Processing helix chain '2' and resid 345 through 354 Processing helix chain '2' and resid 396 through 407 removed outlier: 3.643A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 removed outlier: 3.932A pdb=" N GLU 2 422 " --> pdb=" O ALA 2 418 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 418 through 422' Processing helix chain '2' and resid 426 through 442 removed outlier: 3.825A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 94 through 99 removed outlier: 3.661A pdb=" N VAL 3 98 " --> pdb=" O ASN 3 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 94 through 99' Processing helix chain '3' and resid 102 through 113 Processing helix chain '3' and resid 117 through 127 removed outlier: 4.128A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 128 through 132 removed outlier: 3.823A pdb=" N VAL 3 132 " --> pdb=" O LYS 3 129 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 Processing helix chain '3' and resid 173 through 187 removed outlier: 4.064A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 205 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.625A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.814A 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: 3.677A pdb=" N LYS 3 251 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 272 Processing helix chain '3' and resid 277 through 284 removed outlier: 4.237A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 3.605A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 removed outlier: 3.658A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.514A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.663A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 4.153A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.890A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 97 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 124 Processing helix chain '4' and resid 131 through 150 removed outlier: 3.829A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 176 removed outlier: 4.248A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 Processing helix chain '4' and resid 192 through 234 removed outlier: 4.001A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 258 removed outlier: 3.514A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.827A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 5.273A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.708A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.485A 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 88 through 106 removed outlier: 3.972A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.158A 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: 3.955A 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: 3.649A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE 6 120 " --> pdb=" O PHE 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 3.867A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 67 removed outlier: 4.010A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 67' Processing helix chain '7' and resid 83 through 104 removed outlier: 3.554A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 7 103 " --> pdb=" O GLU 7 99 " (cutoff:3.500A) Processing helix chain '7' and resid 110 through 114 removed outlier: 3.879A 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 removed outlier: 3.565A pdb=" N THR 7 145 " --> pdb=" O TYR 7 141 " (cutoff:3.500A) 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 removed outlier: 3.550A pdb=" N TYR 7 161 " --> pdb=" O VAL 7 157 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 187 Processing helix chain '8' and resid 26 through 31 removed outlier: 3.946A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.889A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 44 Processing helix chain '8' and resid 44 through 78 removed outlier: 3.803A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 19 through 24 removed outlier: 3.802A pdb=" N PHE 9 24 " --> pdb=" O ALA 9 20 " (cutoff:3.500A) Processing helix chain '9' and resid 32 through 55 removed outlier: 3.607A pdb=" N TYR 9 36 " --> pdb=" O SER 9 32 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 94 removed outlier: 3.520A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU 9 92 " --> pdb=" O GLU 9 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 removed outlier: 4.055A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.290A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.601A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.009A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.638A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.113A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 92 removed outlier: 3.642A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.053A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.942A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.585A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 4.611A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.453A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 removed outlier: 3.651A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 4.107A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.749A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.386A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.631A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.013A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.260A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.589A pdb=" N SER G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.823A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.359A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.048A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.895A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 92 removed outlier: 3.601A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY I 79 " --> pdb=" O GLY I 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 Processing helix chain 'I' and resid 97 through 124 removed outlier: 3.505A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.803A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.173A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 96 removed outlier: 3.678A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 96' Processing helix chain 'J' and resid 97 through 126 removed outlier: 3.784A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.105A 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 144 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 201 removed outlier: 3.555A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 230 removed outlier: 4.471A pdb=" N LEU M 224 " --> pdb=" O ILE M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 258 removed outlier: 4.251A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.599A pdb=" N LEU M 265 " --> pdb=" O LEU M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 309 removed outlier: 4.056A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 64 removed outlier: 3.583A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.936A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 126 removed outlier: 3.759A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (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 147 removed outlier: 4.117A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.815A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 210 through 229 removed outlier: 3.612A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL P 226 " --> pdb=" O VAL P 222 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'R' and resid 29 through 41 removed outlier: 4.147A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 54 Processing helix chain 'R' and resid 157 through 169 removed outlier: 4.399A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA R 169 " --> pdb=" O ALA R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 4.107A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.672A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.464A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 130 removed outlier: 3.760A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR S 130 " --> pdb=" O THR S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 146 through 151 removed outlier: 3.912A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 212 through 217 Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.759A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 315 removed outlier: 3.753A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU S 314 " --> pdb=" O GLY S 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 76 removed outlier: 3.678A pdb=" N LYS T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.107A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER T 76 " --> pdb=" O GLU T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.912A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 246 Processing helix chain 'T' and resid 267 through 280 