Starting phenix.real_space_refine on Tue Nov 19 20:30:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rec_4849/11_2024/6rec_4849.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rec_4849/11_2024/6rec_4849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rec_4849/11_2024/6rec_4849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rec_4849/11_2024/6rec_4849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rec_4849/11_2024/6rec_4849.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rec_4849/11_2024/6rec_4849.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34301 2.51 5 N 9113 2.21 5 O 10174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 385 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 53756 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 29.73, per 1000 atoms: 0.55 Number of scatterers: 53756 At special positions: 0 Unit cell: (214.812, 134.784, 263.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10174 8.00 N 9113 7.00 C 34301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.61 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13088 Finding SS restraints... Secondary structure from input PDB file: 316 helices and 0 sheets defined 58.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.734A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 3 through 8' Processing helix chain '0' and resid 17 through 31 Processing helix chain '0' and resid 43 through 49 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.532A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 96 through 100 removed outlier: 3.573A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.591A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 4.165A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 202 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: 3.929A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.564A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.770A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 316 Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 4.057A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.717A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.636A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.792A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.732A pdb=" N ASN 1 450 " --> pdb=" O ASN 1 446 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 removed outlier: 3.845A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 515 removed outlier: 3.829A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.650A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 removed outlier: 3.508A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 577 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '1' and resid 610 through 614 Processing helix chain '2' and resid 7 through 19 Processing helix chain '2' and resid 25 through 39 Processing helix chain '2' and resid 44 through 57 removed outlier: 4.028A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.572A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.524A pdb=" N TYR 2 121 " --> pdb=" O ASN 2 117 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 155 through 168 removed outlier: 3.674A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 197 removed outlier: 3.782A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 200 No H-bonds generated for 'chain '2' and resid 198 through 200' Processing helix chain '2' and resid 206 through 220 removed outlier: 3.725A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 235 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.523A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.597A pdb=" N PHE 2 262 " --> pdb=" O ASP 2 258 " (cutoff:3.500A) Proline residue: 2 271 - end of helix removed outlier: 3.541A pdb=" N ALA 2 276 " --> pdb=" O ALA 2 272 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 295 removed outlier: 3.627A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 3.574A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS 2 321 " --> pdb=" O ALA 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 Processing helix chain '2' and resid 345 through 354 Processing helix chain '2' and resid 396 through 408 removed outlier: 3.774A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 442 removed outlier: 3.652A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 97 through 101 removed outlier: 3.781A pdb=" N GLU 3 100 " --> pdb=" O ASN 3 97 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE 3 101 " --> pdb=" O VAL 3 98 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 97 through 101' Processing helix chain '3' and resid 102 through 113 removed outlier: 3.608A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 129 removed outlier: 4.360A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 3 129 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 removed outlier: 3.551A pdb=" N ALA 3 134 " --> pdb=" O LYS 3 131 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU 3 135 " --> pdb=" O VAL 3 132 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 131 through 135' Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 removed outlier: 