Starting phenix.real_space_refine on Wed Sep 25 04:34:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/09_2024/6rdr_4828.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/09_2024/6rdr_4828.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/09_2024/6rdr_4828.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/09_2024/6rdr_4828.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/09_2024/6rdr_4828.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdr_4828/09_2024/6rdr_4828.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 404 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.57, per 1000 atoms: 0.44 Number of scatterers: 53748 At special positions: 0 Unit cell: (208.494, 133.731, 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 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.61 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... Secondary structure from input PDB file: 310 helices and 37 sheets defined 57.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain '0' and resid 3 through 9 removed outlier: 3.949A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 31 Processing helix chain '0' and resid 43 through 49 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.559A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 73 Processing helix chain '1' and resid 96 through 100 removed outlier: 3.730A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) Processing helix chain '1' and resid 103 through 105 No H-bonds generated for 'chain '1' and resid 103 through 105' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.701A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 4.024A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 203 removed outlier: 3.909A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) Processing helix chain '1' and resid 204 through 205 No H-bonds generated for 'chain '1' and resid 204 through 205' 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: 3.613A pdb=" N SER 1 214 " --> pdb=" O ALA 1 210 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.518A pdb=" N ALA 1 245 " --> pdb=" O SER 1 241 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.996A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 removed outlier: 3.713A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 4.065A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 335 removed outlier: 4.444A pdb=" N GLU 1 334 " --> pdb=" O LYS 1 330 " (cutoff:3.500A) 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: 3.977A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 Processing helix chain '1' and resid 392 through 421 removed outlier: 3.776A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 431 Processing helix chain '1' and resid 435 through 444 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 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.959A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.618A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 removed outlier: 3.607A pdb=" N ILE 1 553 " --> pdb=" O ASP 1 549 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '2' and resid 7 through 19 Processing helix chain '2' and resid 25 through 38 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.916A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 2 58 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 removed outlier: 3.696A pdb=" N ALA 2 91 " --> pdb=" O LEU 2 87 " (cutoff:3.500A) Processing helix chain '2' and resid 99 through 113 removed outlier: 3.604A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.946A pdb=" N LYS 2 131 " --> pdb=" O VAL 2 127 " (cutoff:3.500A) Processing helix chain '2' and resid 132 through 135 Processing helix chain '2' and resid 136 through 149 Processing helix chain '2' and resid 154 through 166 removed outlier: 3.817A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 3.531A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 220 removed outlier: 3.645A 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 255 removed outlier: 3.521A pdb=" N GLY 2 255 " --> pdb=" O LEU 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.988A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 295 removed outlier: 3.681A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 4.340A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.613A 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 355 Processing helix chain '2' and resid 396 through 408 removed outlier: 3.726A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 426 through 442 removed outlier: 3.871A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 89 removed outlier: 3.593A pdb=" N LYS 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.751A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 125 removed outlier: 4.804A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 Processing helix chain '3' and resid 173 through 187 removed outlier: 3.597A 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: 4.052A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.849A 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 250 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.669A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 287 removed outlier: 4.130A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 3.674A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 removed outlier: 3.739A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 4.338A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE 4 14 " --> pdb=" O GLU 4 10 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 9 through 14' Processing helix chain '4' and resid 20 through 35 removed outlier: 3.708A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 69 removed outlier: 4.062A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.591A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 78 through 96 removed outlier: 4.655A pdb=" N VAL 4 82 " --> pdb=" O GLY 4 78 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS 4 83 " --> pdb=" O SER 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 removed outlier: 3.532A pdb=" N VAL 4 122 " --> pdb=" O THR 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 150 removed outlier: 3.806A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 4.072A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 Processing helix chain '4' and resid 193 through 234 removed outlier: 3.922A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.873A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 284 Processing helix chain '5' and resid 7 through 30 removed outlier: 3.714A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 59 removed outlier: 3.916A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 removed outlier: 3.715A pdb=" N SER 5 67 " --> pdb=" O ASP 5 63 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 87 through 106 removed outlier: 4.038A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 113 through 118 removed outlier: 3.900A pdb=" N TRP 5 116 " --> pdb=" O VAL 5 113 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 removed outlier: 3.814A 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 117 removed outlier: 4.033A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '7' and resid 63 through 70 removed outlier: 3.804A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER 7 70 " --> pdb=" O LEU 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 102 Processing helix chain '7' and resid 110 through 114 removed outlier: 3.566A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 165 Processing helix chain '7' and resid 174 through 187 Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 removed outlier: 3.875A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 40 through 78 removed outlier: 7.020A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 36 through 55 removed outlier: 4.169A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 removed outlier: 4.502A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.863A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.662A pdb=" N ALA A 70 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 71 " --> pdb=" O THR A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 71' Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.735A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 removed outlier: 3.551A pdb=" N ALA A 96 " --> pdb=" O PRO A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 93 through 96' Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.632A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.778A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.662A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 127 removed outlier: 3.685A pdb=" N VAL B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 66 removed outlier: 4.198A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 70 through 90 removed outlier: 4.142A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.564A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.972A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.310A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.507A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 3.634A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 90 removed outlier: 3.805A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 98 through 127 removed outlier: 3.809A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU E 125 " --> pdb=" O VAL E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.991A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.922A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 127 removed outlier: 4.847A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 125 " --> pdb=" O VAL F 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.900A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.482A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 124 removed outlier: 3.512A pdb=" N VAL G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 124 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 67 Processing helix chain 'H' and resid 70 through 92 removed outlier: 3.995A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.792A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.583A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.082A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 