removed outlier: 3.585A pdb=" N VAL T 273 " --> pdb=" O VAL T 269 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.156A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 353 through 363 Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.574A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS T 415 " --> pdb=" O GLU T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.677A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.664A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 457 removed outlier: 3.621A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 removed outlier: 4.103A pdb=" N GLN T 461 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.538A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU T 482 " --> pdb=" O ALA T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.659A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS T 506 " --> pdb=" O TYR T 502 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 removed outlier: 3.589A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 546 through 556 Processing helix chain 'U' and resid 41 through 48 removed outlier: 3.604A pdb=" N LEU U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 71 removed outlier: 4.459A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.577A 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 72 through 74 No H-bonds generated for 'chain 'U' and resid 72 through 74' Processing helix chain 'U' and resid 134 through 138 removed outlier: 4.100A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.560A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.836A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.544A pdb=" N ARG U 283 " --> pdb=" O GLY U 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 280 through 283' Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.787A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 340 removed outlier: 3.660A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) 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: 3.758A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 414 removed outlier: 3.651A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 455 removed outlier: 3.560A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA U 451 " --> pdb=" O LYS U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.701A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 468 Processing helix chain 'U' and resid 469 through 484 removed outlier: 3.677A pdb=" N LEU U 474 " --> pdb=" O THR U 470 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 removed outlier: 3.604A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 506 removed outlier: 3.535A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.938A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.779A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 545 through 554 removed outlier: 3.628A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 removed outlier: 3.521A pdb=" N LEU V 48 " --> pdb=" O LEU V 45 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 45 through 49' Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.889A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.825A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.689A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.928A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 removed outlier: 3.670A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 280 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 4.264A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.595A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) 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: 3.687A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.848A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 415 removed outlier: 3.548A pdb=" N PHE V 413 " --> pdb=" O GLU V 409 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 454 removed outlier: 4.087A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 485 removed outlier: 3.766A pdb=" N LEU V 474 " --> pdb=" O THR V 470 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU V 484 " --> pdb=" O LEU V 480 " (cutoff:3.500A) Processing helix chain 'V' and resid 494 through 507 removed outlier: 3.775A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY V 507 " --> pdb=" O ALA V 503 " (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: 3.617A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.560A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 554 removed outlier: 4.338A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.858A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 260 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.900A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER X 298 " --> pdb=" O ASN X 294 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.628A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 395 through 418 removed outlier: 4.419A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 444 removed outlier: 3.672A pdb=" N ALA X 434 " --> pdb=" O LYS X 430 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER X 444 " --> pdb=" O GLN X 440 " (cutoff:3.500A) Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 removed outlier: 3.533A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 483 through 487 removed outlier: 3.629A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 507 removed outlier: 3.769A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 removed outlier: 3.628A pdb=" N VAL X 531 " --> pdb=" O LEU X 527 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 237 through 242 removed outlier: 4.187A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 4.838A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 removed outlier: 3.536A pdb=" N PHE Y 290 " --> pdb=" O ASN Y 286 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.816A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 392 through 412 removed outlier: 4.281A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 430 through 443 removed outlier: 4.096A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 447 through 449 No H-bonds generated for 'chain 'Y' and resid 447 through 449' Processing helix chain 'Y' and resid 450 through 455 removed outlier: 3.526A pdb=" N GLY Y 455 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.912A 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 492 through 503 removed outlier: 3.835A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 510 removed outlier: 3.848A pdb=" N ARG Y 509 " --> pdb=" O ASP Y 505 " (cutoff:3.500A) Processing helix chain 'Y' and resid 518 through 523 removed outlier: 4.148A pdb=" N LYS Y 522 " --> pdb=" O SER Y 518 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP Y 523 " --> pdb=" O GLU Y 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 518 through 523' Processing helix chain 'Y' and resid 526 through 532 removed outlier: 3.552A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER Y 532 " --> pdb=" O ASP Y 528 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 554 removed outlier: 4.081A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.605A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 204 removed outlier: 4.543A pdb=" N LYS Z 202 " --> pdb=" O ASN Z 198 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA Z 203 " --> pdb=" O ASN Z 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.995A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.642A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.938A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.760A 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 348 through 355 Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 371 Processing helix chain 'Z' and resid 393 through 413 removed outlier: 3.507A pdb=" N LEU Z 413 " --> pdb=" O ASP Z 409 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 3.531A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 422 through 425 Processing helix chain 'Z' and resid 426 through 443 removed outlier: 3.707A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 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 508 removed outlier: 3.702A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.679A pdb=" N VAL Z 531 " --> pdb=" O LEU Z 527 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) 2588 hydrogen bonds defined for protein. 7578 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: 14.64 Time building geometry restraints manager: 11.