3.784A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.615A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 169 through 172' Processing helix chain '3' and resid 173 through 187 removed outlier: 3.968A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 205 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.749A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 245 through 251 removed outlier: 3.723A pdb=" N LYS 3 251 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 272 removed outlier: 3.917A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 284 removed outlier: 4.082A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 4.032A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.638A pdb=" N LEU 4 12 " --> pdb=" O LYS 4 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.716A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 3.525A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.745A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 removed outlier: 3.755A pdb=" N THR 4 126 " --> pdb=" O VAL 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 150 removed outlier: 4.089A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.849A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 Processing helix chain '4' and resid 192 through 234 removed outlier: 3.640A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.513A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.585A pdb=" N GLU 4 266 " --> pdb=" O ALA 4 262 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 3.809A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.588A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 87 through 106 removed outlier: 4.444A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 removed outlier: 3.612A pdb=" N LYS 5 119 " --> pdb=" O ILE 5 115 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 Processing helix chain '6' and resid 72 through 94 Processing helix chain '6' and resid 98 through 117 removed outlier: 3.705A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.191A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 105 removed outlier: 3.746A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.781A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 removed outlier: 3.665A pdb=" N THR 7 145 " --> pdb=" O TYR 7 141 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 165 removed outlier: 4.091A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL 7 157 " --> pdb=" O LEU 7 153 " (cutoff:3.500A) Proline residue: 7 159 - end of helix Processing helix chain '7' and resid 174 through 187 Processing helix chain '8' and resid 26 through 31 removed outlier: 3.639A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.641A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 44 Processing helix chain '8' and resid 44 through 78 Processing helix chain '9' and resid 2 through 17 removed outlier: 3.648A pdb=" N LEU 9 7 " --> pdb=" O VAL 9 3 " (cutoff:3.500A) Processing helix chain '9' and resid 33 through 55 removed outlier: 3.950A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 removed outlier: 3.780A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.337A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.776A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 4.241A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.756A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.977A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.483A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.409A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.394A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.783A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 4.220A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.591A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.257A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.458A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 92 Processing helix chain 'E' and resid 95 through 126 removed outlier: 4.494A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.043A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 90 removed outlier: 3.569A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 95 through 126 removed outlier: 3.507A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.985A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.680A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 3.571A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.954A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.336A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 124 removed outlier: 4.205A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.539A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.233A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.235A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.905A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.239A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 126 removed outlier: 4.665A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL J 121 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 144 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.851A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.581A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 