3.638A pdb=" N VAL I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 66 removed outlier: 3.865A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 69 No H-bonds generated for 'chain 'J' and resid 67 through 69' Processing helix chain 'J' and resid 70 through 90 removed outlier: 4.036A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.595A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE J 126 " --> pdb=" O PHE J 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.624A pdb=" N TRP M 151 " --> pdb=" O SER M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.815A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 259 removed outlier: 4.097A pdb=" N LEU M 224 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.527A pdb=" N PHE M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.640A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 65 removed outlier: 3.993A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS P 63 " --> pdb=" O GLN P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.812A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU P 79 " --> pdb=" O TYR P 75 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE P 81 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.611A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.879A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER P 106 " --> pdb=" O THR P 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 122 Processing helix chain 'P' and resid 123 through 128 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 150 removed outlier: 3.681A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU P 144 " --> pdb=" O ASN P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.723A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 229 removed outlier: 3.681A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 228 " --> pdb=" O LYS P 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 12 removed outlier: 3.511A pdb=" N ALA Q 12 " --> pdb=" O PHE Q 8 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.232A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 42 removed outlier: 3.751A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.649A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 168 removed outlier: 4.253A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 4.001A pdb=" N ALA R 197 " --> pdb=" O SER R 193 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.960A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 71 " --> pdb=" O LYS S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 removed outlier: 4.479A pdb=" N GLU S 76 " --> pdb=" O GLN S 72 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 removed outlier: 3.897A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 129 removed outlier: 3.663A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 4.010A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 148' Processing helix chain 'S' and resid 149 through 154 removed outlier: 4.173A pdb=" N ILE S 153 " --> pdb=" O GLN S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 Processing helix chain 'S' and resid 216 through 221 removed outlier: 3.549A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.515A pdb=" N VAL S 242 " --> pdb=" O GLU S 238 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP S 245 " --> pdb=" O ASP S 241 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE S 307 " --> pdb=" O GLU S 303 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 76 Proline residue: T 68 - end of helix removed outlier: 3.680A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.374A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 211 removed outlier: 3.627A pdb=" N ALA T 211 " --> pdb=" O LYS T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.853A pdb=" N ALA T 238 " --> pdb=" O VAL T 234 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN T 244 " --> pdb=" O ILE T 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN T 246 " --> pdb=" O GLN T 242 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 284 Processing helix chain 'T' and resid 295 through 316 removed outlier: 3.741A pdb=" N LEU T 301 " --> pdb=" O PRO T 297 " (cutoff:3.500A) Proline residue: T 303 - end of helix removed outlier: 3.616A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 339 removed outlier: 4.024A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.582A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU T 363 " --> pdb=" O SER T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 removed outlier: 3.551A pdb=" N ASN T 397 " --> pdb=" O TYR T 393 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL T 398 " --> pdb=" O ILE T 394 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER T 400 " --> pdb=" O THR T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.892A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 443 removed outlier: 4.032A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) Processing helix chain 'T' and resid 445 through 458 removed outlier: 3.525A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 459 through 463 removed outlier: 4.050A pdb=" N PHE T 462 " --> pdb=" O PHE T 459 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 482 Processing helix chain 'T' and resid 494 through 506 removed outlier: 4.026A pdb=" N THR T 498 " --> pdb=" O ILE T 494 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL T 499 " --> pdb=" O GLU T 495 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 527 removed outlier: 4.965A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL T 524 " --> pdb=" O ALA T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 540 removed outlier: 4.053A pdb=" N LYS T 534 " --> pdb=" O PRO T 530 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 552 removed outlier: 4.537A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 47 through 49 No H-bonds generated for 'chain 'U' and resid 47 through 49' Processing helix chain 'U' and resid 58 through 64 Processing helix chain 'U' and resid 65 through 73 removed outlier: 3.722A pdb=" N ALA U 69 " --> pdb=" O LYS U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.990A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.507A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 removed outlier: 3.526A pdb=" N VAL U 269 " --> pdb=" O LYS U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.549A 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: 3.655A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 340 Processing helix chain 'U' and resid 353 through 363 Processing helix chain 'U' and resid 393 through 400 removed outlier: 3.651A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 409 through 415 Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.417A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.611A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 494 through 506 removed outlier: 3.815A pdb=" N VAL U 499 " --> pdb=" O GLU U 495 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS U 506 " --> pdb=" O TYR U 502 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.554A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.885A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY U 540 " --> pdb=" O LEU U 536 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 4.282A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU U 554 " --> pdb=" O LEU U 550 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 removed outlier: 3.726A pdb=" N ARG V 49 " --> pdb=" O ASP V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 57 No H-bonds generated for 'chain 'V' and resid 55 through 57' Processing helix chain 'V' and resid 58 through 67 Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 4.121A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 4.305A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 248 through 249 No H-bonds generated for 'chain 'V' and resid 248 through 249' Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 284 Processing helix chain 'V' and resid 295 through 315 Proline residue: V 303 - end of helix removed outlier: 3.826A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.509A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 411 through 415 removed outlier: 3.714A pdb=" N TYR V 414 " --> pdb=" O GLU V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.231A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 457 removed outlier: 3.695A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 3.734A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 507 removed outlier: 3.979A 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 521 Processing helix chain 'V' and resid 521 through 526 Processing helix chain 'V' and resid 529 through 540 removed outlier: 4.388A pdb=" N PHE V 533 " --> pdb=" O ASN V 529 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY V 540 " --> pdb=" O LEU V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.521A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 5.141A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 removed outlier: 3.731A pdb=" N GLU X 229 " --> pdb=" O ARG X 225 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 242 removed outlier: 3.529A pdb=" N ASN X 241 " --> pdb=" O GLU X 238 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER X 242 " --> pdb=" O ARG X 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 238 through 242' Processing helix chain 'X' and resid 256 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.571A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 299 removed outlier: 3.719A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 366 through 371 Processing helix chain 'X' and resid 393 through 420 removed outlier: 4.998A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.619A pdb=" N LEU X 443 " --> pdb=" O ILE X 439 " (cutoff:3.500A) Processing helix chain 'X' and resid 449 through 453 removed outlier: 3.742A pdb=" N VAL X 452 " --> pdb=" O VAL X 449 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 483 through 487 Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.595A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 532 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.101A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER Y 242 " --> pdb=" O ARG Y 239 