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16612 1.34 - 1.45: 7554 1.45 - 1.57: 30253 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54694 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.04e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.53e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 73690 3.68 - 7.36: 424 7.36 - 11.05: 46 11.05 - 14.73: 8 14.73 - 18.41: 4 Bond angle restraints: 74172 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 121.46 18.41 1.00e+00 1.00e+00 3.39e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.53 17.34 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 121.18 15.65 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 122.20 14.63 1.00e+00 1.00e+00 2.14e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.89: 32199 31.89 - 63.78: 748 63.78 - 95.67: 78 95.67 - 127.56: 1 127.56 - 159.46: 4 Dihedral angle restraints: 33030 sinusoidal: 12669 harmonic: 20361 Sorted by residual: dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -126.90 -53.10 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -128.33 -51.67 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual 180.00 -128.88 -51.12 0 5.00e+00 4.00e-02 1.05e+02 ... (remaining 33027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 6875 0.061 - 0.123: 1558 0.123 - 0.184: 232 0.184 - 0.245: 20 0.245 - 0.306: 5 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE H 95 " pdb=" CA ILE H 95 " pdb=" CG1 ILE H 95 " pdb=" CG2 ILE H 95 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB ILE S 183 " pdb=" CA ILE S 183 " pdb=" CG1 ILE S 183 " pdb=" CG2 ILE S 183 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.033 2.00e-02 2.50e+03 6.36e-02 4.05e+01 pdb=" C ALA X 503 " 0.110 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.041 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C ALA Z 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.052 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO 1 93 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.044 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 7966 2.76 - 3.29: 50860 3.29 - 3.83: 93369 3.83 - 4.36: 113020 4.36 - 4.90: 191314 Nonbonded interactions: 456529 Sorted by model distance: nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.220 2.170 nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.224 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.230 2.170 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.241 2.170 ... (remaining 456524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.060 Extract box with map and model: 1.730 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 94.930 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.006 0.084 54694 Z= 0.374 Angle : 0.856 18.411 74172 Z= 0.494 Chirality : 0.053 0.306 8690 Planarity : 0.007 0.080 9512 Dihedral : 14.207 159.456 19942 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.38 % Favored : 95.50 % Rotamer: Outliers : 0.14 % Allowed : 4.99 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.82 (0.08), residues: 7039 helix: -2.81 (0.06), residues: 3808 sheet: -1.52 (0.20), residues: 564 loop : -2.02 (0.10), residues: 2667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Z 141 HIS 0.008 0.001 HIS R 104 PHE 0.028 0.002 PHE A 122 TYR 0.025 0.002 TYR 4 211 ARG 0.009 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1240 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8622 (ttpt) cc_final: 0.7768 (tptt) REVERT: 1 32 THR cc_start: 0.8971 (p) cc_final: 0.8750 (p) REVERT: 1 212 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7405 (mp0) REVERT: 1 438 GLN cc_start: 0.8381 (tp-100) cc_final: 0.8118 (tp40) REVERT: 1 503 SER cc_start: 0.8549 (t) cc_final: 0.8142 (m) REVERT: 2 190 LYS cc_start: 0.8218 (mppt) cc_final: 0.7468 (tptt) REVERT: 2 192 THR cc_start: 0.8185 (m) cc_final: 0.7969 (p) REVERT: 3 276 GLU cc_start: 0.7509 (tp30) cc_final: 0.7000 (tp30) REVERT: 3 279 GLU cc_start: 0.7764 (pt0) cc_final: 0.7488 (pt0) REVERT: 8 5 GLU cc_start: 0.7595 (tt0) cc_final: 0.7305 (tt0) REVERT: A 81 MET cc_start: 0.7765 (ttp) cc_final: 0.7380 (ttp) REVERT: A 97 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8319 (pttp) REVERT: C 60 LYS cc_start: 0.8097 (mttp) cc_final: 0.7510 (mttp) REVERT: C 81 MET cc_start: 0.8660 (ttp) cc_final: 0.8379 (ttm) REVERT: C 94 ASN cc_start: 0.8371 (p0) cc_final: 0.8052 (m110) REVERT: C 126 PHE cc_start: 0.6790 (m-80) cc_final: 0.6583 (m-10) REVERT: E 60 LYS cc_start: 0.7777 (mttp) cc_final: 0.7158 (mtpt) REVERT: G 94 ASN cc_start: 0.8529 (t0) cc_final: 0.8311 (t0) REVERT: H 81 MET cc_start: 0.8277 (ttp) cc_final: 0.7982 (ttp) REVERT: I 60 LYS cc_start: 0.8066 (mttp) cc_final: 0.7537 (mtpt) REVERT: I 91 ARG cc_start: 0.8200 (ttm110) cc_final: 0.7760 (ttm-80) REVERT: J 122 PHE cc_start: 0.7311 (m-10) cc_final: 0.6422 (t80) REVERT: P 75 TYR cc_start: 0.8115 (m-80) cc_final: 0.7150 (m-80) REVERT: P 206 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7719 (ttp-170) REVERT: P 220 ASN cc_start: 0.8924 (m110) cc_final: 0.8705 (m-40) REVERT: Q 35 PHE cc_start: 0.6948 (m-80) cc_final: 0.6738 (m-80) REVERT: Q 40 GLN cc_start: 0.8196 (pm20) cc_final: 0.7991 (mm-40) REVERT: Q 42 ARG cc_start: 0.7362 (ptp90) cc_final: 0.7025 (ptp-170) REVERT: Q 48 ARG cc_start: 0.8450 (ptt-90) cc_final: 0.8028 (ptt-90) REVERT: R 54 TYR cc_start: 0.8173 (m-80) cc_final: 0.7431 (m-80) REVERT: R 117 GLU cc_start: 0.7659 (tt0) cc_final: 0.7379 (tt0) REVERT: S 271 MET cc_start: 0.7809 (ttp) cc_final: 0.7605 (ttp) REVERT: S 275 GLU cc_start: 0.7032 (tp30) cc_final: 0.6788 (tp30) REVERT: T 294 ASP cc_start: 0.6938 (m-30) cc_final: 0.6646 (m-30) REVERT: U 53 PHE cc_start: 0.6782 (p90) cc_final: 0.6030 (p90) REVERT: U 559 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6852 (pp) REVERT: X 386 MET cc_start: 0.7053 (mmm) cc_final: 0.6763 (mmp) REVERT: Y 168 ASP cc_start: 0.7559 (m-30) cc_final: 0.7246 (m-30) REVERT: Y 345 ASP cc_start: 0.8012 (t0) cc_final: 0.7751 (t0) REVERT: Y 382 SER cc_start: 0.8637 (m) cc_final: 0.8331 (m) REVERT: Z 51 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7065 (ttm170) REVERT: Z 82 ASP cc_start: 0.7087 (t0) cc_final: 0.6687 (t0) REVERT: Z 215 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7064 (mm-30) outliers start: 8 outliers final: 1 residues processed: 1243 average time/residue: 0.5515 time to fit residues: 1121.2394 Evaluate side-chains 689 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 687 time to evaluate : 4.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain U residue 559 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 2.9990 chunk 529 optimal weight: 0.9980 chunk 293 optimal weight: 0.4980 chunk 180 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 547 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 332 optimal weight: 0.6980 chunk 407 optimal weight: 0.9990 chunk 633 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 1 166 ASN 1 257 HIS 1 285 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 394 GLN 1 428 HIS 1 482 ASN 1 587 ASN 2 122 ASN 2 243 GLN 2 432 GLN 3 206 ASN 3 229 ASN 4 240 GLN 5 107 ASN 6 40 ASN 6 74 GLN 7 24 GLN 7 86 HIS 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 9 35 GLN 9 41 HIS 9 60 ASN 9 80 GLN G 92 ASN I 98 GLN M 108 ASN M 163 ASN P 52 GLN P 59 GLN P 220 ASN P 223 ASN R 38 ASN R 73 ASN R 85 GLN R 137 HIS R 154 GLN S 262 ASN S 267 HIS T 64 GLN T 134 ASN ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 244 ASN T 278 GLN T 358 HIS T 386 GLN T 441 GLN T 497 GLN T 539 ASN U 60 GLN U 196 GLN U 241 HIS U 242 GLN U 248 GLN U 497 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 139 HIS V 152 ASN V 196 GLN V 219 GLN V 241 HIS V 242 GLN V 244 ASN V 435 GLN V 486 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN X 337 GLN Y 68 HIS Y 199 ASN Y 278 GLN Y 294 ASN Y 404 GLN Y 408 GLN Y 414 GLN Y 440 GLN Z 42 GLN Z 199 ASN Z 440 GLN Z 574 ASN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 54694 Z= 0.172 Angle : 0.553 12.081 74172 Z= 0.288 Chirality : 0.041 0.176 8690 Planarity : 0.005 0.064 9512 Dihedral : 6.707 147.643 7674 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.35 % Favored : 96.53 % Rotamer: Outliers : 1.79 % Allowed : 10.62 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.78 (0.09), residues: 7039 helix: -0.88 (0.08), residues: 3877 sheet: -1.17 (0.20), residues: 595 loop : -1.40 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.007 0.001 HIS U 61 PHE 0.027 0.001 PHE A 122 TYR 0.025 0.001 TYR 4 211 ARG 0.005 0.000 ARG 1 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 854 time to evaluate : 4.