230 removed outlier: 3.556A pdb=" N GLU M 225 " --> pdb=" O PHE M 221 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 265 removed outlier: 4.154A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.699A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 62 Processing helix chain 'P' and resid 66 through 84 removed outlier: 4.047A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.796A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 removed outlier: 4.029A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.902A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 147 removed outlier: 3.932A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.660A pdb=" N ARG P 167 " --> pdb=" O ASP P 163 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 226 removed outlier: 3.575A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 40 removed outlier: 4.329A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 44 removed outlier: 3.782A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 41 through 44' Processing helix chain 'R' and resid 29 through 41 removed outlier: 3.730A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 156 through 168 removed outlier: 3.818A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 3.508A pdb=" N GLU R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.652A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 79 Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.466A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 removed outlier: 3.787A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 151 removed outlier: 3.501A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR S 151 " --> pdb=" O ARG S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 183 Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.769A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER S 272 " --> pdb=" O ALA S 268 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 313 " --> pdb=" O ALA S 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 64 Processing helix chain 'T' and resid 66 through 76 removed outlier: 4.239A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.076A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 212 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.736A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 removed outlier: 3.514A pdb=" N VAL T 269 " --> pdb=" O LYS T 265 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN T 271 " --> pdb=" O SER T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 315 Proline residue: T 303 - end of helix removed outlier: 4.168A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 341 removed outlier: 3.529A pdb=" N GLN T 330 " --> pdb=" O ASP T 326 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 352 No H-bonds generated for 'chain 'T' and resid 351 through 352' Processing helix chain 'T' and resid 353 through 363 Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 410 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.878A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 456 removed outlier: 3.723A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL T 442 " --> pdb=" O GLY T 438 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY T 444 " --> pdb=" O LYS T 440 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR T 445 " --> pdb=" O GLN T 441 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 Processing helix chain 'T' and resid 469 through 482 removed outlier: 3.968A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.635A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.810A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 48 removed outlier: 3.639A pdb=" N LEU U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 73 removed outlier: 3.652A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix removed outlier: 3.591A pdb=" N GLU U 72 " --> pdb=" O PRO U 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP U 73 " --> pdb=" O ALA U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 77 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.940A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE U 138 " --> pdb=" O ASP U 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 134 through 138' Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.577A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 212 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.790A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 283 removed outlier: 3.728A 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: 3.793A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.719A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER U 331 " --> pdb=" O LEU U 327 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.789A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 412 through 416 removed outlier: 3.878A pdb=" N GLY U 416 " --> pdb=" O PHE U 413 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 455 removed outlier: 3.590A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU U 449 " --> pdb=" O THR U 445 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.724A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 4.385A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 