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 260 through 275 Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.856A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 356 removed outlier: 3.892A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Y 356 " --> pdb=" O ALA Y 352 " (cutoff:3.500A) Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 414 removed outlier: 3.771A pdb=" N TYR Y 397 " --> pdb=" O GLY Y 393 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 removed outlier: 3.899A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) Processing helix chain 'Y' and resid 449 through 453 removed outlier: 4.112A pdb=" N VAL Y 452 " --> pdb=" O VAL Y 449 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 482 through 487 removed outlier: 3.961A pdb=" N ALA Y 485 " --> pdb=" O PRO Y 482 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE Y 486 " --> pdb=" O GLU Y 483 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 507 removed outlier: 3.892A pdb=" N ASP Y 500 " --> pdb=" O LYS Y 496 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 removed outlier: 3.826A pdb=" N LEU Y 530 " --> pdb=" O SER Y 526 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU Y 533 " --> pdb=" O LYS Y 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 555 removed outlier: 3.901A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 165 through 170 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.727A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN Z 241 " --> pdb=" O GLU Z 238 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.521A pdb=" N THR Z 264 " --> pdb=" O ARG Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.645A pdb=" N PHE Z 290 " --> pdb=" O ASN Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.227A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 366 through 371 Processing helix chain 'Z' and resid 388 through 393 removed outlier: 3.717A pdb=" N GLY Z 393 " --> pdb=" O PRO Z 389 " (cutoff:3.500A) Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.612A pdb=" N ASN Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) Processing helix chain 'Z' and resid 415 through 420 Processing helix chain 'Z' and resid 426 through 440 removed outlier: 3.789A pdb=" N LEU Z 431 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR Z 432 " --> pdb=" O GLU Z 428 " (cutoff:3.500A) Processing helix chain 'Z' and resid 447 through 451 removed outlier: 3.605A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.875A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 505 removed outlier: 3.735A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Z 503 " --> pdb=" O ALA Z 499 " (cutoff:3.500A) Processing helix chain 'Z' and resid 506 through 510 removed outlier: 4.367A pdb=" N LYS Z 510 " --> pdb=" O ALA Z 507 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 6.435A pdb=" N LYS 2 376 " --> pdb=" O ALA 2 412 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 35 through 38 Processing sheet with id=AA5, first strand: chain '7' and resid 45 through 47 Processing sheet with id=AA6, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'P' and resid 189 through 190 Processing sheet with id=AA8, first strand: chain 'Q' and resid 45 through 49 removed outlier: 3.571A pdb=" N PHE Q 47 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 85 through 86 removed outlier: 7.264A pdb=" N ILE R 108 " --> pdb=" O GLU S 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 96 through 100 removed outlier: 6.831A pdb=" N VAL R 115 " --> pdb=" O PRO R 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 136 through 137 removed outlier: 7.282A pdb=" N VAL S 140 " --> pdb=" O SER S 100 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL S 102 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE S 142 " --> pdb=" O VAL S 102 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA S 104 " --> pdb=" O ILE S 142 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL S 139 " --> pdb=" O LEU S 160 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ILE S 162 " --> pdb=" O VAL S 139 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER S 141 " --> pdb=" O ILE S 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 136 through 137 removed outlier: 5.717A pdb=" N ASN S 195 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS S 204 " --> pdb=" O LYS S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.557A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB5, first strand: chain 'T' and resid 85 through 91 removed outlier: 6.557A pdb=" N ARG T 96 " --> pdb=" O LEU T 88 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL T 90 " --> pdb=" O ILE T 94 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE T 94 " --> pdb=" O VAL T 90 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN T 121 " --> pdb=" O GLY T 128 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL T 130 " --> pdb=" O ALA T 119 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA T 119 " --> pdb=" O VAL T 130 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 116 through 122 current: chain 'Y' and resid 62 through 65 removed outlier: 4.711A pdb=" N LEU Y 72 " --> pdb=" O VAL Y 65 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL Y 76 " --> pdb=" O ILE Y 88 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE Y 88 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL Y 47 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Y 43 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASP Y 49 " --> pdb=" O SER Y 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 38 through 44 current: chain 'T' and resid 144 through 150 Processing sheet with id=AB6, first strand: chain 'T' and resid 152 through 155 Processing sheet with id=AB7, first strand: chain 'T' and resid 286 through 291 removed outlier: 6.042A pdb=" N TYR T 256 " --> pdb=" O LEU T 321 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE T 323 " --> pdb=" O TYR T 256 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL T 258 " --> pdb=" O ILE T 323 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASP T 325 " --> pdb=" O VAL T 258 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL T 260 " --> pdb=" O ASP T 325 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 85 through 91 removed outlier: 6.728A pdb=" N ARG U 96 " --> pdb=" O LEU U 88 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL U 90 " --> pdb=" O ILE U 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE U 94 " --> pdb=" O VAL U 90 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS U 126 " --> pdb=" O LEU U 122 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LEU U 122 " --> pdb=" O HIS U 126 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLY U 128 " --> pdb=" O LEU U 120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU U 107 " --> pdb=" O ALA U 119 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU U 108 " --> pdb=" O THR U 147 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 152 through 155 Processing sheet with id=AC1, first strand: chain 'U' and resid 382 through 384 removed outlier: 6.717A pdb=" N LEU U 222 " --> pdb=" O ILE U 406 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU U 408 " --> pdb=" O LEU U 222 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE U 224 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 285 through 290 removed outlier: 3.538A pdb=" N LEU U 321 " --> pdb=" O TYR U 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 116 through 122 removed outlier: 4.027A pdb=" N GLU V 107 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU V 108 " --> pdb=" O THR V 147 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG V 86 " --> pdb=" O TYR V 98 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG V 96 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL V 130 " --> pdb=" O ALA V 119 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ALA V 119 " --> pdb=" O VAL V 130 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU Z 64 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL Z 76 " --> pdb=" O ILE Z 88 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE Z 88 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN Z 78 " --> pdb=" O ARG Z 86 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR Z 84 " --> pdb=" O MET Z 80 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL Z 43 " --> pdb=" O VAL Z 47 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASP Z 49 " --> pdb=" O SER Z 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 152 through 155 Processing sheet with id=AC5, first strand: chain 'V' and resid 163 through 164 removed outlier: 6.234A pdb=" N THR V 164 " --> pdb=" O SER V 289 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 201 through 202 removed outlier: 4.315A pdb=" N ILE V 215 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'V' and resid 382 through 385 removed outlier: 8.025A pdb=" N ILE V 383 " --> pdb=" O GLU V 221 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE V 223 " --> pdb=" O ILE V 383 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR V 385 " --> pdb=" O ILE V 223 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY V 225 " --> pdb=" O THR V 385 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU V 222 " --> pdb=" O GLY V 404 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'X' and resid 39 through 44 removed outlier: 6.653A pdb=" N ASP X 49 " --> pdb=" O SER X 41 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL X 43 " --> pdb=" O VAL X 47 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR X 84 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N HIS X 79 " --> pdb=" O THR X 84 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARG X 86 " --> pdb=" O ALA X 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 110 through 113 Processing sheet with id=AD1, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.066A pdb=" N MET X 122 " --> pdb=" O TYR X 248 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER X 208 " --> pdb=" O THR X 245 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL X 247 " --> pdb=" O SER X 208 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE X 210 " --> pdb=" O VAL X 247 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY X 249 " --> pdb=" O PHE X 210 