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8560 (ttpt) cc_final: 0.7732 (tptt) REVERT: 1 32 THR cc_start: 0.8784 (p) cc_final: 0.8545 (p) REVERT: 1 503 SER cc_start: 0.8521 (t) cc_final: 0.8243 (m) REVERT: 2 187 ARG cc_start: 0.6566 (mtp85) cc_final: 0.6226 (mmm-85) REVERT: 2 189 ASP cc_start: 0.7952 (t0) cc_final: 0.7639 (t0) REVERT: 2 190 LYS cc_start: 0.8202 (mppt) cc_final: 0.7536 (tptt) REVERT: 2 192 THR cc_start: 0.8190 (m) cc_final: 0.7965 (p) REVERT: 3 93 GLU cc_start: 0.6015 (mp0) cc_final: 0.5689 (mp0) REVERT: 3 276 GLU cc_start: 0.7534 (tp30) cc_final: 0.7043 (tp30) REVERT: 3 279 GLU cc_start: 0.7758 (pt0) cc_final: 0.7420 (pt0) REVERT: 4 266 GLU cc_start: 0.7964 (mp0) cc_final: 0.7757 (mp0) REVERT: 7 128 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7813 (mttp) REVERT: 8 5 GLU cc_start: 0.7593 (tt0) cc_final: 0.7309 (tt0) REVERT: 8 62 ASP cc_start: 0.7520 (p0) cc_final: 0.7222 (p0) REVERT: A 81 MET cc_start: 0.7663 (ttp) cc_final: 0.7332 (ttp) REVERT: A 97 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8322 (pttp) REVERT: C 60 LYS cc_start: 0.8006 (mttp) cc_final: 0.7670 (mttp) REVERT: C 81 MET cc_start: 0.8536 (ttp) cc_final: 0.8323 (ttm) REVERT: C 92 ASN cc_start: 0.8204 (t0) cc_final: 0.7932 (t0) REVERT: C 94 ASN cc_start: 0.8346 (p0) cc_final: 0.8022 (m110) REVERT: I 60 LYS cc_start: 0.7994 (mttp) cc_final: 0.7595 (mtpt) REVERT: I 91 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7776 (ttm-80) REVERT: J 122 PHE cc_start: 0.7184 (m-10) cc_final: 0.6556 (t80) REVERT: P 206 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7608 (ttp-170) REVERT: Q 52 TYR cc_start: 0.7434 (m-80) cc_final: 0.7205 (m-80) REVERT: R 31 LYS cc_start: 0.7571 (ptpp) cc_final: 0.7221 (mmmt) REVERT: R 37 TRP cc_start: 0.6638 (t60) cc_final: 0.6340 (t60) REVERT: R 117 GLU cc_start: 0.7580 (tt0) cc_final: 0.7265 (tt0) REVERT: R 171 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6838 (pp30) REVERT: T 541 LYS cc_start: 0.7340 (ttpt) cc_final: 0.7008 (tmtt) REVERT: U 53 PHE cc_start: 0.6622 (p90) cc_final: 0.6338 (p90) REVERT: V 353 ASP cc_start: 0.8481 (p0) cc_final: 0.8056 (p0) REVERT: V 483 MET cc_start: 0.6685 (tpp) cc_final: 0.6233 (tpp) REVERT: X 194 MET cc_start: 0.7071 (mmt) cc_final: 0.6711 (mmp) REVERT: X 386 MET cc_start: 0.7203 (mmm) cc_final: 0.6904 (mmp) REVERT: X 414 GLN cc_start: 0.6758 (mm-40) cc_final: 0.6469 (tp-100) REVERT: X 430 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7039 (mtmt) REVERT: X 431 LEU cc_start: 0.7774 (tt) cc_final: 0.7214 (mp) REVERT: X 487 TYR cc_start: 0.7956 (t80) cc_final: 0.7492 (t80) REVERT: Y 168 ASP cc_start: 0.7730 (m-30) cc_final: 0.7385 (m-30) REVERT: Y 278 GLN cc_start: 0.7214 (mt0) cc_final: 0.6807 (mt0) REVERT: Z 51 ARG cc_start: 0.7802 (ttm-80) cc_final: 0.6712 (ttm170) outliers start: 101 outliers final: 49 residues processed: 920 average time/residue: 0.5213 time to fit residues: 807.8848 Evaluate side-chains 691 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 640 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 195 LYS Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 7 residue 183 THR Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 146 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 473 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 430 LYS Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 497 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 527 optimal weight: 10.0000 chunk 431 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 635 optimal weight: 1.9990 chunk 685 optimal weight: 0.9980 chunk 565 optimal weight: 0.0980 chunk 629 optimal weight: 10.0000 chunk 216 optimal weight: 0.0070 chunk 509 optimal weight: 5.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 430 GLN 1 590 HIS 3 256 GLN 5 107 ASN 8 29 GLN 9 80 GLN F 94 ASN J 98 GLN P 59 GLN P 71 GLN Q 49 GLN R 66 HIS R 178 GLN T 104 GLN T 134 ASN T 248 GLN T 471 GLN T 529 ASN T 539 ASN U 248 GLN U 452 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 ASN X 241 ASN Y 278 GLN Z 448 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 54694 Z= 0.165 Angle : 0.527 11.140 74172 Z= 0.271 Chirality : 0.041 0.223 8690 Planarity : 0.004 0.057 9512 Dihedral : 6.135 148.141 7674 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 1.90 % Allowed : 12.89 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.84 (0.10), residues: 7039 helix: -0.02 (0.08), residues: 3873 sheet: -1.06 (0.20), residues: 623 loop : -1.08 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.010 0.001 HIS V 61 PHE 0.042 0.001 PHE A 122 TYR 0.025 0.001 TYR 4 211 ARG 0.006 0.000 ARG Z 366 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 745 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8565 (ttpt) cc_final: 0.7880 (tptt) REVERT: 1 32 THR cc_start: 0.8780 (p) cc_final: 0.8498 (p) REVERT: 1 438 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7822 (tp40) REVERT: 1 503 SER cc_start: 0.8602 (t) cc_final: 0.8377 (m) REVERT: 2 187 ARG cc_start: 0.6494 (mtp85) cc_final: 0.6248 (mtp180) REVERT: 2 189 ASP cc_start: 0.8138 (t0) cc_final: 0.7883 (t0) REVERT: 2 190 LYS cc_start: 0.8175 (mppt) cc_final: 0.7609 (tptt) REVERT: 2 192 THR cc_start: 0.8205 (m) cc_final: 0.7994 (p) REVERT: 3 93 GLU cc_start: 0.6072 (mp0) cc_final: 0.5823 (mp0) REVERT: 3 276 GLU cc_start: 0.7516 (tp30) cc_final: 0.7184 (tp30) REVERT: 3 279 GLU cc_start: 0.7801 (pt0) cc_final: 0.7563 (pt0) REVERT: 4 266 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: 4 269 LEU cc_start: 0.8088 (mt) cc_final: 0.7494 (mt) REVERT: 5 104 ASP cc_start: 0.7439 (m-30) cc_final: 0.7228 (m-30) REVERT: 7 78 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7941 (mt-10) REVERT: 7 128 LYS cc_start: 0.8096 (mmtm) cc_final: 0.7887 (mttm) REVERT: 8 5 GLU cc_start: 0.7633 (tt0) cc_final: 0.7351 (tt0) REVERT: 9 50 ASN cc_start: 0.8315 (m-40) cc_final: 0.8091 (m-40) REVERT: A 81 MET cc_start: 0.7719 (ttp) cc_final: 0.7356 (ttp) REVERT: A 102 TYR cc_start: 0.7344 (m-80) cc_final: 0.6581 (m-80) REVERT: A 122 PHE cc_start: 0.5975 (p90) cc_final: 0.5626 (p90) REVERT: C 60 LYS cc_start: 0.8063 (mttp) cc_final: 0.7689 (mttp) REVERT: C 81 MET cc_start: 0.8557 (ttp) cc_final: 0.8338 (ttm) REVERT: C 92 ASN cc_start: 0.8271 (t0) cc_final: 0.7971 (t0) REVERT: C 94 ASN cc_start: 0.8361 (p0) cc_final: 0.8137 (m110) REVERT: E 60 LYS cc_start: 0.7756 (mttp) cc_final: 0.7185 (mtpt) REVERT: F 61 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7403 (mmt) REVERT: I 60 LYS cc_start: 0.7974 (mttp) cc_final: 0.7617 (mtpt) REVERT: I 91 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7802 (ttm-80) REVERT: J 120 VAL cc_start: 0.7350 (t) cc_final: 0.7139 (t) REVERT: J 122 PHE cc_start: 0.7214 (m-10) cc_final: 0.6849 (t80) REVERT: M 271 VAL cc_start: 0.7537 (OUTLIER) cc_final: 0.7099 (t) REVERT: P 59 GLN cc_start: 0.8151 (mt0) cc_final: 0.7924 (mt0) REVERT: P 190 ILE cc_start: 0.8398 (pt) cc_final: 0.8100 (mm) REVERT: P 206 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7527 (ttp-170) REVERT: P 209 MET cc_start: 0.8380 (mmm) cc_final: 0.8065 (mmt) REVERT: Q 32 LYS cc_start: 0.6853 (mmtm) cc_final: 0.6463 (mmtp) REVERT: R 31 LYS cc_start: 0.7520 (ptpp) cc_final: 0.7317 (mmpt) REVERT: R 37 TRP cc_start: 0.6615 (t60) cc_final: 0.6270 (t60) REVERT: R 117 GLU cc_start: 0.7625 (tt0) cc_final: 0.7311 (tt0) REVERT: R 171 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6882 (pp30) REVERT: S 115 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7106 (mp) REVERT: U 515 GLN cc_start: 0.7784 (mp10) cc_final: 0.7579 (tt0) REVERT: U 549 HIS cc_start: 0.4786 (OUTLIER) cc_final: 0.4556 (t-90) REVERT: U 559 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7044 (pp) REVERT: X 310 TYR cc_start: 0.8604 (m-80) cc_final: 0.8374 (m-80) REVERT: X 386 MET cc_start: 0.7268 (mmm) cc_final: 0.6962 (mmp) REVERT: X 414 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6421 (tp-100) REVERT: X 431 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7254 (mp) REVERT: X 488 MET cc_start: 0.7216 (mmm) cc_final: 0.6853 (mmm) REVERT: Z 51 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7366 (ttm170) REVERT: Z 115 ARG cc_start: 0.8400 (ttm110) cc_final: 0.7508 (mtt-85) REVERT: Z 175 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7353 (tpt170) REVERT: Z 276 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7344 (mm-30) outliers start: 107 outliers final: 61 residues processed: 812 average time/residue: 0.5343 time to fit residues: 731.4970 Evaluate side-chains 696 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 627 time to evaluate : 4.