484 removed outlier: 4.108A pdb=" N ALA U 478 " --> pdb=" O LEU U 474 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 Processing helix chain 'U' and resid 501 through 506 Processing helix chain 'U' and resid 513 through 515 No H-bonds generated for 'chain 'U' and resid 513 through 515' Processing helix chain 'U' and resid 516 through 528 removed outlier: 4.215A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA U 523 " --> pdb=" O ALA U 519 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL U 528 " --> pdb=" O VAL U 524 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 4.057A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.899A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 48 removed outlier: 3.732A pdb=" N GLU V 47 " --> pdb=" O ALA V 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.683A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.664A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.944A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 279 Processing helix chain 'V' and resid 280 through 283 Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 4.384A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 removed outlier: 3.549A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.517A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.832A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.936A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 414 Processing helix chain 'V' and resid 438 through 454 removed outlier: 3.616A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 470 through 485 removed outlier: 4.035A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.536A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.803A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 555 removed outlier: 4.148A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 201 Processing helix chain 'X' and resid 216 through 229 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG X 239 " --> pdb=" O GLY X 236 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 297 removed outlier: 3.737A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL X 297 " --> pdb=" O ALA X 293 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.608A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) Processing helix chain 'X' and resid 365 through 370 removed outlier: 3.613A pdb=" N ALA X 369 " --> pdb=" O SER X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 393 through 421 removed outlier: 3.523A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 443 removed outlier: 3.593A pdb=" N ALA X 436 " --> pdb=" O THR X 432 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 447 through 451 removed outlier: 3.864A pdb=" N GLU X 451 " --> pdb=" O GLN X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 482 through 487 removed outlier: 3.645A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 508 removed outlier: 4.006A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 204 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.601A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 5.091A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.731A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 removed outlier: 3.721A pdb=" N ASP Y 344 " --> pdb=" O VAL Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 371 removed outlier: 3.610A pdb=" N LEU Y 371 " --> pdb=" O SER Y 367 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 412 removed outlier: 7.242A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) Processing helix chain 'Y' and resid 412 through 420 removed outlier: 4.065A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 427 through 442 removed outlier: 4.615A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.958A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 504 removed outlier: 3.742A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 518 through 522 removed outlier: 3.589A pdb=" N LEU Y 521 " --> pdb=" O SER Y 518 " (cutoff:3.500A) Processing helix chain 'Y' and resid 544 through 554 removed outlier: 4.175A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.522A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 removed outlier: 3.578A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 201 Processing helix chain 'Z' and resid 216 through 229 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.117A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 259 Processing helix chain 'Z' and resid 260 through 275 removed outlier: 3.587A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.855A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 removed outlier: 3.602A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 372 removed outlier: 3.527A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 412 removed outlier: 3.620A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 420 Processing helix chain 'Z' and resid 421 through 425 removed outlier: 4.076A pdb=" N GLU Z 424 " --> pdb=" O GLY Z 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 421 through 425' Processing helix chain 'Z' and resid 429 through 440 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.690A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 486 Processing helix chain 'Z' and resid 492 through 500 removed outlier: 3.641A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 508 removed outlier: 3.580A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 509 through 511 No H-bonds generated for 'chain 'Z' and resid 509 through 511' Processing helix chain 'Z' and resid 527 through 533 2576 hydrogen bonds defined for protein. 