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY X 212 " --> pdb=" O GLY X 249 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL X 209 " --> pdb=" O PHE X 283 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ASP X 285 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ALA X 211 " --> pdb=" O ASP X 285 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE X 179 " --> pdb=" O GLN X 337 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL X 339 " --> pdb=" O ILE X 179 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU X 181 " --> pdb=" O VAL X 339 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LYS X 178 " --> pdb=" O ALA X 360 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR X 362 " --> pdb=" O LYS X 178 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY X 180 " --> pdb=" O THR X 362 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 159 through 160 removed outlier: 4.253A pdb=" N TYR X 173 " --> pdb=" O LEU X 160 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 559 through 561 Processing sheet with id=AD4, first strand: chain 'Y' and resid 110 through 111 Processing sheet with id=AD5, first strand: chain 'Y' and resid 121 through 122 removed outlier: 5.860A pdb=" N MET Y 122 " --> pdb=" O TYR Y 248 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE Y 179 " --> pdb=" O GLN Y 337 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA Y 360 " --> pdb=" O LYS Y 178 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR Y 383 " --> pdb=" O THR Y 361 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.349A pdb=" N TYR Y 173 " --> pdb=" O LEU Y 160 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Z' and resid 110 through 113 removed outlier: 3.594A pdb=" N ASP Z 139 " --> pdb=" O VAL Z 113 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 121 through 122 removed outlier: 6.511A pdb=" N VAL Z 280 " --> pdb=" O THR Z 334 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL Z 336 " --> pdb=" O VAL Z 280 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU Z 282 " --> pdb=" O VAL Z 336 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA Z 338 " --> pdb=" O LEU Z 282 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL Z 284 " --> pdb=" O ALA Z 338 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE Z 179 " --> pdb=" O GLN Z 337 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Z' and resid 159 through 160 removed outlier: 4.559A pdb=" N TYR Z 173 " --> pdb=" O LEU Z 160 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 559 through 561 2818 hydrogen bonds defined for protein. 8211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.08 Time building geometry restraints manager: 12.81 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: 17172 1.34 - 1.46: 10554 1.46 - 1.58: 26685 1.58 - 1.70: 21 1.70 - 1.82: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.61e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.24e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.64: 73844 4.64 - 9.27: 291 9.27 - 13.91: 19 13.91 - 18.55: 3 18.55 - 23.18: 4 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 116.69 23.18 1.00e+00 1.00e+00 5.38e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 117.28 22.59 1.00e+00 1.00e+00 5.10e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 119.00 20.87 1.00e+00 1.00e+00 4.36e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.89 18.94 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 119.79 17.04 1.00e+00 1.00e+00 2.90e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.60: 31447 26.60 - 53.19: 1408 53.19 - 79.79: 134 79.79 - 106.39: 33 106.39 - 132.99: 3 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -120.84 -59.16 0 5.00e+00 4.00e-02 1.40e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -123.55 -56.45 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -123.79 -56.21 0 5.00e+00 4.00e-02 1.26e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 6944 0.066 - 0.132: 1532 0.132 - 0.198: 193 0.198 - 0.264: 15 0.264 - 0.329: 5 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL 2 41 " pdb=" CA VAL 2 41 " pdb=" CG1 VAL 2 41 " pdb=" CG2 VAL 2 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CB VAL 2 357 " pdb=" CA VAL 2 357 " pdb=" CG1 VAL 2 357 " pdb=" CG2 VAL 2 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL U 137 " pdb=" CA VAL U 137 " pdb=" CG1 VAL U 137 " pdb=" CG2 VAL U 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.88e-02 3.46e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO 3 211 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 1 611 " -0.051 5.00e-02 4.00e+02 7.77e-02 9.67e+00 pdb=" N PRO 1 612 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO 1 612 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO 1 612 " -0.042 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 385 2.51 - 3.10: 37217 3.10 - 3.70: 86292 3.70 - 4.30: 120271 4.30 - 4.90: 197908 Nonbonded interactions: 442073 Sorted by model distance: nonbonded pdb=" CZ PHE I 107 " pdb=" OE2 GLU I 111 " model vdw 1.908 3.340 nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.068 2.170 nonbonded pdb=" O2B ADP X 601 " pdb="MG MG X 602 " model vdw 2.117 2.170 nonbonded pdb=" O GLN P 187 " pdb=" O GLU P 188 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.174 2.170 ... (remaining 442068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.850 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: 0.070 Extract box with map and model: 1.630 Check model and map are aligned: 0.320 Set scattering table: 0.400 Process input model: 109.520 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.340 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.109 54686 Z= 0.430 Angle : 0.937 23.184 74161 Z= 0.542 Chirality : 0.055 0.329 8689 Planarity : 0.007 0.083 9510 Dihedral : 15.030 132.986 19939 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.19 % Favored : 94.63 % Rotamer: Outliers : 0.44 % Allowed : 9.70 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.08), residues: 7038 helix: -2.96 (0.06), residues: 3782 sheet: -2.07 (0.19), residues: 621 loop : -2.41 (0.10), residues: 2635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP Z 141 HIS 0.010 0.002 HIS U 549 PHE 0.039 0.002 PHE X 355 TYR 0.031 0.002 TYR 4 211 ARG 0.007 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1252 time to evaluate : 4.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 71 MET cc_start: 0.8890 (mtp) cc_final: 0.8352 (mtp) REVERT: 1 269 LEU cc_start: 0.9393 (mt) cc_final: 0.9190 (mt) REVERT: 1 273 GLU cc_start: 0.8270 (mp0) cc_final: 0.7903 (mp0) REVERT: 1 566 ASP cc_start: 0.7930 (p0) cc_final: 0.7417 (p0) REVERT: 1 586 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8401 (mm-30) REVERT: 2 378 LEU cc_start: 0.8239 (mt) cc_final: 0.7872 (tt) REVERT: 2 394 LYS cc_start: 0.8080 (mmmm) cc_final: 0.7672 (mttt) REVERT: 3 108 TYR cc_start: 0.7822 (t80) cc_final: 0.6976 (t80) REVERT: 3 159 THR cc_start: 0.8257 (m) cc_final: 0.8054 (t) REVERT: 5 79 ASN cc_start: 0.9073 (m-40) cc_final: 0.8863 (t0) REVERT: 5 90 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7702 (tm-30) REVERT: 5 107 ASN cc_start: 0.7958 (t0) cc_final: 0.7694 (t0) REVERT: 6 54 ILE cc_start: 0.9385 (mt) cc_final: 0.9133 (mt) REVERT: 7 20 PHE cc_start: 0.8939 (m-80) cc_final: 0.8616 (m-10) REVERT: 8 8 LEU cc_start: 0.9529 (mt) cc_final: 0.9291 (mt) REVERT: 8 66 ASP cc_start: 0.7107 (t70) cc_final: 0.6881 (t70) REVERT: 9 1 MET cc_start: 0.2282 (ptt) cc_final: 0.1286 (mmt) REVERT: 9 73 TRP cc_start: 0.7476 (m100) cc_final: 0.7228 (m100) REVERT: M 230 THR cc_start: 0.8980 (t) cc_final: 0.8759 (m) REVERT: M 232 ARG cc_start: 0.8351 (ptp-170) cc_final: 0.7954 (ptp-170) REVERT: M 301 ILE cc_start: 0.9541 (mm) cc_final: 0.9125 (mt) REVERT: M 306 TYR cc_start: 0.9181 (m-10) cc_final: 0.8786 (m-80) REVERT: P 58 TRP cc_start: 0.8731 (t60) cc_final: 0.8176 (t60) REVERT: P 122 PHE cc_start: 0.8843 (m-10) cc_final: 0.8533 (m-80) REVERT: P 142 GLU cc_start: 0.8569 (pp20) cc_final: 0.8368 (pp20) REVERT: R 133 PHE cc_start: 0.7282 (m-80) cc_final: 0.6908 (m-10) REVERT: R 144 ILE cc_start: 0.6900 (mm) cc_final: 0.6593 (mt) REVERT: S 315 MET cc_start: 0.6888 (ppp) cc_final: 0.6432 (ptt) REVERT: T 98 TYR cc_start: 0.7473 (t80) cc_final: 0.7083 (t80) REVERT: T 171 ILE cc_start: 0.7944 (pt) cc_final: 0.7641 (tt) REVERT: U 456 VAL cc_start: 0.8633 (m) cc_final: 0.8407 (p) REVERT: V 48 LEU cc_start: 0.8483 (mp) cc_final: 0.8014 (mp) REVERT: V 64 GLN cc_start: 0.7911 (mt0) cc_final: 0.7708 (tp40) REVERT: V 120 LEU cc_start: 0.9218 (mt) cc_final: 0.9016 (tp) REVERT: V 326 ASP cc_start: 0.6983 (t0) cc_final: 0.5480 (t0) REVERT: V 418 ARG cc_start: 0.6444 (mtt180) cc_final: 0.5775 (mtt180) REVERT: V 481 THR cc_start: 0.8156 (p) cc_final: 0.7870 (m) REVERT: X 187 VAL cc_start: 0.8564 (m) cc_final: 0.8313 (t) REVERT: X 264 THR cc_start: 0.8639 (m) cc_final: 0.8332 (m) REVERT: X 325 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7839 (mt) REVERT: Y 102 VAL cc_start: 0.9024 (t) cc_final: 0.8787 (p) REVERT: Y 181 LEU cc_start: 0.8775 (mt) cc_final: 0.8211 (pp) REVERT: Y 233 ILE cc_start: 0.7404 (mt) cc_final: 0.7012 (mt) REVERT: Y 286 ASN cc_start: 0.5968 (m-40) cc_final: 0.5361 (m-40) REVERT: Y 386 MET cc_start: 0.7643 (mmm) cc_final: 0.6910 (tpp) REVERT: Z 422 MET cc_start: 0.4370 (tmm) cc_final: 0.3542 (ttm) REVERT: Z 484 MET cc_start: 0.7252 (mmm) cc_final: 0.6966 (tmm) outliers start: 25 outliers final: 12 residues processed: 1273 average time/residue: 0.5284 time to fit residues: 1114.5299 Evaluate side-chains 671 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 658 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 9.9990 chunk 529 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 547 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 332 optimal weight: 0.0270 chunk 407 optimal weight: 3.9990 chunk 633 optimal weight: 10.0000 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 65 GLN 1 82 HIS 1 100 GLN 1 209 ASN 1 285 GLN ** 1 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 316 ASN 1 365 GLN 1 606 ASN 2 122 ASN 2 243 GLN 2 289 HIS 2 380 GLN 3 164 ASN 3 179 GLN 3 188 ASN 3 206 ASN 4 38 GLN 4 240 GLN 5 38 HIS ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 117 GLN 6 74 GLN ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 