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 195 LYS Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 19 ASP Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 4 residue 266 GLU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 109 LYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 483 MET Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 549 HIS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 233 ILE Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 0.1980 chunk 477 optimal weight: 8.9990 chunk 329 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 303 optimal weight: 0.0570 chunk 426 optimal weight: 2.9990 chunk 637 optimal weight: 0.0570 chunk 674 optimal weight: 0.8980 chunk 332 optimal weight: 0.7980 chunk 603 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 107 ASN 7 24 GLN 9 80 GLN I 92 ASN P 52 GLN T 134 ASN T 241 HIS ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 278 GLN U 149 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN V 386 GLN ** V 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 54694 Z= 0.132 Angle : 0.502 9.726 74172 Z= 0.256 Chirality : 0.040 0.235 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.713 153.247 7674 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.22 % Favored : 96.69 % Rotamer: Outliers : 1.81 % Allowed : 13.87 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.21 (0.10), residues: 7039 helix: 0.50 (0.09), residues: 3865 sheet: -0.77 (0.20), residues: 631 loop : -0.83 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 9 73 HIS 0.007 0.001 HIS V 61 PHE 0.039 0.001 PHE A 122 TYR 0.025 0.001 TYR 4 211 ARG 0.004 0.000 ARG P 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 758 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8523 (ttpt) cc_final: 0.7863 (tptt) REVERT: 1 32 THR cc_start: 0.8724 (p) cc_final: 0.8444 (p) REVERT: 1 604 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.7201 (mtm110) REVERT: 2 189 ASP cc_start: 0.8170 (t0) cc_final: 0.7778 (t0) REVERT: 2 190 LYS cc_start: 0.8187 (mppt) cc_final: 0.7643 (tptt) REVERT: 2 192 THR cc_start: 0.8076 (m) cc_final: 0.7806 (p) REVERT: 2 346 ARG cc_start: 0.7368 (mtm-85) cc_final: 0.7026 (mtm-85) REVERT: 3 93 GLU cc_start: 0.6099 (mp0) cc_final: 0.5858 (mp0) REVERT: 3 276 GLU cc_start: 0.7493 (tp30) cc_final: 0.7176 (tp30) REVERT: 3 297 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7830 (mt) REVERT: 4 266 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: 7 78 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7875 (mt-10) REVERT: 8 5 GLU cc_start: 0.7559 (tt0) cc_final: 0.7286 (tt0) REVERT: 8 62 ASP cc_start: 0.7692 (p0) cc_final: 0.7483 (p0) REVERT: A 81 MET cc_start: 0.7667 (ttp) cc_final: 0.7372 (ttp) REVERT: C 60 LYS cc_start: 0.8001 (mttp) cc_final: 0.7675 (mttp) REVERT: C 81 MET cc_start: 0.8543 (ttp) cc_final: 0.8306 (ttp) REVERT: C 92 ASN cc_start: 0.8280 (t0) cc_final: 0.7880 (t0) REVERT: C 94 ASN cc_start: 0.8347 (p0) cc_final: 0.8128 (m110) REVERT: E 60 LYS cc_start: 0.7809 (mttp) cc_final: 0.7352 (mtpt) REVERT: E 61 MET cc_start: 0.8163 (mmm) cc_final: 0.7924 (mmt) REVERT: F 61 MET cc_start: 0.7510 (mmm) cc_final: 0.7237 (mmt) REVERT: F 119 LEU cc_start: 0.7983 (tt) cc_final: 0.6155 (mm) REVERT: I 60 LYS cc_start: 0.7916 (mttp) cc_final: 0.7535 (mtpt) REVERT: I 91 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7917 (ttm-80) REVERT: J 120 VAL cc_start: 0.7328 (t) cc_final: 0.7126 (t) REVERT: J 122 PHE cc_start: 0.7204 (m-10) cc_final: 0.6811 (t80) REVERT: M 271 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.6981 (t) REVERT: P 59 GLN cc_start: 0.8197 (mt0) cc_final: 0.7935 (mt0) REVERT: P 190 ILE cc_start: 0.8402 (pt) cc_final: 0.8126 (mm) REVERT: P 206 ARG cc_start: 0.8235 (ttp80) cc_final: 0.8004 (ttp-170) REVERT: Q 32 LYS cc_start: 0.6859 (mmtm) cc_final: 0.6561 (mmtp) REVERT: R 37 TRP cc_start: 0.6467 (t60) cc_final: 0.6227 (t60) REVERT: R 54 TYR cc_start: 0.7749 (m-80) cc_final: 0.7197 (m-80) REVERT: R 171 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6939 (pp30) REVERT: S 115 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7154 (mp) REVERT: S 220 LEU cc_start: 0.8061 (mm) cc_final: 0.7639 (tp) REVERT: U 393 TYR cc_start: 0.8338 (t80) cc_final: 0.8086 (t80) REVERT: U 515 GLN cc_start: 0.7807 (mp10) cc_final: 0.7567 (tt0) REVERT: U 559 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7052 (pp) REVERT: V 287 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: X 386 MET cc_start: 0.7175 (mmm) cc_final: 0.6886 (mmp) REVERT: X 414 GLN cc_start: 0.6654 (mm-40) cc_final: 0.6209 (tp-100) REVERT: X 431 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7418 (mp) REVERT: X 488 MET cc_start: 0.7115 (mmm) cc_final: 0.6802 (mmm) outliers start: 102 outliers final: 57 residues processed: 822 average time/residue: 0.5239 time to fit residues: 728.9404 Evaluate side-chains 693 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 628 time to evaluate : 4.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 549 ASP Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 3 residue 297 LEU Chi-restraints excluded: chain 4 residue 266 GLU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 102 SER Chi-restraints excluded: chain T residue 186 GLU Chi-restraints excluded: chain U residue 288 VAL Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 502 optimal weight: 4.9990 chunk 278 optimal weight: 5.9990 chunk 575 optimal weight: 9.9990 chunk 466 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 344 optimal weight: 0.8980 chunk 605 optimal weight: 2.9990 chunk 170 optimal weight: 0.2980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 428 HIS ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 256 GLN 5 107 ASN 7 24 GLN 7 184 ASN G 94 ASN P 66 GLN P 83 GLN T 134 ASN T 241 HIS ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 149 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 54694 Z= 0.188 Angle : 0.522 10.760 74172 Z= 0.266 Chirality : 0.041 0.255 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.700 164.815 7674 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % Rotamer: Outliers : 2.31 % Allowed : 14.52 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.01 (0.10), residues: 7039 helix: 0.68 (0.09), residues: 3859 sheet: -0.69 (0.21), residues: 628 loop : -0.74 (0.13), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP U 73 HIS 0.007 0.001 HIS T 241 PHE 0.033 0.001 PHE A 122 TYR 0.023 0.001 TYR 4 211 ARG 0.006 0.000 ARG 1 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 656 time to evaluate : 4.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8566 (ttpt) cc_final: 0.7893 (tptt) REVERT: 1 32 THR cc_start: 0.8817 (p) cc_final: 0.8531 (p) REVERT: 2 189 ASP cc_start: 0.8161 (t0) cc_final: 0.7709 (t0) REVERT: 2 190 LYS cc_start: 0.8175 (mppt) cc_final: 0.7643 (tptt) REVERT: 2 192 THR cc_start: 0.8144 (m) cc_final: 0.7935 (p) REVERT: 3 93 GLU cc_start: 0.6054 (mp0) cc_final: 0.5804 (mp0) REVERT: 3 276 GLU cc_start: 0.7397 (tp30) cc_final: 0.7057 (tp30) REVERT: 4 266 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: 9 26 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8495 (tt) REVERT: 9 80 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7581 (mm-40) REVERT: A 81 MET cc_start: 0.7700 (ttp) cc_final: 0.7351 (ttp) REVERT: C 81 MET cc_start: 0.8531 (ttp) cc_final: 0.8314 (ttp) REVERT: C 92 ASN cc_start: 0.8311 (t0) cc_final: 0.8010 (t0) REVERT: E 60 LYS cc_start: 0.7847 (mttp) cc_final: 0.7607 (mttm) REVERT: E 61 MET cc_start: 0.8373 (mmm) cc_final: 0.7993 (mmt) REVERT: E 111 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: F 61 MET cc_start: 0.7637 (mmm) cc_final: 0.7425 (mmt) REVERT: F 102 TYR cc_start: 0.8495 (m-10) cc_final: 0.8254 (m-10) REVERT: F 119 LEU cc_start: 0.8123 (tt) cc_final: 0.6178 (mm) REVERT: I 60 LYS cc_start: 0.7992 (mttp) cc_final: 0.7558 (mtpt) REVERT: I 91 ARG cc_start: 0.8095 (ttm110) cc_final: 0.7873 (ttm-80) REVERT: J 120 VAL cc_start: 0.7273 (t) cc_final: 0.7063 (t) REVERT: J 122 PHE cc_start: 0.7268 (m-10) cc_final: 0.6849 (t80) REVERT: M 271 VAL cc_start: 0.7341 (OUTLIER) cc_final: 0.6934 (t) REVERT: P 59 GLN cc_start: 0.8177 (mt0) cc_final: 0.7895 (mt0) REVERT: P 83 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7810 (mm110) REVERT: P 190 ILE cc_start: 0.8448 (pt) cc_final: 0.8134 (mm) REVERT: P 206 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7816 (ttt-90) REVERT: Q 32 LYS cc_start: 0.6897 (mmtm) cc_final: 0.6559 (mmtp) REVERT: R 37 TRP cc_start: 0.6540 (t60) cc_final: 0.6309 (t60) REVERT: R 117 GLU cc_start: 0.7554 (tt0) cc_final: 0.7328 (tt0) REVERT: R 171 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.6964 (pp30) REVERT: S 115 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7119 (mp) REVERT: U 393 TYR cc_start: 0.8381 (t80) cc_final: 0.8066 (t80) REVERT: U 559 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7058 (pp) REVERT: V 287 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.8117 (ttm) REVERT: X 227 MET cc_start: 0.6979 (ttp) cc_final: 0.6696 (ttp) REVERT: X 386 MET cc_start: 0.7199 (mmm) cc_final: 0.6821 (mmp) REVERT: X 414 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6187 (tp-100) REVERT: X 431 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7419 (mp) REVERT: X 488 MET cc_start: 0.7115 (mmm) cc_final: 0.6807 (mmm) REVERT: Z 175 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7198 (tpt170) outliers start: 130 outliers final: 79 residues processed: 741 average time/residue: 0.5124 time to fit residues: 645.4886 Evaluate side-chains 698 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 610 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 329 LEU Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 4 residue 266 GLU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 294 ASP Chi-restraints excluded: chain T residue 483 MET Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 288 VAL Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 2.9990 chunk 607 optimal weight: 8.9990 chunk 133 optimal weight: 0.6980 chunk 396 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 675 optimal weight: 1.9990 chunk 560 optimal weight: 3.9990 chunk 312 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN 7 24 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN T 134 ASN T 241 HIS ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 123 GLN V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 54694 Z= 0.243 Angle : 0.547 11.027 74172 Z= 0.279 Chirality : 0.042 0.271 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.870 179.763 7674 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.55 % Favored : 96.39 % Rotamer: Outliers : 2.34 % Allowed : 15.22 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.02 (0.10), residues: 7039 helix: 0.66 (0.09), residues: 3882 sheet: -0.62 (0.21), residues: 616 loop : -0.69 (0.13), residues: 2541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP U 73 HIS 0.007 0.001 HIS V 61 PHE 0.031 0.001 PHE A 122 TYR 0.023 0.001 TYR 4 211 ARG 0.006 0.000 ARG V 479 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 635 time to evaluate : 4.