7536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.13 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13556 1.33 - 1.45: 9967 1.45 - 1.57: 30896 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54694 Sorted by residual: bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.81e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.70e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.455 -0.067 1.00e-02 1.00e+04 4.54e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.327 0.060 1.00e-02 1.00e+04 3.65e+01 bond pdb=" C5 ATP T1001 " pdb=" N7 ATP T1001 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.19e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 73323 3.54 - 7.07: 765 7.07 - 10.61: 65 10.61 - 14.15: 15 14.15 - 17.69: 4 Bond angle restraints: 74172 Sorted by residual: angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 122.18 17.69 1.00e+00 1.00e+00 3.13e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.51 17.36 1.00e+00 1.00e+00 3.01e+02 angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 124.30 15.57 1.00e+00 1.00e+00 2.42e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.81 13.02 1.00e+00 1.00e+00 1.69e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 125.05 11.78 1.00e+00 1.00e+00 1.39e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.25: 31973 30.25 - 60.50: 978 60.50 - 90.75: 75 90.75 - 121.00: 1 121.00 - 151.25: 3 Dihedral angle restraints: 33030 sinusoidal: 12669 harmonic: 20361 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -122.82 -57.18 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual 180.00 -133.04 -46.96 0 5.00e+00 4.00e-02 8.82e+01 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 -134.40 -45.60 0 5.00e+00 4.00e-02 8.32e+01 ... (remaining 33027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 6917 0.075 - 0.151: 1597 0.151 - 0.226: 150 0.226 - 0.301: 23 0.301 - 0.377: 3 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB ILE Y 524 " pdb=" CA ILE Y 524 " pdb=" CG1 ILE Y 524 " pdb=" CG2 ILE Y 524 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU U 202 " pdb=" CB LEU U 202 " pdb=" CD1 LEU U 202 " pdb=" CD2 LEU U 202 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.22e-02 3.87e+01 pdb=" C ALA Z 503 " -0.108 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA X 503 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C ALA X 503 " 0.100 2.00e-02 2.50e+03 pdb=" O ALA X 503 " -0.037 2.00e-02 2.50e+03 pdb=" N LYS X 504 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL Z 341 " -0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO Z 342 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO Z 342 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Z 342 " -0.047 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1709 2.69 - 3.24: 51715 3.24 - 3.80: 89558 3.80 - 4.35: 119069 4.35 - 4.90: 197168 Nonbonded interactions: 459219 Sorted by model distance: nonbonded pdb=" OG1 THR X 190 " pdb="MG MG X 602 " model vdw 2.140 2.170 nonbonded pdb=" OH TYR 9 90 " pdb=" CE LYS 9 94 " model vdw 2.168 3.440 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.197 2.170 nonbonded pdb=" O3G ATP U1001 " pdb="MG MG U1002 " model vdw 2.218 2.170 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.241 3.040 ... (remaining 459214 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.140 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: 0.000 Extract box with map and model: 1.340 Check model and map are aligned: 0.380 Set scattering table: 0.430 Process input model: 122.180 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.121 54694 Z= 0.745 Angle : 1.022 17.687 74172 Z= 0.576 Chirality : 0.062 0.377 8690 Planarity : 0.008 0.086 9512 Dihedral : 14.479 151.251 19942 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.06 % Rotamer: Outliers : 0.37 % Allowed : 6.85 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.08), residues: 7039 helix: -2.90 (0.06), residues: 3824 sheet: -1.50 (0.20), residues: 606 loop : -2.11 (0.10), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 7 107 HIS 0.013 0.002 HIS 4 233 PHE 0.038 0.003 PHE 4 90 TYR 0.032 0.003 TYR 4 211 ARG 0.008 0.001 ARG M 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 1093 time to evaluate : 6.