26 HIS 9 60 ASN A 94 ASN C 98 GLN F 94 ASN I 94 ASN M 108 ASN M 163 ASN P 52 GLN P 65 ASN P 220 ASN P 223 ASN Q 21 ASN Q 40 GLN Q 46 HIS R 38 ASN R 53 ASN R 83 GLN R 171 GLN S 96 ASN S 174 GLN ** S 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 262 ASN S 297 GLN T 64 GLN T 386 GLN T 435 GLN T 441 GLN U 61 HIS U 123 GLN U 140 GLN U 179 ASN U 242 GLN U 246 ASN U 248 GLN U 319 HIS U 358 HIS U 397 ASN U 497 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS V 64 GLN V 104 GLN V 152 ASN ** V 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 GLN V 497 GLN V 515 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 68 HIS ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN X 278 GLN X 322 GLN X 337 GLN X 388 ASN X 390 ASN X 445 GLN Y 68 HIS Y 79 HIS Y 83 ASN Y 144 HIS Y 157 GLN Y 278 GLN Z 199 ASN Z 250 GLN Z 278 GLN Z 294 ASN Total number of N/Q/H flips: 88 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 54686 Z= 0.209 Angle : 0.640 13.419 74161 Z= 0.332 Chirality : 0.043 0.235 8689 Planarity : 0.005 0.057 9510 Dihedral : 6.562 106.988 7670 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.09), residues: 7038 helix: -1.26 (0.08), residues: 3850 sheet: -1.61 (0.20), residues: 585 loop : -1.99 (0.11), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 141 HIS 0.009 0.001 HIS S 185 PHE 0.028 0.002 PHE X 283 TYR 0.029 0.002 TYR R 75 ARG 0.011 0.001 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 910 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8907 (p) cc_final: 0.8660 (p) REVERT: 0 36 THR cc_start: 0.7567 (t) cc_final: 0.7363 (t) REVERT: 1 46 LEU cc_start: 0.8929 (tt) cc_final: 0.8726 (tt) REVERT: 1 61 MET cc_start: 0.8978 (ttm) cc_final: 0.8755 (tpp) REVERT: 2 394 LYS cc_start: 0.8205 (mmmm) cc_final: 0.7704 (mttt) REVERT: 3 108 TYR cc_start: 0.7691 (t80) cc_final: 0.6897 (t80) REVERT: 5 51 TYR cc_start: 0.8909 (t80) cc_final: 0.8462 (t80) REVERT: 5 90 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7846 (tm-30) REVERT: 6 41 GLU cc_start: 0.8254 (pp20) cc_final: 0.8042 (mt-10) REVERT: 7 113 MET cc_start: 0.7930 (mtt) cc_final: 0.7337 (mtt) REVERT: 8 46 TYR cc_start: 0.8263 (m-80) cc_final: 0.7968 (m-80) REVERT: 8 66 ASP cc_start: 0.7037 (t70) cc_final: 0.6795 (t70) REVERT: 9 1 MET cc_start: 0.2168 (ptt) cc_final: 0.1701 (mmt) REVERT: 9 93 TRP cc_start: 0.8219 (t60) cc_final: 0.7903 (t60) REVERT: B 110 THR cc_start: 0.8736 (m) cc_final: 0.8461 (t) REVERT: M 244 MET cc_start: 0.8130 (mmm) cc_final: 0.7810 (mmm) REVERT: M 272 PRO cc_start: 0.7041 (Cg_endo) cc_final: 0.6818 (Cg_exo) REVERT: M 301 ILE cc_start: 0.9469 (mm) cc_final: 0.9119 (mt) REVERT: M 306 TYR cc_start: 0.9169 (m-10) cc_final: 0.8784 (m-80) REVERT: P 53 ILE cc_start: 0.9088 (mp) cc_final: 0.8740 (tt) REVERT: P 144 LEU cc_start: 0.8531 (tp) cc_final: 0.8066 (tp) REVERT: R 75 TYR cc_start: 0.6052 (m-80) cc_final: 0.5678 (m-80) REVERT: S 315 MET cc_start: 0.7035 (ppp) cc_final: 0.6492 (ptt) REVERT: T 98 TYR cc_start: 0.7406 (t80) cc_final: 0.7114 (t80) REVERT: T 171 ILE cc_start: 0.7840 (pt) cc_final: 0.7528 (tt) REVERT: T 275 LEU cc_start: 0.8610 (tt) cc_final: 0.8311 (tp) REVERT: U 112 ASP cc_start: 0.8293 (p0) cc_final: 0.7987 (p0) REVERT: U 401 ILE cc_start: 0.8540 (mt) cc_final: 0.8322 (mt) REVERT: V 73 TRP cc_start: 0.8031 (m-10) cc_final: 0.7718 (m-10) REVERT: V 326 ASP cc_start: 0.7176 (t0) cc_final: 0.6590 (t0) REVERT: V 418 ARG cc_start: 0.6476 (mtt180) cc_final: 0.5819 (mtt180) REVERT: V 481 THR cc_start: 0.8290 (p) cc_final: 0.7876 (m) REVERT: X 187 VAL cc_start: 0.8519 (m) cc_final: 0.8319 (t) REVERT: X 368 ILE cc_start: 0.7850 (tt) cc_final: 0.7195 (tt) REVERT: Y 181 LEU cc_start: 0.8672 (mt) cc_final: 0.8176 (pp) REVERT: Y 196 LEU cc_start: 0.8707 (mt) cc_final: 0.8386 (mm) REVERT: Y 327 THR cc_start: 0.7246 (m) cc_final: 0.6938 (p) REVERT: Y 386 MET cc_start: 0.7608 (mmm) cc_final: 0.6822 (tpp) REVERT: Z 125 ILE cc_start: 0.8316 (pt) cc_final: 0.8075 (pt) REVERT: Z 251 MET cc_start: 0.7622 (mtp) cc_final: 0.7214 (mtp) REVERT: Z 422 MET cc_start: 0.5143 (tmm) cc_final: 0.4119 (ttm) REVERT: Z 484 MET cc_start: 0.7450 (mmm) cc_final: 0.7007 (tmm) outliers start: 3 outliers final: 2 residues processed: 913 average time/residue: 0.5514 time to fit residues: 866.1854 Evaluate side-chains 581 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 579 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 527 optimal weight: 8.9990 chunk 431 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 635 optimal weight: 10.0000 chunk 685 optimal weight: 8.9990 chunk 565 optimal weight: 2.9990 chunk 629 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 509 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 68 HIS 4 233 HIS ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 40 ASN ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 HIS R 178 GLN T 126 HIS ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 61 HIS U 139 HIS U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 153 GLN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 471 GLN Z 132 GLN Z 199 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 54686 Z= 0.217 Angle : 0.616 12.644 74161 Z= 0.317 Chirality : 0.043 0.208 8689 Planarity : 0.004 0.052 9510 Dihedral : 6.146 96.380 7670 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.42 % Favored : 95.42 % Rotamer: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.10), residues: 7038 helix: -0.44 (0.08), residues: 3838 sheet: -1.31 (0.21), residues: 583 loop : -1.68 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 141 HIS 0.004 0.001 HIS Y 204 PHE 0.024 0.002 PHE T 489 TYR 0.024 0.002 TYR 4 211 ARG 0.006 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 830 time to evaluate : 5.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8884 (p) cc_final: 0.8608 (p) REVERT: 0 36 THR cc_start: 0.7657 (t) cc_final: 0.7418 (t) REVERT: 0 68 VAL cc_start: 0.8851 (t) cc_final: 0.8457 (t) REVERT: 0 71 MET cc_start: 0.8884 (mtp) cc_final: 0.8532 (mtp) REVERT: 1 273 GLU cc_start: 0.8337 (mp0) cc_final: 0.8016 (mt-10) REVERT: 1 586 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8402 (mm-30) REVERT: 2 246 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8421 (mm-30) REVERT: 2 394 LYS cc_start: 0.8246 (mmmm) cc_final: 0.7787 (mttt) REVERT: 3 108 TYR cc_start: 0.7708 (t80) cc_final: 0.6880 (t80) REVERT: 3 292 TYR cc_start: 0.5694 (m-80) cc_final: 0.5493 (m-80) REVERT: 3 299 GLU cc_start: 0.6930 (pt0) cc_final: 0.6661 (pt0) REVERT: 5 1 MET cc_start: 0.6797 (ptt) cc_final: 0.6427 (ptt) REVERT: 5 51 TYR cc_start: 0.8878 (t80) cc_final: 0.8632 (t80) REVERT: 5 90 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7895 (tm-30) REVERT: 6 41 GLU cc_start: 0.8382 (pp20) cc_final: 0.8040 (mt-10) REVERT: 7 113 MET cc_start: 0.7694 (mtt) cc_final: 0.7489 (mtt) REVERT: 8 66 ASP cc_start: 0.7031 (t70) cc_final: 0.6824 (t70) REVERT: 9 1 MET cc_start: 0.2200 (ptt) cc_final: 0.1703 (mmt) REVERT: B 110 THR cc_start: 0.8624 (m) cc_final: 0.8389 (t) REVERT: G 92 ASN cc_start: 0.5407 (p0) cc_final: 0.5205 (p0) REVERT: H 82 PHE cc_start: 0.5672 (m-10) cc_final: 0.5306 (m-10) REVERT: M 301 ILE cc_start: 0.9487 (mm) cc_final: 0.9167 (mt) REVERT: M 306 TYR cc_start: 0.9131 (m-10) cc_final: 0.8765 (m-80) REVERT: P 55 THR cc_start: 0.9403 (m) cc_final: 0.9187 (t) REVERT: R 75 TYR cc_start: 0.6139 (m-80) cc_final: 0.5733 (m-80) REVERT: S 195 ASN cc_start: 0.5679 (m-40) cc_final: 0.5390 (t0) REVERT: S 315 MET cc_start: 0.6536 (ppp) cc_final: 0.6192 (ptt) REVERT: T 98 TYR cc_start: 0.7354 (t80) cc_final: 0.7005 (t80) REVERT: T 452 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7884 (mm-40) REVERT: T 483 MET cc_start: 0.7833 (tpp) cc_final: 0.7242 (tmm) REVERT: U 112 ASP cc_start: 0.8317 (p0) cc_final: 0.8080 (p0) REVERT: U 455 GLU cc_start: 0.7523 (pt0) cc_final: 0.6441 (tp30) REVERT: V 73 TRP cc_start: 0.8137 (m-10) cc_final: 0.7863 (m-10) REVERT: V 418 ARG cc_start: 0.6159 (mtt180) cc_final: 0.5532 (mtt180) REVERT: X 153 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5580 (tp-100) REVERT: Y 80 MET cc_start: 0.8276 (mmm) cc_final: 0.7666 (tpp) REVERT: Y 290 PHE cc_start: 0.7769 (t80) cc_final: 0.7563 (t80) REVERT: Y 327 THR cc_start: 0.7073 (m) cc_final: 0.6825 (p) REVERT: Y 386 MET cc_start: 0.7628 (mmm) cc_final: 0.6740 (tpp) REVERT: Y 502 MET cc_start: 0.8171 (tpp) cc_final: 0.7059 (ptt) REVERT: Z 80 MET cc_start: 0.7608 (mmm) cc_final: 0.7388 (mtp) REVERT: Z 251 MET cc_start: 0.8008 (mtp) cc_final: 0.7774 (mtp) REVERT: Z 422 MET cc_start: 0.5022 (tmm) cc_final: 0.3999 (ttm) REVERT: Z 484 MET cc_start: 0.7290 (mmm) cc_final: 0.6870 (tpp) outliers start: 2 outliers final: 0 residues processed: 832 average time/residue: 0.4847 time to fit residues: 698.6487 Evaluate side-chains 544 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 543 time to evaluate : 4.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 6.9990 chunk 477 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 303 optimal weight: 0.4980 chunk 426 optimal weight: 0.0270 chunk 637 optimal weight: 9.9990 chunk 674 optimal weight: 9.9990 chunk 332 optimal weight: 2.9990 chunk 603 optimal weight: 0.0870 chunk 181 optimal weight: 2.