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8606 (ttpt) cc_final: 0.7900 (tptt) REVERT: 1 32 THR cc_start: 0.8906 (p) cc_final: 0.8627 (p) REVERT: 2 74 ASN cc_start: 0.7751 (t0) cc_final: 0.7469 (t0) REVERT: 2 189 ASP cc_start: 0.8154 (t0) cc_final: 0.7724 (t0) REVERT: 2 190 LYS cc_start: 0.8194 (mppt) cc_final: 0.7657 (tptt) REVERT: 3 93 GLU cc_start: 0.5955 (mp0) cc_final: 0.5727 (mp0) REVERT: 6 76 LYS cc_start: 0.7837 (mtmt) cc_final: 0.6972 (tttm) REVERT: 8 5 GLU cc_start: 0.7674 (tt0) cc_final: 0.7375 (tt0) REVERT: 8 62 ASP cc_start: 0.7610 (p0) cc_final: 0.7327 (p0) REVERT: 9 26 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8422 (tt) REVERT: 9 80 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7545 (mm-40) REVERT: A 81 MET cc_start: 0.7777 (ttp) cc_final: 0.7429 (ttp) REVERT: C 60 LYS cc_start: 0.8130 (mttp) cc_final: 0.7826 (mttp) REVERT: C 81 MET cc_start: 0.8537 (ttp) cc_final: 0.8304 (ttm) REVERT: E 60 LYS cc_start: 0.7934 (mttp) cc_final: 0.7678 (mttm) REVERT: E 61 MET cc_start: 0.8350 (mmm) cc_final: 0.8119 (mmt) REVERT: E 111 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: F 119 LEU cc_start: 0.8300 (tt) cc_final: 0.7933 (tp) REVERT: I 60 LYS cc_start: 0.8078 (mttp) cc_final: 0.7601 (mtpt) REVERT: I 91 ARG cc_start: 0.8156 (ttm110) cc_final: 0.7906 (ttm-80) REVERT: J 120 VAL cc_start: 0.7414 (t) cc_final: 0.7188 (t) REVERT: J 122 PHE cc_start: 0.7258 (m-10) cc_final: 0.6844 (t80) REVERT: M 202 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5700 (m-80) REVERT: M 271 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7076 (t) REVERT: P 59 GLN cc_start: 0.8175 (mt0) cc_final: 0.7884 (mt0) REVERT: P 190 ILE cc_start: 0.8465 (pt) cc_final: 0.8105 (mm) REVERT: P 205 ARG cc_start: 0.7861 (ptp90) cc_final: 0.6923 (ptt-90) REVERT: P 209 MET cc_start: 0.8711 (mmm) cc_final: 0.8465 (mmt) REVERT: Q 14 MET cc_start: 0.7729 (ttm) cc_final: 0.7492 (ttt) REVERT: Q 32 LYS cc_start: 0.6919 (mmtm) cc_final: 0.6556 (mmtp) REVERT: R 171 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6917 (pp30) REVERT: S 115 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7282 (mp) REVERT: T 522 GLU cc_start: 0.7031 (pp20) cc_final: 0.6797 (pp20) REVERT: U 393 TYR cc_start: 0.8405 (t80) cc_final: 0.8168 (t80) REVERT: U 449 GLU cc_start: 0.6039 (tt0) cc_final: 0.5788 (tp30) REVERT: U 559 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7072 (pp) REVERT: V 287 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: X 386 MET cc_start: 0.7243 (mmm) cc_final: 0.6903 (mmp) REVERT: X 414 GLN cc_start: 0.6666 (mm-40) cc_final: 0.6165 (tp-100) REVERT: X 431 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7453 (mp) REVERT: X 488 MET cc_start: 0.6952 (mmm) cc_final: 0.6670 (mmm) REVERT: Z 175 ARG cc_start: 0.7638 (tpp80) cc_final: 0.7148 (tpt170) outliers start: 132 outliers final: 98 residues processed: 720 average time/residue: 0.5784 time to fit residues: 714.5093 Evaluate side-chains 697 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 590 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 329 LEU Chi-restraints excluded: chain 2 residue 385 SER Chi-restraints excluded: chain 2 residue 398 HIS Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 294 ASP Chi-restraints excluded: chain T residue 483 MET Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 288 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 514 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 235 LEU Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 384 optimal weight: 3.9990 chunk 493 optimal weight: 4.9990 chunk 382 optimal weight: 1.9990 chunk 568 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 672 optimal weight: 0.6980 chunk 421 optimal weight: 4.9990 chunk 410 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 83 GLN T 134 ASN ** T 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54694 Z= 0.223 Angle : 0.541 10.738 74172 Z= 0.275 Chirality : 0.042 0.292 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.780 166.933 7674 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.48 % Rotamer: Outliers : 2.49 % Allowed : 15.73 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.10), residues: 7039 helix: 0.76 (0.09), residues: 3866 sheet: -0.56 (0.21), residues: 611 loop : -0.61 (0.13), residues: 2562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP U 73 HIS 0.007 0.001 HIS V 61 PHE 0.041 0.001 PHE A 122 TYR 0.023 0.001 TYR 4 211 ARG 0.006 0.000 ARG Y 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 632 time to evaluate : 4.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8588 (ttpt) cc_final: 0.7900 (tptt) REVERT: 1 32 THR cc_start: 0.8885 (p) cc_final: 0.8603 (p) REVERT: 2 74 ASN cc_start: 0.7724 (t0) cc_final: 0.7438 (t0) REVERT: 2 190 LYS cc_start: 0.8214 (mppt) cc_final: 0.7648 (tptt) REVERT: 3 93 GLU cc_start: 0.5940 (mp0) cc_final: 0.5720 (mp0) REVERT: 4 124 ASN cc_start: 0.7910 (m110) cc_final: 0.7625 (m-40) REVERT: 6 76 LYS cc_start: 0.7841 (mtmt) cc_final: 0.6975 (tttm) REVERT: 8 5 GLU cc_start: 0.7631 (tt0) cc_final: 0.7309 (tt0) REVERT: 8 62 ASP cc_start: 0.7595 (p0) cc_final: 0.7321 (p0) REVERT: 9 26 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8484 (tt) REVERT: 9 80 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7456 (mm-40) REVERT: A 81 MET cc_start: 0.7772 (ttp) cc_final: 0.7431 (ttp) REVERT: C 81 MET cc_start: 0.8553 (ttp) cc_final: 0.8318 (ttm) REVERT: C 92 ASN cc_start: 0.8397 (t0) cc_final: 0.7983 (t0) REVERT: E 60 LYS cc_start: 0.7876 (mttp) cc_final: 0.7644 (mttm) REVERT: E 61 MET cc_start: 0.8453 (mmm) cc_final: 0.8242 (mmt) REVERT: I 60 LYS cc_start: 0.8008 (mttp) cc_final: 0.7494 (mtpt) REVERT: I 91 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7925 (ttm-80) REVERT: J 120 VAL cc_start: 0.7545 (t) cc_final: 0.7321 (t) REVERT: J 122 PHE cc_start: 0.7227 (m-10) cc_final: 0.6841 (t80) REVERT: M 110 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8821 (mm) REVERT: M 202 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: M 271 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7142 (t) REVERT: P 59 GLN cc_start: 0.8173 (mt0) cc_final: 0.7895 (mt0) REVERT: P 190 ILE cc_start: 0.8480 (pt) cc_final: 0.8103 (mm) REVERT: P 206 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.7707 (ttp-170) REVERT: Q 32 LYS cc_start: 0.6970 (mmtm) cc_final: 0.6643 (mmtp) REVERT: R 171 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6952 (pp30) REVERT: S 115 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7395 (mp) REVERT: T 118 MET cc_start: 0.8237 (ttt) cc_final: 0.7933 (ttt) REVERT: U 393 TYR cc_start: 0.8380 (t80) cc_final: 0.8140 (t80) REVERT: U 471 GLN cc_start: 0.6210 (tm-30) cc_final: 0.5957 (tp-100) REVERT: U 559 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7045 (pp) REVERT: V 287 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (ttm) REVERT: X 122 MET cc_start: 0.7085 (mtm) cc_final: 0.6656 (mtm) REVERT: X 386 MET cc_start: 0.7290 (mmm) cc_final: 0.6953 (mmp) REVERT: X 414 GLN cc_start: 0.6708 (mm-40) cc_final: 0.6238 (tp-100) REVERT: X 431 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7417 (mp) REVERT: X 488 MET cc_start: 0.6916 (mmm) cc_final: 0.6629 (mmm) REVERT: Y 456 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7994 (m) REVERT: Y 539 ILE cc_start: 0.6350 (mt) cc_final: 0.6136 (mt) REVERT: Z 175 ARG cc_start: 0.7648 (tpp80) cc_final: 0.7156 (tpt170) outliers start: 140 outliers final: 111 residues processed: 725 average time/residue: 0.5039 time to fit residues: 622.5164 Evaluate side-chains 716 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 595 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 572 ASP Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 329 LEU Chi-restraints excluded: chain 2 residue 385 SER Chi-restraints excluded: chain 2 residue 398 HIS Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 160 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 294 ASP Chi-restraints excluded: chain T residue 483 MET Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 