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 103 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7700 (mtmm) REVERT: 1 441 PHE cc_start: 0.7895 (m-80) cc_final: 0.7681 (m-80) REVERT: 1 456 LYS cc_start: 0.7862 (tmmt) cc_final: 0.7606 (ttpp) REVERT: 1 472 LYS cc_start: 0.8178 (tptt) cc_final: 0.7953 (tppt) REVERT: 1 508 ASP cc_start: 0.7187 (m-30) cc_final: 0.6882 (m-30) REVERT: 4 31 LYS cc_start: 0.7585 (mtpt) cc_final: 0.7146 (pttt) REVERT: 4 218 GLU cc_start: 0.8033 (tp30) cc_final: 0.7729 (tp30) REVERT: 4 220 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7997 (mptt) REVERT: 4 232 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7776 (mtp180) REVERT: 5 35 MET cc_start: 0.8758 (mmt) cc_final: 0.8556 (mmp) REVERT: 5 111 LYS cc_start: 0.8045 (tttt) cc_final: 0.7764 (mmmt) REVERT: 5 118 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8662 (m) REVERT: 5 119 LYS cc_start: 0.7667 (mmtp) cc_final: 0.7151 (mtmt) REVERT: 8 69 LYS cc_start: 0.8518 (mttt) cc_final: 0.6356 (tmtt) REVERT: 9 13 LYS cc_start: 0.7335 (mtmt) cc_final: 0.6737 (mtpp) REVERT: 9 35 GLN cc_start: 0.8004 (pt0) cc_final: 0.7801 (pt0) REVERT: A 61 MET cc_start: 0.6553 (mmt) cc_final: 0.6182 (mmt) REVERT: B 61 MET cc_start: 0.7404 (mtt) cc_final: 0.7172 (mtt) REVERT: C 92 ASN cc_start: 0.8838 (t0) cc_final: 0.8515 (t0) REVERT: F 97 LYS cc_start: 0.8788 (tttt) cc_final: 0.8559 (tttm) REVERT: H 61 MET cc_start: 0.7804 (mmt) cc_final: 0.7543 (mmp) REVERT: M 288 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7905 (mm-30) REVERT: P 163 ASP cc_start: 0.8195 (m-30) cc_final: 0.7956 (m-30) REVERT: Q 14 MET cc_start: 0.8322 (ttm) cc_final: 0.8090 (ttm) REVERT: Q 19 TYR cc_start: 0.8665 (t80) cc_final: 0.8460 (t80) REVERT: Q 42 ARG cc_start: 0.8169 (ptp90) cc_final: 0.7926 (ptt-90) REVERT: R 95 ASP cc_start: 0.8608 (m-30) cc_final: 0.8367 (m-30) REVERT: R 177 GLU cc_start: 0.7615 (mp0) cc_final: 0.7342 (mp0) REVERT: S 83 ASP cc_start: 0.7747 (p0) cc_final: 0.7458 (p0) REVERT: S 118 ASN cc_start: 0.7812 (t0) cc_final: 0.7529 (t0) REVERT: S 121 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7478 (mmtm) REVERT: S 144 ASP cc_start: 0.7192 (p0) cc_final: 0.6807 (p0) REVERT: S 159 GLN cc_start: 0.7915 (mp10) cc_final: 0.7490 (mm110) REVERT: S 260 LEU cc_start: 0.8885 (tp) cc_final: 0.8527 (mt) REVERT: S 291 ASP cc_start: 0.7858 (t0) cc_final: 0.7550 (m-30) REVERT: T 329 LYS cc_start: 0.8876 (mttt) cc_final: 0.8473 (mmmt) REVERT: U 75 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7723 (mtpp) REVERT: U 439 MET cc_start: 0.7644 (tpp) cc_final: 0.7308 (tpp) REVERT: V 66 LEU cc_start: 0.8327 (mt) cc_final: 0.7997 (mt) REVERT: V 112 ASP cc_start: 0.8287 (p0) cc_final: 0.8012 (p0) REVERT: X 252 ASN cc_start: 0.8109 (p0) cc_final: 0.7672 (p0) REVERT: X 456 THR cc_start: 0.7608 (m) cc_final: 0.7392 (p) REVERT: Y 101 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8156 (tptt) REVERT: Z 91 ASP cc_start: 0.7966 (t70) cc_final: 0.7724 (t70) REVERT: Z 195 GLU cc_start: 0.7513 (tp30) cc_final: 0.7255 (tp30) outliers start: 21 outliers final: 8 residues processed: 1110 average time/residue: 0.6929 time to fit residues: 1264.6506 Evaluate side-chains 665 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 656 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 5 residue 118 VAL Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 10.0000 chunk 529 optimal weight: 0.0370 chunk 293 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 356 optimal weight: 0.5980 chunk 282 optimal weight: 1.9990 chunk 547 optimal weight: 7.9990 chunk 211 optimal weight: 0.8980 chunk 332 optimal weight: 6.9990 chunk 407 optimal weight: 3.9990 chunk 633 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 65 GLN 1 257 HIS 1 298 GLN 1 316 ASN 1 365 GLN 1 482 ASN 1 587 ASN 1 606 ASN 2 68 ASN 2 243 GLN 3 87 ASN 3 206 ASN 3 229 ASN 4 52 GLN 4 135 ASN 4 240 GLN 5 29 GLN 5 59 ASN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 117 GLN 6 40 ASN 6 74 GLN 7 86 HIS 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 184 ASN 8 26 HIS A 94 ASN E 94 ASN G 92 ASN M 108 ASN M 163 ASN P 52 GLN ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 223 ASN R 38 ASN R 66 HIS R 73 ASN R 83 GLN R 85 GLN ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 154 GLN S 52 ASN ** S 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN S 188 GLN ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 267 HIS T 64 GLN ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 241 HIS T 386 GLN T 435 GLN T 497 GLN T 529 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 196 GLN U 244 ASN U 386 GLN U 422 ASN U 497 GLN V 64 GLN V 126 HIS V 139 HIS V 152 ASN V 196 GLN V 241 HIS V 242 GLN V 244 ASN V 386 GLN V 435 GLN V 486 GLN V 497 GLN ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN Y 199 ASN ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 294 ASN ** Y 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 404 GLN Z 42 GLN Z 68 HIS Z 199 ASN Z 278 GLN Z 337 GLN Z 388 ASN Z 440 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54694 Z= 0.180 Angle : 0.582 10.821 74172 Z= 0.304 Chirality : 0.042 0.210 8690 Planarity : 0.005 0.063 9512 Dihedral : 6.712 136.865 7681 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 1.67 % Allowed : 11.40 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.09), residues: 7039 helix: -1.06 (0.08), residues: 3845 sheet: -1.21 (0.20), residues: 588 loop : -1.50 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.032 0.001 PHE G 107 TYR 0.028 0.001 TYR 4 211 ARG 0.011 0.001 ARG T 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 811 time to evaluate : 6.