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 298 GLN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 206 ASN 4 233 HIS 5 29 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 ASN M 171 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 228 GLN T 253 GLN ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 529 ASN V 539 ASN ** X 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 357 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54686 Z= 0.164 Angle : 0.578 11.547 74161 Z= 0.294 Chirality : 0.042 0.175 8689 Planarity : 0.004 0.068 9510 Dihedral : 5.757 90.125 7670 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7038 helix: 0.00 (0.09), residues: 3832 sheet: -1.11 (0.22), residues: 586 loop : -1.49 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 9 93 HIS 0.007 0.001 HIS Y 204 PHE 0.036 0.001 PHE X 355 TYR 0.023 0.001 TYR 4 211 ARG 0.007 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 853 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8833 (p) cc_final: 0.8592 (p) REVERT: 0 36 THR cc_start: 0.7576 (t) cc_final: 0.7363 (t) REVERT: 0 71 MET cc_start: 0.8813 (mtp) cc_final: 0.8522 (mtp) REVERT: 1 298 GLN cc_start: 0.8149 (tp-100) cc_final: 0.7921 (tp-100) REVERT: 1 586 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8374 (mm-30) REVERT: 2 394 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7767 (mttt) REVERT: 3 108 TYR cc_start: 0.7651 (t80) cc_final: 0.6859 (t80) REVERT: 4 231 ASP cc_start: 0.7724 (m-30) cc_final: 0.7341 (m-30) REVERT: 5 1 MET cc_start: 0.6588 (ptt) cc_final: 0.6156 (ptt) REVERT: 5 51 TYR cc_start: 0.8807 (t80) cc_final: 0.8554 (t80) REVERT: 5 90 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7747 (tm-30) REVERT: 7 20 PHE cc_start: 0.8961 (m-80) cc_final: 0.8521 (m-10) REVERT: 7 85 LEU cc_start: 0.9415 (tp) cc_final: 0.9160 (tp) REVERT: 8 46 TYR cc_start: 0.8226 (m-80) cc_final: 0.7925 (m-80) REVERT: 8 70 LYS cc_start: 0.8817 (tttm) cc_final: 0.8289 (mmtt) REVERT: 9 1 MET cc_start: 0.1800 (ptt) cc_final: 0.1434 (mmt) REVERT: A 61 MET cc_start: 0.6946 (mmm) cc_final: 0.6693 (tmm) REVERT: B 110 THR cc_start: 0.8543 (m) cc_final: 0.8308 (t) REVERT: M 281 LEU cc_start: 0.8740 (mt) cc_final: 0.8303 (mt) REVERT: M 301 ILE cc_start: 0.9482 (mm) cc_final: 0.9185 (mt) REVERT: P 144 LEU cc_start: 0.8357 (tp) cc_final: 0.8137 (tp) REVERT: Q 14 MET cc_start: 0.3885 (ttt) cc_final: 0.3470 (ptm) REVERT: R 75 TYR cc_start: 0.5962 (m-80) cc_final: 0.5631 (m-80) REVERT: S 92 PHE cc_start: 0.6130 (m-10) cc_final: 0.5811 (m-10) REVERT: S 315 MET cc_start: 0.6445 (ppp) cc_final: 0.6140 (ptt) REVERT: T 98 TYR cc_start: 0.7201 (t80) cc_final: 0.6896 (t80) REVERT: T 171 ILE cc_start: 0.7728 (pt) cc_final: 0.7485 (tt) REVERT: T 452 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7880 (mm-40) REVERT: U 204 THR cc_start: 0.8592 (p) cc_final: 0.8286 (t) REVERT: U 455 GLU cc_start: 0.7441 (pt0) cc_final: 0.6321 (tp30) REVERT: V 73 TRP cc_start: 0.8139 (m-10) cc_final: 0.7929 (m-10) REVERT: V 326 ASP cc_start: 0.7370 (t0) cc_final: 0.6868 (t0) REVERT: V 418 ARG cc_start: 0.6111 (mtt180) cc_final: 0.5522 (mtt180) REVERT: X 488 MET cc_start: 0.6606 (mmt) cc_final: 0.6373 (mmt) REVERT: Y 80 MET cc_start: 0.8232 (mmm) cc_final: 0.7801 (tpp) REVERT: Y 290 PHE cc_start: 0.7716 (t80) cc_final: 0.7511 (t80) REVERT: Y 327 THR cc_start: 0.6949 (m) cc_final: 0.6743 (p) REVERT: Y 371 LEU cc_start: 0.7718 (mm) cc_final: 0.7409 (pp) REVERT: Y 386 MET cc_start: 0.7634 (mmm) cc_final: 0.6738 (tpp) REVERT: Y 405 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7634 (tptt) REVERT: Y 502 MET cc_start: 0.8080 (tpp) cc_final: 0.7086 (ptt) REVERT: Z 80 MET cc_start: 0.7510 (mmm) cc_final: 0.7282 (mtp) REVERT: Z 251 MET cc_start: 0.8016 (mtp) cc_final: 0.7797 (mtp) REVERT: Z 386 MET cc_start: 0.6685 (mtt) cc_final: 0.6261 (mtt) REVERT: Z 422 MET cc_start: 0.5031 (tmm) cc_final: 0.3871 (ttm) REVERT: Z 484 MET cc_start: 0.7113 (mmm) cc_final: 0.6715 (tpp) outliers start: 2 outliers final: 0 residues processed: 853 average time/residue: 0.4808 time to fit residues: 708.3510 Evaluate side-chains 564 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 8.9990 chunk 382 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 502 optimal weight: 0.0270 chunk 278 optimal weight: 1.9990 chunk 575 optimal weight: 5.9990 chunk 466 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 344 optimal weight: 0.6980 chunk 605 optimal weight: 0.4980 chunk 170 optimal weight: 0.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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** 3 206 ASN 5 9 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 74 GLN ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 529 ASN V 539 ASN X 157 GLN ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 286 ASN ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 54686 Z= 0.157 Angle : 0.566 10.602 74161 Z= 0.287 Chirality : 0.042 0.211 8689 Planarity : 0.004 0.055 9510 Dihedral : 5.513 86.399 7670 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.02 % Favored : 95.89 % Rotamer: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.10), residues: 7038 helix: 0.23 (0.09), residues: 3844 sheet: -1.07 (0.21), residues: 598 loop : -1.40 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Z 141 HIS 0.005 0.001 HIS T 241 PHE 0.027 0.001 PHE X 355 TYR 0.015 0.001 TYR 4 249 ARG 0.009 0.000 ARG T 364 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 837 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8872 (p) cc_final: 0.8603 (p) REVERT: 0 36 THR cc_start: 0.7583 (t) cc_final: 0.7315 (t) REVERT: 0 71 MET cc_start: 0.8771 (mtp) cc_final: 0.8522 (mtp) REVERT: 1 586 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8338 (mm-30) REVERT: 2 118 TYR cc_start: 0.7476 (m-80) cc_final: 0.7165 (m-80) REVERT: 2 394 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7884 (mttt) REVERT: 3 108 TYR cc_start: 0.7665 (t80) cc_final: 0.6896 (t80) REVERT: 5 1 MET cc_start: 0.6455 (ptt) cc_final: 0.6001 (ptt) REVERT: 5 90 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7654 (tm-30) REVERT: 7 20 PHE cc_start: 0.8932 (m-80) cc_final: 0.8514 (m-10) REVERT: 7 85 LEU cc_start: 0.9374 (tp) cc_final: 0.9100 (tp) REVERT: 7 113 MET cc_start: 0.7493 (mtp) cc_final: 0.7174 (mtt) REVERT: 8 34 THR cc_start: 0.9348 (m) cc_final: 0.8887 (m) REVERT: 8 38 LYS cc_start: 0.9120 (mtmm) cc_final: 0.8848 (mtmm) REVERT: 8 70 LYS cc_start: 0.8800 (tttm) cc_final: 0.8023 (mmtt) REVERT: 9 1 MET cc_start: 0.1798 (ptt) cc_final: 0.1427 (mmt) REVERT: 9 80 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7878 (mm-40) REVERT: 9 89 MET cc_start: 0.7910 (mtp) cc_final: 0.7652 (mtp) REVERT: G 116 PHE cc_start: 0.0923 (m-80) cc_final: 0.0657 (m-10) REVERT: M 182 THR cc_start: 0.8782 (p) cc_final: 0.8527 (t) REVERT: M 278 CYS cc_start: 0.8040 (m) cc_final: 0.7821 (m) REVERT: M 281 LEU cc_start: 0.8852 (mt) cc_final: 0.8364 (mt) REVERT: M 301 ILE cc_start: 0.9456 (mm) cc_final: 0.9162 (mt) REVERT: P 78 ILE cc_start: 0.9284 (mt) cc_final: 0.8945 (mt) REVERT: P 144 LEU cc_start: 0.8317 (tp) cc_final: 0.8057 (tp) REVERT: Q 14 MET cc_start: 0.4232 (ttt) cc_final: 0.3590 (tmm) REVERT: R 75 TYR cc_start: 0.5951 (m-80) cc_final: 0.5586 (m-80) REVERT: S 315 MET cc_start: 0.6369 (ppp) cc_final: 0.5982 (ptt) REVERT: T 98 TYR cc_start: 0.7170 (t80) cc_final: 0.6912 (t80) REVERT: T 171 ILE cc_start: 0.7828 (pt) cc_final: 0.7503 (tt) REVERT: T 275 LEU cc_start: 0.8480 (tt) cc_final: 0.8276 (tp) REVERT: T 452 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7742 (mm-40) REVERT: U 112 ASP cc_start: 0.8184 (p0) cc_final: 0.7820 (p0) REVERT: U 204 THR cc_start: 0.8652 (p) cc_final: 0.8394 (t) REVERT: U 403 ASP cc_start: 0.7469 (m-30) cc_final: 0.7250 (m-30) REVERT: U 455 GLU cc_start: 0.7556 (pt0) cc_final: 0.6348 (tp30) REVERT: V 73 TRP cc_start: 0.8162 (m-10) cc_final: 0.7868 (m-10) REVERT: V 418 ARG cc_start: 0.6106 (mtt180) cc_final: 0.5479 (mtt180) REVERT: V 439 MET cc_start: 0.6075 (mmt) cc_final: 0.5861 (mmm) REVERT: X 248 TYR cc_start: 0.5967 (m-80) cc_final: 0.5740 (m-80) REVERT: Y 80 MET cc_start: 0.8285 (mmm) cc_final: 0.7673 (tpp) REVERT: Y 386 MET cc_start: 0.7614 (mmm) cc_final: 0.6763 (tpp) REVERT: Y 405 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7654 (tptt) REVERT: Y 468 SER cc_start: 0.6727 (m) cc_final: 0.6111 (p) REVERT: Y 502 MET cc_start: 0.8051 (tpp) cc_final: 0.7100 (ptt) REVERT: Z 80 MET cc_start: 0.7558 (mmm) cc_final: 0.7105 (mtp) REVERT: Z 251 MET cc_start: 0.7915 (mtp) cc_final: 0.7689 (mtp) REVERT: Z 386 MET cc_start: 0.6751 (mtt) cc_final: 0.6264 (ttt) REVERT: Z 422 MET cc_start: 0.4963 (tmm) cc_final: 0.3749 (ttm) REVERT: Z 484 MET cc_start: 0.7180 (mmm) cc_final: 0.6726 (tpp) outliers start: 1 outliers final: 0 residues processed: 837 average time/residue: 0.4905 time to fit residues: 717.6022 Evaluate side-chains 568 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 6.9990 chunk 607 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 396 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 675 optimal weight: 8.9990 chunk 560 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 354 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** 3 206 ASN 5 29 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 91 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 HIS U 169 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 445 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54686 Z= 0.216 Angle : 0.602 11.608 74161 Z= 0.305 Chirality : 0.043 0.192 8689 Planarity : 0.004 0.053 9510 Dihedral : 5.506 83.443 7670 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.65 % Favored : 95.27 % Rotamer: Outliers : 0.02 % Allowed : 2.49 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 7038 helix: 0.37 (0.09), residues: 3840 sheet: -0.97 (0.21), residues: 613 loop : -1.29 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Z 141 HIS 0.007 0.001 HIS 5 25 PHE 0.052 0.002 PHE E 116 TYR 0.029 0.001 TYR 2 180 ARG 0.009 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 773 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8910 (p) cc_final: 0.8652 (p) REVERT: 0 36 THR cc_start: 0.7535 (t) cc_final: 0.7325 (t) REVERT: 0 71 MET cc_start: 0.8805 (mtp) cc_final: 0.8503 (mtp) REVERT: 1 298 GLN cc_start: 0.8064 (tp40) cc_final: 0.7812 (tp40) REVERT: 1 586 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8451 (mm-30) REVERT: 2 394 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7887 (mttt) REVERT: 3 108 TYR cc_start: 0.7681 (t80) cc_final: 0.6860 (t80) REVERT: 4 231 ASP cc_start: 0.7927 (m-30) cc_final: 0.7507 (m-30) REVERT: 5 1 MET cc_start: 0.6634 (ptt) cc_final: 0.6199 (ptt) REVERT: 5 90 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7882 (tm-30) REVERT: 7 20 PHE cc_start: 0.8987 (m-80) cc_final: 0.8506 (m-10) REVERT: 8 70 LYS cc_start: 0.8776 (tttm) cc_final: 0.8093 (mmtt) REVERT: 9 1 MET cc_start: 0.1741 (ptt) cc_final: 0.1335 (mmt) REVERT: 9 80 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7668 (mm-40) REVERT: 9 89 MET cc_start: 0.7944 (mtp) cc_final: 0.7624 (mtp) REVERT: M 278 CYS cc_start: 0.8116 (m) cc_final: 0.7826 (m) REVERT: M 281 LEU cc_start: 0.8930 (mt) cc_final: 0.8445 (mt) REVERT: P 45 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7343 (tm-30) REVERT: R 75 TYR cc_start: 0.6165 (m-80) cc_final: 0.5666 (m-80) REVERT: R 133 PHE cc_start: 0.7103 (m-10) cc_final: 0.6665 (m-10) REVERT: R 144 ILE cc_start: 0.6131 (mp) cc_final: 0.5789 (mt) REVERT: S 315 MET cc_start: 0.6411 (ppp) cc_final: 0.6196 (ptt) REVERT: T 98 TYR cc_start: 0.7264 (t80) cc_final: 0.6968 (t80) REVERT: T 452 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7714 (mm-40) REVERT: U 57 TYR cc_start: 0.6478 (p90) cc_final: 0.6095 (p90) REVERT: U 359 SER cc_start: 0.8610 (t) cc_final: 0.8358 (p) REVERT: U 401 ILE cc_start: 0.8509 (mt) cc_final: 0.8229 (mt) REVERT: V 73 TRP cc_start: 0.8197 (m-10) cc_final: 0.7930 (m-10) REVERT: V 484 LEU cc_start: 0.8867 (mt) cc_final: 0.8469 (mt) REVERT: Y 80 MET cc_start: 0.8446 (mmm) cc_final: 0.7784 (tpp) REVERT: Y 286 ASN cc_start: 0.6067 (m-40) cc_final: 0.5863 (m-40) REVERT: Y 290 PHE cc_start: 0.7791 (t80) cc_final: 0.7531 (t80) REVERT: Y 370 GLU cc_start: 0.7114 (mp0) cc_final: 0.6910 (tm-30) REVERT: Y 371 LEU cc_start: 0.7737 (mm) cc_final: 0.7450 (pp) REVERT: Y 386 MET cc_start: 0.7684 (mmm) cc_final: 0.6853 (tpp) REVERT: Y 405 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7570 (tptt) REVERT: Y 502 MET cc_start: 0.8112 (tpp) cc_final: 0.7131 (ptt) REVERT: Z 80 MET cc_start: 0.7616 (mmm) cc_final: 0.7375 (mtm) REVERT: Z 386 MET cc_start: 0.6675 (mtt) cc_final: 0.6240 (ttt) REVERT: Z 422 MET cc_start: 0.5017 (tmm) cc_final: 0.3900 (ttm) REVERT: Z 484 MET cc_start: 0.7146 (mmm) cc_final: 0.6704 (tpp) outliers start: 1 outliers final: 0 residues processed: 774 average time/residue: 0.4893 time to fit residues: 667.7169 Evaluate side-chains 535 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 384 optimal weight: 0.6980 chunk 493 optimal weight: 0.9990 chunk 382 optimal weight: 0.9980 chunk 568 optimal weight: 0.6980 chunk 377 optimal weight: 7.9990 chunk 672 optimal weight: 0.9980 chunk 421 optimal weight: 9.9990 chunk 410 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 562 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 9 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 HIS S 72 GLN ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 358 HIS ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 54686 Z= 0.161 Angle : 0.579 10.552 74161 Z= 0.291 Chirality : 0.042 0.274 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.390 84.941 7670 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 0.02 % Allowed : 1.37 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.10), residues: 7038 helix: 0.49 (0.09), residues: 3851 sheet: -0.90 (0.21), residues: 614 loop : -1.23 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 5 116 HIS 0.005 0.001 HIS T 241 PHE 0.038 0.001 PHE E 116 TYR 0.021 0.001 TYR S 122 ARG 0.006 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 808 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8876 (p) cc_final: 0.8612 (p) REVERT: 0 36 THR cc_start: 0.7350 (t) cc_final: 0.7110 (t) REVERT: 0 71 MET cc_start: 0.8787 (mtp) cc_final: 0.8500 (mtp) REVERT: 0 81 HIS cc_start: 0.7521 (m90) cc_final: 0.5434 (p90) REVERT: 1 298 GLN cc_start: 0.8060 (tp40) cc_final: 0.7822 (tp40) REVERT: 1 586 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8388 (mm-30) REVERT: 2 118 TYR cc_start: 0.7487 (m-80) cc_final: 0.7246 (m-80) REVERT: 2 209 ASP cc_start: 0.7865 (m-30) cc_final: 0.7660 (m-30) REVERT: 2 394 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7890 (mttt) REVERT: 3 108 TYR cc_start: 0.7626 (t80) cc_final: 0.6838 (t80) REVERT: 3 177 LEU cc_start: 0.9475 (mt) cc_final: 0.9264 (mt) REVERT: 4 99 GLU cc_start: 0.7756 (mp0) cc_final: 0.7517 (mt-10) REVERT: 5 1 MET cc_start: 0.6624 (ptt) cc_final: 0.6099 (ptt) REVERT: 5 90 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7754 (tm-30) REVERT: 7 20 PHE cc_start: 0.8927 (m-80) cc_final: 0.8539 (m-10) REVERT: 7 96 LEU cc_start: 0.9117 (mt) cc_final: 0.8896 (mt) REVERT: 8 34 THR cc_start: 0.9375 (m) cc_final: 0.8878 (m) REVERT: 8 70 LYS cc_start: 0.8749 (tttm) cc_final: 0.8091 (mmtt) REVERT: 9 1 MET cc_start: 0.1686 (ptt) cc_final: 0.1439 (mmt) REVERT: 9 80 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7844 (mm-40) REVERT: 9 89 MET cc_start: 0.7948 (mtp) cc_final: 0.7647 (mtp) REVERT: B 110 THR cc_start: 0.8602 (m) cc_final: 0.8390 (t) REVERT: M 278 CYS cc_start: 0.7950 (m) cc_final: 0.7737 (m) REVERT: M 281 LEU cc_start: 0.8877 (mt) cc_final: 0.8406 (mt) REVERT: R 75 TYR cc_start: 0.6068 (m-80) cc_final: 0.5616 (m-80) REVERT: R 144 ILE cc_start: 0.6201 (mp) cc_final: 0.5825 (mt) REVERT: S 315 MET cc_start: 0.6307 (ppp) cc_final: 0.6090 (ptt) REVERT: T 98 TYR cc_start: 0.7220 (t80) cc_final: 0.6941 (t80) REVERT: T 452 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7700 (mm-40) REVERT: U 57 TYR cc_start: 0.6434 (p90) cc_final: 0.6029 (p90) REVERT: U 112 ASP cc_start: 0.8283 (p0) cc_final: 0.7923 (p0) REVERT: U 359 SER cc_start: 0.8551 (t) cc_final: 0.8347 (p) REVERT: U 401 ILE cc_start: 0.8414 (mt) cc_final: 0.8195 (mt) REVERT: U 403 ASP cc_start: 0.7680 (m-30) cc_final: 0.7353 (m-30) REVERT: V 73 TRP cc_start: 0.8158 (m-10) cc_final: 0.7919 (m-10) REVERT: V 484 LEU cc_start: 0.8776 (mt) cc_final: 0.8452 (mt) REVERT: Y 80 MET cc_start: 0.8580 (mmm) cc_final: 0.7855 (tpp) REVERT: Y 290 PHE cc_start: 0.7727 (t80) cc_final: 0.7473 (t80) REVERT: Y 371 LEU cc_start: 0.7741 (mm) cc_final: 0.7417 (pp) REVERT: Y 386 MET cc_start: 0.7655 (mmm) cc_final: 0.6794 (tpp) REVERT: Y 405 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7552 (tptt) REVERT: Y 468 SER cc_start: 0.6856 (m) cc_final: 0.6248 (p) REVERT: Y 502 MET cc_start: 0.8053 (tpp) cc_final: 0.7148 (ptt) REVERT: Z 80 MET cc_start: 0.7582 (mmm) cc_final: 0.7342 (mtm) REVERT: Z 386 MET cc_start: 0.6529 (mtt) cc_final: 0.6260 (ttt) REVERT: Z 422 MET cc_start: 0.5072 (tmm) cc_final: 0.3968 (ttm) REVERT: Z 484 MET cc_start: 0.7151 (mmm) cc_final: 0.6762 (tpp) outliers start: 1 outliers final: 0 residues processed: 809 average time/residue: 0.5009 time to fit residues: 706.2848 Evaluate side-chains 559 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 401 optimal weight: 7.9990 chunk 202 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 427 optimal weight: 0.8980 chunk 458 optimal weight: 0.8980 chunk 332 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 528 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 50 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 84 HIS ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 42 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 54686 Z= 0.164 Angle : 0.583 10.248 74161 Z= 0.293 Chirality : 0.042 0.243 8689 Planarity : 0.004 0.056 9510 Dihedral : 5.324 85.741 7670 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 7038 helix: 0.57 (0.09), residues: 3839 sheet: -0.79 (0.21), residues: 608 loop : -1.16 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Z 141 HIS 0.004 0.001 HIS T 241 PHE 0.024 0.001 PHE X 355 TYR 0.018 0.001 TYR 2 180 ARG 0.007 0.000 ARG 4 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 4.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8889 (p) cc_final: 0.8636 (p) REVERT: 0 36 THR cc_start: 0.7415 (t) cc_final: 0.7149 (t) REVERT: 0 71 MET cc_start: 0.8741 (mtp) cc_final: 0.8501 (mtp) REVERT: 0 81 HIS cc_start: 0.7385 (m90) cc_final: 0.5407 (p90) REVERT: 1 298 GLN cc_start: 0.8030 (tp40) cc_final: 0.7822 (tp-100) REVERT: 1 586 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8361 (mm-30) REVERT: 2 118 TYR cc_start: 0.7519 (m-80) cc_final: 0.7293 (m-80) REVERT: 2 209 ASP cc_start: 0.7958 (m-30) cc_final: 0.7640 (m-30) REVERT: 2 394 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7904 (mttt) REVERT: 3 108 TYR cc_start: 0.7655 (t80) cc_final: 0.6895 (t80) REVERT: 3 177 LEU cc_start: 0.9404 (mt) cc_final: 0.9184 (mt) REVERT: 3 205 CYS cc_start: 0.8764 (m) cc_final: 0.8555 (m) REVERT: 5 1 MET cc_start: 0.6541 (ptt) cc_final: 0.6069 (ptt) REVERT: 5 75 GLN cc_start: 0.8397 (mt0) cc_final: 0.8185 (mm-40) REVERT: 5 90 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7745 (tm-30) REVERT: 6 51 LEU cc_start: 0.9368 (tp) cc_final: 0.9163 (tp) REVERT: 6 104 ASN cc_start: 0.8301 (t0) cc_final: 0.7924 (t0) REVERT: 7 20 PHE cc_start: 0.8908 (m-80) cc_final: 0.8503 (m-10) REVERT: 8 70 LYS cc_start: 0.8819 (tttm) cc_final: 0.8183 (mmtt) REVERT: 9 1 MET cc_start: 0.1546 (ptt) cc_final: 0.1285 (mmt) REVERT: 9 80 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7715 (mm-40) REVERT: B 74 VAL cc_start: 0.7296 (t) cc_final: 0.7079 (p) REVERT: M 278 CYS cc_start: 0.7735 (m) cc_final: 0.7469 (m) REVERT: M 281 LEU cc_start: 0.8834 (mt) cc_final: 0.8391 (mt) REVERT: P 45 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7235 (tm-30) REVERT: P 123 GLU cc_start: 0.7068 (pt0) cc_final: 0.6584 (pt0) REVERT: R 75 TYR cc_start: 0.6021 (m-80) cc_final: 0.5533 (m-80) REVERT: R 133 PHE cc_start: 0.7620 (m-10) cc_final: 0.7223 (m-10) REVERT: R 144 ILE cc_start: 0.6168 (mp) cc_final: 0.5843 (mt) REVERT: S 245 ASP cc_start: 0.6863 (m-30) cc_final: 0.6426 (m-30) REVERT: S 315 MET cc_start: 0.6337 (ppp) cc_final: 0.6107 (ptt) REVERT: T 98 TYR cc_start: 0.7228 (t80) cc_final: 0.6885 (t80) REVERT: T 452 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7768 (mm-40) REVERT: U 57 TYR cc_start: 0.6476 (p90) cc_final: 0.6140 (p90) REVERT: U 112 ASP cc_start: 0.8274 (p0) cc_final: 0.7908 (p0) REVERT: V 73 TRP cc_start: 0.8167 (m-10) cc_final: 0.7955 (m-10) REVERT: V 384 GLU cc_start: 0.7636 (mp0) cc_final: 0.6824 (mp0) REVERT: V 484 LEU cc_start: 0.8622 (mt) cc_final: 0.8232 (mt) REVERT: Y 80 MET cc_start: 0.8504 (mmm) cc_final: 0.7891 (tpp) REVERT: Y 290 PHE cc_start: 0.7706 (t80) cc_final: 0.7425 (t80) REVERT: Y 361 THR cc_start: 0.8369 (p) cc_final: 0.8099 (p) REVERT: Y 386 MET cc_start: 0.7624 (mmm) cc_final: 0.6763 (tpp) REVERT: Y 405 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7587 (tptt) REVERT: Y 468 SER cc_start: 0.6979 (m) cc_final: 0.6394 (p) REVERT: Y 502 MET cc_start: 0.8014 (tpp) cc_final: 0.7152 (ptt) REVERT: Z 125 ILE cc_start: 0.8168 (pt) cc_final: 0.7955 (pt) REVERT: Z 386 MET cc_start: 0.6551 (mtt) cc_final: 0.6237 (ttt) REVERT: Z 422 MET cc_start: 0.5504 (tmm) cc_final: 0.4053 (ttm) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 0.4883 time to fit residues: 697.4393 Evaluate side-chains 571 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 571 time to evaluate : 4.