274 ASP Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 414 GLN Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 401 optimal weight: 7.9990 chunk 202 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 427 optimal weight: 7.9990 chunk 458 optimal weight: 0.9990 chunk 332 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 528 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN S 159 GLN T 134 ASN T 248 GLN V 441 GLN V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 54694 Z= 0.160 Angle : 0.523 9.434 74172 Z= 0.266 Chirality : 0.041 0.296 8690 Planarity : 0.004 0.060 9512 Dihedral : 5.494 147.787 7674 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Rotamer: Outliers : 2.36 % Allowed : 16.16 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.36 (0.10), residues: 7039 helix: 0.92 (0.09), residues: 3888 sheet: -0.52 (0.21), residues: 613 loop : -0.50 (0.13), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP U 73 HIS 0.007 0.001 HIS V 61 PHE 0.042 0.001 PHE A 122 TYR 0.023 0.001 TYR 4 211 ARG 0.009 0.000 ARG U 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 675 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8560 (ttpt) cc_final: 0.7861 (tptt) REVERT: 1 32 THR cc_start: 0.8823 (p) cc_final: 0.8546 (p) REVERT: 1 604 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7230 (mtm110) REVERT: 2 74 ASN cc_start: 0.7652 (t0) cc_final: 0.7257 (t0) REVERT: 2 190 LYS cc_start: 0.8192 (mppt) cc_final: 0.7669 (tptt) REVERT: 6 76 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7210 (mttm) REVERT: 8 5 GLU cc_start: 0.7629 (tt0) cc_final: 0.7361 (tt0) REVERT: 9 22 GLU cc_start: 0.7601 (pp20) cc_final: 0.7388 (mm-30) REVERT: 9 26 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8535 (tt) REVERT: 9 80 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7368 (mm-40) REVERT: 9 85 LYS cc_start: 0.8060 (pttt) cc_final: 0.7855 (ptmt) REVERT: A 81 MET cc_start: 0.7760 (ttp) cc_final: 0.7425 (ttp) REVERT: C 81 MET cc_start: 0.8537 (ttp) cc_final: 0.8331 (ttp) REVERT: C 92 ASN cc_start: 0.8312 (t0) cc_final: 0.7891 (t0) REVERT: E 60 LYS cc_start: 0.7856 (mttp) cc_final: 0.7623 (mttm) REVERT: F 119 LEU cc_start: 0.8129 (tt) cc_final: 0.6214 (mm) REVERT: I 60 LYS cc_start: 0.7873 (mttp) cc_final: 0.7382 (mtpt) REVERT: I 91 ARG cc_start: 0.8093 (ttm110) cc_final: 0.7584 (ttp-110) REVERT: J 120 VAL cc_start: 0.7359 (t) cc_final: 0.7149 (t) REVERT: J 122 PHE cc_start: 0.7232 (m-10) cc_final: 0.6872 (t80) REVERT: M 202 PHE cc_start: 0.6453 (OUTLIER) cc_final: 0.5762 (m-80) REVERT: M 271 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7124 (t) REVERT: P 59 GLN cc_start: 0.8227 (mt0) cc_final: 0.7978 (mt0) REVERT: P 117 ILE cc_start: 0.8270 (mm) cc_final: 0.7974 (tt) REVERT: P 190 ILE cc_start: 0.8378 (pt) cc_final: 0.8109 (mm) REVERT: P 206 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: Q 14 MET cc_start: 0.7589 (ttm) cc_final: 0.7335 (ttt) REVERT: Q 32 LYS cc_start: 0.6978 (mmtm) cc_final: 0.6677 (mmtp) REVERT: R 171 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6916 (pp30) REVERT: S 115 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7361 (mp) REVERT: T 118 MET cc_start: 0.8136 (ttt) cc_final: 0.7812 (ttt) REVERT: T 522 GLU cc_start: 0.7015 (pp20) cc_final: 0.6775 (pp20) REVERT: U 213 VAL cc_start: 0.7826 (m) cc_final: 0.7433 (p) REVERT: U 559 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7024 (pp) REVERT: V 287 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: X 122 MET cc_start: 0.7092 (mtm) cc_final: 0.6670 (mtm) REVERT: X 414 GLN cc_start: 0.6436 (mm-40) cc_final: 0.6023 (tp-100) REVERT: X 431 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7476 (mp) REVERT: X 488 MET cc_start: 0.6909 (mmm) cc_final: 0.6637 (mmm) REVERT: Y 456 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.7993 (m) REVERT: Y 539 ILE cc_start: 0.6351 (mt) cc_final: 0.6139 (mt) outliers start: 133 outliers final: 99 residues processed: 757 average time/residue: 0.5121 time to fit residues: 657.5151 Evaluate side-chains 731 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 623 time to evaluate : 4.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 329 LEU Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 60 GLN Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 160 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 LYS Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 294 ASP Chi-restraints excluded: chain T residue 483 MET Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 484 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.8980 chunk 644 optimal weight: 3.9990 chunk 588 optimal weight: 1.9990 chunk 626 optimal weight: 6.9990 chunk 377 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 492 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 566 optimal weight: 3.9990 chunk 592 optimal weight: 2.9990 chunk 624 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 243 ASN P 52 GLN P 83 GLN T 134 ASN V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN Y 252 ASN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54694 Z= 0.207 Angle : 0.543 11.533 74172 Z= 0.276 Chirality : 0.042 0.314 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.469 127.618 7674 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 2.24 % Allowed : 16.44 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 7039 helix: 0.93 (0.09), residues: 3876 sheet: -0.51 (0.21), residues: 618 loop : -0.44 (0.13), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP U 73 HIS 0.008 0.001 HIS V 61 PHE 0.042 0.001 PHE A 122 TYR 0.023 0.001 TYR 4 211 ARG 0.005 0.000 ARG Z 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 634 time to evaluate : 4.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8587 (ttpt) cc_final: 0.7910 (tptt) REVERT: 1 32 THR cc_start: 0.8855 (p) cc_final: 0.8576 (p) REVERT: 2 74 ASN cc_start: 0.7735 (t0) cc_final: 0.7428 (t0) REVERT: 2 190 LYS cc_start: 0.8168 (mppt) cc_final: 0.7658 (tptt) REVERT: 4 124 ASN cc_start: 0.7915 (m110) cc_final: 0.7662 (m-40) REVERT: 6 76 LYS cc_start: 0.7852 (mtmt) cc_final: 0.7285 (mttm) REVERT: 8 5 GLU cc_start: 0.7604 (tt0) cc_final: 0.7279 (tt0) REVERT: 9 1 MET cc_start: 0.2433 (ptt) cc_final: -0.0821 (mpp) REVERT: 9 22 GLU cc_start: 0.7618 (pp20) cc_final: 0.7388 (mm-30) REVERT: 9 26 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8474 (tt) REVERT: 9 80 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7367 (mm-40) REVERT: A 81 MET cc_start: 0.7805 (ttp) cc_final: 0.7428 (ttp) REVERT: A 102 TYR cc_start: 0.7089 (m-80) cc_final: 0.6742 (m-80) REVERT: A 111 GLU cc_start: 0.7509 (tp30) cc_final: 0.7232 (mm-30) REVERT: C 81 MET cc_start: 0.8549 (ttp) cc_final: 0.8313 (ttm) REVERT: C 92 ASN cc_start: 0.8338 (t0) cc_final: 0.7908 (t0) REVERT: E 60 LYS cc_start: 0.7967 (mttp) cc_final: 0.7708 (mttm) REVERT: F 119 LEU cc_start: 0.8132 (tt) cc_final: 0.6254 (mm) REVERT: I 60 LYS cc_start: 0.7921 (mttp) cc_final: 0.7440 (mtpt) REVERT: I 91 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7575 (ttp-110) REVERT: J 120 VAL cc_start: 0.7402 (t) cc_final: 0.7170 (t) REVERT: J 122 PHE cc_start: 0.7179 (m-10) cc_final: 0.6875 (t80) REVERT: M 110 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8755 (mm) REVERT: M 202 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5776 (m-80) REVERT: M 231 PHE cc_start: 0.8386 (t80) cc_final: 0.7992 (t80) REVERT: M 271 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7118 (t) REVERT: P 59 GLN cc_start: 0.8226 (mt0) cc_final: 0.7955 (mt0) REVERT: P 183 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7795 (pttp) REVERT: P 190 ILE cc_start: 0.8372 (pt) cc_final: 0.8110 (mm) REVERT: P 206 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7650 (ttp-170) REVERT: Q 32 LYS cc_start: 0.6994 (mmtm) cc_final: 0.6697 (mmtp) REVERT: R 171 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6932 (pp30) REVERT: S 115 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7398 (mp) REVERT: S 156 GLN cc_start: 0.7471 (pm20) cc_final: 0.7205 (mp10) REVERT: U 213 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7559 (p) REVERT: U 471 GLN cc_start: 0.6415 (tm-30) cc_final: 0.5834 (tp-100) REVERT: U 559 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7119 (pp) REVERT: V 287 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8130 (ttm) REVERT: X 122 MET cc_start: 0.7049 (mtm) cc_final: 0.6609 (mtm) REVERT: X 414 GLN cc_start: 0.6464 (mm-40) cc_final: 0.6028 (tp-100) REVERT: X 431 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7473 (mp) REVERT: X 488 MET cc_start: 0.6927 (mmm) cc_final: 0.6664 (mmm) REVERT: Y 456 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8020 (m) REVERT: Y 539 ILE cc_start: 0.6375 (mt) cc_final: 0.6154 (mt) outliers start: 126 outliers final: 106 residues processed: 715 average time/residue: 0.5157 time to fit residues: 628.3195 Evaluate side-chains 712 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 595 time to evaluate : 4.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 195 LYS Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 329 LEU Chi-restraints excluded: chain 2 residue 348 GLU Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 109 GLN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 7 residue 175 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 160 GLU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 294 ASP Chi-restraints excluded: chain T residue 483 MET Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 169 GLN Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 502 MET Chi-restraints excluded: chain Z residue 568 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 1.9990 chunk 662 optimal weight: 4.9990 chunk 404 optimal weight: 5.9990 chunk 314 optimal weight: 0.0170 chunk 460 optimal weight: 0.6980 chunk 695 optimal weight: 9.9990 chunk 640 optimal weight: 9.9990 chunk 553 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 427 optimal weight: 0.8980 chunk 339 optimal weight: 9.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 107 ASN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN T 134 ASN U 104 GLN U 441 GLN V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 250 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 54694 Z= 0.155 Angle : 0.526 11.800 74172 Z= 0.267 Chirality : 0.041 0.317 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.233 102.485 7674 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 2.15 % Allowed : 16.81 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 7039 helix: 1.08 (0.09), residues: 3875 sheet: -0.43 (0.22), residues: 596 loop : -0.35 (0.13), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP U 73 HIS 0.009 0.001 HIS V 61 PHE 0.052 0.001 PHE A 107 TYR 0.023 0.001 TYR 4 211 ARG 0.007 0.000 ARG V 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 644 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8552 (ttpt) cc_final: 0.7848 (tptt) REVERT: 1 32 THR cc_start: 0.8718 (p) cc_final: 0.8463 (p) REVERT: 1 604 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7209 (mtm110) REVERT: 2 190 LYS cc_start: 0.8123 (mppt) cc_final: 0.7636 (tptt) REVERT: 2 346 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6788 (mtm-85) REVERT: 4 124 ASN cc_start: 0.7994 (m110) cc_final: 0.7751 (m-40) REVERT: 6 76 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7211 (mttm) REVERT: 7 24 GLN cc_start: 0.8380 (tp40) cc_final: 0.8007 (tm-30) REVERT: 8 5 GLU cc_start: 0.7560 (tt0) cc_final: 0.7242 (tt0) REVERT: 9 1 MET cc_start: 0.2091 (ptt) cc_final: -0.0843 (mpp) REVERT: 9 22 GLU cc_start: 0.7678 (pp20) cc_final: 0.7451 (mm-30) REVERT: 9 26 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (tt) REVERT: 9 80 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7380 (mm110) REVERT: A 81 MET cc_start: 0.7818 (ttp) cc_final: 0.7452 (ttp) REVERT: A 102 TYR cc_start: 0.7011 (m-80) cc_final: 0.6740 (m-80) REVERT: B 107 PHE cc_start: 0.8316 (t80) cc_final: 0.7994 (t80) REVERT: C 81 MET cc_start: 0.8547 (ttp) cc_final: 0.8343 (ttp) REVERT: C 92 ASN cc_start: 0.8341 (t0) cc_final: 0.7890 (t0) REVERT: E 60 LYS cc_start: 0.7833 (mttp) cc_final: 0.7581 (mttm) REVERT: F 119 LEU cc_start: 0.8004 (tt) cc_final: 0.6208 (mm) REVERT: I 91 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7494 (ttp-110) REVERT: J 120 VAL cc_start: 0.7360 (t) cc_final: 0.7132 (t) REVERT: J 122 PHE cc_start: 0.7204 (m-10) cc_final: 0.6907 (t80) REVERT: M 110 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8618 (mm) REVERT: M 202 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.5821 (m-80) REVERT: M 271 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7079 (t) REVERT: P 59 GLN cc_start: 0.8228 (mt0) cc_final: 0.7995 (mt0) REVERT: P 117 ILE cc_start: 0.8254 (mm) cc_final: 0.7963 (tt) REVERT: P 183 LYS cc_start: 0.8163 (mmtm) cc_final: 0.7755 (pttp) REVERT: P 190 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8091 (mm) REVERT: P 206 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7587 (ttp-170) REVERT: Q 32 LYS cc_start: 0.6991 (mmtm) cc_final: 0.6764 (mmtp) REVERT: R 171 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7007 (pp30) REVERT: S 115 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7356 (mp) REVERT: S 117 SER cc_start: 0.7998 (p) cc_final: 0.7682 (m) REVERT: S 203 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7333 (m-10) REVERT: T 522 GLU cc_start: 0.6969 (pp20) cc_final: 0.6745 (pp20) REVERT: U 213 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7578 (p) REVERT: U 559 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7105 (pp) REVERT: V 287 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8144 (ttm) REVERT: X 122 MET cc_start: 0.7109 (mtm) cc_final: 0.6704 (mtm) REVERT: X 310 TYR cc_start: 0.8546 (m-80) cc_final: 0.8323 (m-80) REVERT: X 414 GLN cc_start: 0.6404 (mm-40) cc_final: 0.5996 (tp-100) REVERT: X 431 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7526 (mp) REVERT: X 488 MET cc_start: 0.6849 (mmm) cc_final: 0.6594 (mmm) REVERT: Y 456 THR cc_start: 0.8239 (OUTLIER) cc_final: 0.8019 (m) outliers start: 121 outliers final: 98 residues processed: 718 average time/residue: 0.5100 time to fit residues: 625.8204 Evaluate side-chains 729 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 618 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 188 VAL Chi-restraints excluded: chain 1 residue 195 LYS Chi-restraints excluded: chain 1 residue 258 GLU Chi-restraints excluded: chain 1 residue 418 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 2 residue 98 LEU Chi-restraints excluded: chain 2 residue 290 VAL Chi-restraints excluded: chain 2 residue 329 LEU Chi-restraints excluded: chain 2 residue 348 GLU Chi-restraints excluded: chain 3 residue 82 VAL Chi-restraints excluded: chain 3 residue 116 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 133 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 107 ASN Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 72 SER Chi-restraints excluded: chain 7 residue 83 SER Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 38 LYS Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 26 LEU Chi-restraints excluded: chain 9 residue 30 LEU Chi-restraints excluded: chain 9 residue 76 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 202 PHE Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 171 GLN Chi-restraints excluded: chain S residue 56 ILE Chi-restraints excluded: chain S residue 75 VAL Chi-restraints excluded: chain S residue 102 VAL Chi-restraints excluded: chain S residue 112 CYS Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain S residue 124 ARG Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 243 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 272 LEU Chi-restraints excluded: chain T residue 294 ASP Chi-restraints excluded: chain U residue 54 SER Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 287 MET Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 247 VAL Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 103 VAL Chi-restraints excluded: chain Y residue 226 GLU Chi-restraints excluded: chain Y residue 233 ILE Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 440 GLN Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Y residue 461 VAL Chi-restraints excluded: chain Z residue 61 SER Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 162 THR Chi-restraints excluded: chain Z residue 204 HIS Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 484 MET Chi-restraints excluded: chain Z residue 502 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.8980 chunk 589 optimal weight: 0.0670 chunk 169 optimal weight: 0.7980 chunk 510 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 554 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 569 optimal weight: 0.8980 chunk 70 optimal weight: 0.0000 chunk 102 optimal weight: 0.0470 overall best weight: 0.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 380 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 336 GLN V 539 ASN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107834 restraints weight = 87069.579| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.01 r_work: 0.3103 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 54694 Z= 0.143 Angle : 0.528 15.153 74172 Z= 0.267 Chirality : 0.040 0.315 8690 Planarity : 0.004 0.053 9512 Dihedral : 5.092 88.798 7674 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.65 % Rotamer: Outliers : 2.02 % Allowed : 17.24 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.70 (0.11), residues: 7039 helix: 1.18 (0.09), residues: 3876 sheet: -0.43 (0.22), residues: 594 loop : -0.28 (0.13), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.001 TRP U 73 HIS 0.009 0.001 HIS V 61 PHE 0.060 0.001 PHE A 107 TYR 0.023 0.001 TYR 4 211 ARG 0.011 0.000 ARG Y 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12912.73 seconds wall clock time: 225 minutes 23.95 seconds (13523.95 seconds total)