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 2.9990 chunk 644 optimal weight: 0.9990 chunk 588 optimal weight: 5.9990 chunk 626 optimal weight: 4.9990 chunk 377 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 492 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 566 optimal weight: 0.9980 chunk 592 optimal weight: 9.9990 chunk 624 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 9 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 HIS ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 HIS U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** V 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 292 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54686 Z= 0.267 Angle : 0.650 12.000 74161 Z= 0.328 Chirality : 0.045 0.212 8689 Planarity : 0.004 0.073 9510 Dihedral : 5.496 89.028 7670 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.96 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.10), residues: 7038 helix: 0.52 (0.09), residues: 3832 sheet: -0.80 (0.21), residues: 611 loop : -1.14 (0.13), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 5 116 HIS 0.006 0.001 HIS 2 289 PHE 0.021 0.002 PHE X 355 TYR 0.022 0.002 TYR F 102 ARG 0.006 0.001 ARG U 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 746 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8945 (p) cc_final: 0.8676 (p) REVERT: 0 81 HIS cc_start: 0.7325 (m90) cc_final: 0.5194 (p-80) REVERT: 2 209 ASP cc_start: 0.7884 (m-30) cc_final: 0.7612 (m-30) REVERT: 2 394 LYS cc_start: 0.8254 (mmmm) cc_final: 0.7889 (mttt) REVERT: 3 108 TYR cc_start: 0.7766 (t80) cc_final: 0.6872 (t80) REVERT: 3 177 LEU cc_start: 0.9441 (mt) cc_final: 0.9235 (mt) REVERT: 3 205 CYS cc_start: 0.8781 (m) cc_final: 0.8415 (m) REVERT: 5 1 MET cc_start: 0.6731 (ptt) cc_final: 0.6316 (ptt) REVERT: 5 75 GLN cc_start: 0.8458 (mt0) cc_final: 0.8209 (mm-40) REVERT: 5 90 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7930 (tm-30) REVERT: 6 104 ASN cc_start: 0.8347 (t0) cc_final: 0.8071 (t0) REVERT: 7 20 PHE cc_start: 0.9006 (m-80) cc_final: 0.8505 (m-10) REVERT: 8 70 LYS cc_start: 0.8789 (tttm) cc_final: 0.8164 (mmtt) REVERT: 9 1 MET cc_start: 0.1785 (ptt) cc_final: 0.1402 (mmt) REVERT: M 278 CYS cc_start: 0.8005 (m) cc_final: 0.7778 (m) REVERT: P 45 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7348 (tm-30) REVERT: P 123 GLU cc_start: 0.7096 (pt0) cc_final: 0.6568 (pt0) REVERT: R 75 TYR cc_start: 0.6208 (m-80) cc_final: 0.5704 (m-80) REVERT: T 98 TYR cc_start: 0.7346 (t80) cc_final: 0.7086 (t80) REVERT: T 422 ASN cc_start: 0.7287 (m-40) cc_final: 0.6972 (t0) REVERT: T 452 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7733 (mm-40) REVERT: U 57 TYR cc_start: 0.6507 (p90) cc_final: 0.6162 (p90) REVERT: U 401 ILE cc_start: 0.8479 (mt) cc_final: 0.8234 (mt) REVERT: U 494 ILE cc_start: 0.5164 (tp) cc_final: 0.4766 (tp) REVERT: V 73 TRP cc_start: 0.8179 (m-10) cc_final: 0.7953 (m-10) REVERT: V 326 ASP cc_start: 0.7095 (t0) cc_final: 0.6749 (t0) REVERT: V 484 LEU cc_start: 0.8736 (mt) cc_final: 0.8341 (mt) REVERT: Y 80 MET cc_start: 0.8710 (mmm) cc_final: 0.8279 (tpp) REVERT: Y 290 PHE cc_start: 0.7940 (t80) cc_final: 0.7714 (t80) REVERT: Y 370 GLU cc_start: 0.7738 (mp0) cc_final: 0.7189 (tm-30) REVERT: Y 386 MET cc_start: 0.7821 (mmm) cc_final: 0.6903 (tpp) REVERT: Y 405 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7561 (tptt) REVERT: Y 468 SER cc_start: 0.7158 (m) cc_final: 0.6582 (p) REVERT: Y 502 MET cc_start: 0.8135 (tpp) cc_final: 0.7200 (ptt) REVERT: Z 125 ILE cc_start: 0.8331 (pt) cc_final: 0.8075 (pt) REVERT: Z 386 MET cc_start: 0.6444 (mtt) cc_final: 0.6171 (ttt) outliers start: 0 outliers final: 0 residues processed: 746 average time/residue: 0.4981 time to fit residues: 654.1636 Evaluate side-chains 530 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 4.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 3.9990 chunk 662 optimal weight: 10.0000 chunk 404 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 460 optimal weight: 1.9990 chunk 695 optimal weight: 6.9990 chunk 640 optimal weight: 8.9990 chunk 553 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 427 optimal weight: 0.0670 chunk 339 optimal weight: 0.6980 overall best weight: 1.5524 ------------------------------------------------------------------------------- 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** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 HIS ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 HIS U 196 GLN U 397 ASN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 139 HIS ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 336 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54686 Z= 0.191 Angle : 0.617 11.859 74161 Z= 0.309 Chirality : 0.043 0.252 8689 Planarity : 0.004 0.063 9510 Dihedral : 5.429 87.436 7670 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.10), residues: 7038 helix: 0.63 (0.09), residues: 3838 sheet: -0.68 (0.22), residues: 602 loop : -1.12 (0.13), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Z 141 HIS 0.012 0.001 HIS R 104 PHE 0.026 0.001 PHE 3 124 TYR 0.019 0.001 TYR T 472 ARG 0.005 0.000 ARG X 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 759 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 19 SER cc_start: 0.8912 (p) cc_final: 0.8629 (p) REVERT: 0 81 HIS cc_start: 0.7299 (m90) cc_final: 0.5173 (p-80) REVERT: 2 209 ASP cc_start: 0.7940 (m-30) cc_final: 0.7674 (m-30) REVERT: 2 394 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7863 (mttt) REVERT: 3 108 TYR cc_start: 0.7682 (t80) cc_final: 0.6855 (t80) REVERT: 3 177 LEU cc_start: 0.9441 (mt) cc_final: 0.9224 (mt) REVERT: 3 205 CYS cc_start: 0.8785 (m) cc_final: 0.8446 (m) REVERT: 4 214 ASP cc_start: 0.6380 (t0) cc_final: 0.6094 (t0) REVERT: 5 1 MET cc_start: 0.6678 (ptt) cc_final: 0.6255 (ptt) REVERT: 5 90 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7880 (tm-30) REVERT: 6 104 ASN cc_start: 0.8394 (t0) cc_final: 0.8178 (t0) REVERT: 7 20 PHE cc_start: 0.8948 (m-80) cc_final: 0.8521 (m-10) REVERT: 8 70 LYS cc_start: 0.8812 (tttm) cc_final: 0.8220 (mmtt) REVERT: 9 83 LYS cc_start: 0.7893 (ttpt) cc_final: 0.7643 (tttt) REVERT: 9 87 LEU cc_start: 0.8734 (tt) cc_final: 0.8245 (tt) REVERT: 9 89 MET cc_start: 0.7193 (mtp) cc_final: 0.6930 (mtp) REVERT: B 110 THR cc_start: 0.8650 (m) cc_final: 0.8413 (t) REVERT: C 126 PHE cc_start: 0.1579 (m-80) cc_final: 0.1248 (t80) REVERT: M 118 ARG cc_start: 0.8803 (tpt90) cc_final: 0.8543 (tpt90) REVERT: M 244 MET cc_start: 0.8192 (mmm) cc_final: 0.7852 (mmm) REVERT: M 278 CYS cc_start: 0.7876 (m) cc_final: 0.7531 (m) REVERT: P 45 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7170 (tm-30) REVERT: P 123 GLU cc_start: 0.7059 (pt0) cc_final: 0.6576 (pt0) REVERT: R 75 TYR cc_start: 0.6164 (m-80) cc_final: 0.5602 (m-80) REVERT: S 92 PHE cc_start: 0.6067 (m-10) cc_final: 0.5590 (m-10) REVERT: T 98 TYR cc_start: 0.7310 (t80) cc_final: 0.6980 (t80) REVERT: T 452 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7712 (mm-40) REVERT: U 57 TYR cc_start: 0.6527 (p90) cc_final: 0.6175 (p90) REVERT: U 401 ILE cc_start: 0.8434 (mt) cc_final: 0.8183 (mt) REVERT: U 555 ARG cc_start: 0.6628 (mpt-90) cc_final: 0.6377 (mpt-90) REVERT: V 73 TRP cc_start: 0.8222 (m-10) cc_final: 0.8004 (m-10) REVERT: V 326 ASP cc_start: 0.7082 (t0) cc_final: 0.6737 (t0) REVERT: V 484 LEU cc_start: 0.8676 (mt) cc_final: 0.8258 (mt) REVERT: X 84 THR cc_start: 0.7672 (p) cc_final: 0.7441 (p) REVERT: X 318 LEU cc_start: 0.8878 (tp) cc_final: 0.8543 (tp) REVERT: X 335 SER cc_start: 0.8611 (t) cc_final: 0.7593 (p) REVERT: X 502 MET cc_start: 0.4806 (ptt) cc_final: 0.4484 (ttt) REVERT: Y 80 MET cc_start: 0.8687 (mmm) cc_final: 0.8209 (tpp) REVERT: Y 290 PHE cc_start: 0.7828 (t80) cc_final: 0.7609 (t80) REVERT: Y 370 GLU cc_start: 0.7741 (mp0) cc_final: 0.7159 (tm-30) REVERT: Y 386 MET cc_start: 0.7713 (mmm) cc_final: 0.6994 (tpp) REVERT: Y 405 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7584 (tptt) REVERT: Y 468 SER cc_start: 0.7221 (m) cc_final: 0.6843 (p) REVERT: Y 502 MET cc_start: 0.8069 (tpp) cc_final: 0.7164 (ptt) REVERT: Z 125 ILE cc_start: 0.8272 (pt) cc_final: 0.8037 (pt) REVERT: Z 386 MET cc_start: 0.6129 (mtt) cc_final: 0.5901 (ttt) REVERT: Z 422 MET cc_start: 0.5382 (tmm) cc_final: 0.3989 (ttm) outliers start: 0 outliers final: 0 residues processed: 759 average time/residue: 0.4767 time to fit residues: 634.6314 Evaluate side-chains 554 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 4.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.0370 chunk 589 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 510 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 153 optimal weight: 9.9990 chunk 554 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 569 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 9 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 80 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 139 HIS ** T 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 HIS U 196 GLN ** U 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 539 ASN X 322 GLN X 337 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 412 ASN ** Y 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.109662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091327 restraints weight = 165587.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.090635 restraints weight = 127117.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.090601 restraints weight = 109770.356| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 54686 Z= 0.267 Angle : 0.665 13.128 74161 Z= 0.334 Chirality : 0.045 0.258 8689 Planarity : 0.004 0.053 9510 Dihedral : 5.565 89.245 7670 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.33 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 7038 helix: 0.53 (0.09), residues: 3833 sheet: -0.69 (0.22), residues: 601 loop : -1.14 (0.13), residues: 2604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Z 141 HIS 0.011 0.001 HIS R 104 PHE 0.047 0.002 PHE E 116 TYR 0.025 0.002 TYR 8 33 ARG 0.015 0.001 ARG V 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12112.36 seconds wall clock time: 210 minutes 58.40 seconds (12658.40 seconds total)