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 MET cc_start: 0.8447 (mtp) cc_final: 0.8231 (mtp) REVERT: 1 378 GLU cc_start: 0.7570 (tp30) cc_final: 0.7204 (tp30) REVERT: 1 441 PHE cc_start: 0.7805 (m-80) cc_final: 0.7599 (m-80) REVERT: 1 456 LYS cc_start: 0.7674 (tmmt) cc_final: 0.7465 (ttpp) REVERT: 1 504 ASP cc_start: 0.7589 (t70) cc_final: 0.7214 (t0) REVERT: 1 508 ASP cc_start: 0.7062 (m-30) cc_final: 0.6810 (m-30) REVERT: 1 586 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7432 (mm-30) REVERT: 4 31 LYS cc_start: 0.7458 (mtpt) cc_final: 0.7087 (pttt) REVERT: 4 178 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7922 (pp) REVERT: 4 232 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7723 (mtp180) REVERT: 5 119 LYS cc_start: 0.7407 (mmtp) cc_final: 0.6986 (mtmt) REVERT: 7 142 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7566 (tt0) REVERT: 8 69 LYS cc_start: 0.8280 (mttt) cc_final: 0.6293 (tmtt) REVERT: 9 13 LYS cc_start: 0.7233 (mtmt) cc_final: 0.6793 (mtpp) REVERT: B 61 MET cc_start: 0.7253 (mtt) cc_final: 0.6981 (mtt) REVERT: C 92 ASN cc_start: 0.8776 (t0) cc_final: 0.8360 (t0) REVERT: F 81 MET cc_start: 0.8697 (ttp) cc_final: 0.8204 (ttp) REVERT: F 97 LYS cc_start: 0.8616 (tttt) cc_final: 0.8382 (tttm) REVERT: I 117 SER cc_start: 0.8317 (m) cc_final: 0.7831 (p) REVERT: J 56 LEU cc_start: 0.6485 (tp) cc_final: 0.6033 (mt) REVERT: M 288 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7683 (mm-30) REVERT: R 95 ASP cc_start: 0.8615 (m-30) cc_final: 0.8383 (m-30) REVERT: S 118 ASN cc_start: 0.7590 (t0) cc_final: 0.7336 (t0) REVERT: S 121 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7435 (mmtm) REVERT: S 159 GLN cc_start: 0.7605 (mp10) cc_final: 0.7318 (mm110) REVERT: S 164 ASP cc_start: 0.7669 (m-30) cc_final: 0.7429 (t70) REVERT: S 220 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7739 (mm) REVERT: S 227 SER cc_start: 0.7807 (t) cc_final: 0.7441 (p) REVERT: S 260 LEU cc_start: 0.8483 (tp) cc_final: 0.8266 (mt) REVERT: S 271 MET cc_start: 0.8105 (ttp) cc_final: 0.7889 (ttt) REVERT: S 291 ASP cc_start: 0.7777 (t0) cc_final: 0.7446 (m-30) REVERT: T 329 LYS cc_start: 0.8558 (mttt) cc_final: 0.8238 (mmmt) REVERT: T 390 VAL cc_start: 0.8962 (m) cc_final: 0.8719 (m) REVERT: T 436 PHE cc_start: 0.7931 (t80) cc_final: 0.7598 (t80) REVERT: U 75 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7664 (mtpp) REVERT: U 439 MET cc_start: 0.7692 (tpp) cc_final: 0.7365 (tpp) REVERT: V 112 ASP cc_start: 0.8205 (p0) cc_final: 0.7845 (p0) REVERT: V 414 TYR cc_start: 0.5848 (m-10) cc_final: 0.5539 (m-10) REVERT: V 521 GLU cc_start: 0.7367 (pp20) cc_final: 0.6909 (pp20) REVERT: X 202 LYS cc_start: 0.6627 (tptt) cc_final: 0.6401 (mmmt) REVERT: X 484 MET cc_start: 0.7104 (tmm) cc_final: 0.6467 (tmm) REVERT: X 488 MET cc_start: 0.7335 (mmm) cc_final: 0.6662 (mmm) REVERT: X 498 LYS cc_start: 0.7778 (tttt) cc_final: 0.7385 (tttt) REVERT: Y 101 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8083 (mmtt) REVERT: Z 91 ASP cc_start: 0.7908 (t70) cc_final: 0.7589 (t0) REVERT: Z 195 GLU cc_start: 0.7516 (tp30) cc_final: 0.7237 (tp30) outliers start: 94 outliers final: 45 residues processed: 877 average time/residue: 0.6518 time to fit residues: 969.4113 Evaluate side-chains 666 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 619 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 155 GLU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 510 ILE Chi-restraints excluded: chain 2 residue 125 SER Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 219 SER Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain P residue 107 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 328 THR Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 365 SER Chi-restraints excluded: chain Z residue 229 GLU Chi-restraints excluded: chain Z residue 538 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.9990 chunk 196 optimal weight: 0.1980 chunk 527 optimal weight: 9.9990 chunk 431 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 635 optimal weight: 8.9990 chunk 685 optimal weight: 0.4980 chunk 565 optimal weight: 5.9990 chunk 629 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 509 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 52 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 106 ASN 7 170 HIS 9 35 GLN G 94 ASN R 85 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 529 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 GLN ** Y 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 292 GLN Y 388 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 54694 Z= 0.193 Angle : 0.555 11.496 74172 Z= 0.288 Chirality : 0.042 0.202 8690 Planarity : 0.004 0.054 9512 Dihedral : 6.037 108.731 7678 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 2.13 % Allowed : 12.61 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 7039 helix: -0.18 (0.08), residues: 3859 sheet: -1.07 (0.21), residues: 585 loop : -1.19 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.032 0.001 PHE G 107 TYR 0.029 0.001 TYR 4 211 ARG 0.010 0.000 ARG T 283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 714 time to evaluate : 5.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 MET cc_start: 0.8403 (mtp) cc_final: 0.8116 (mtp) REVERT: 1 378 GLU cc_start: 0.7542 (tp30) cc_final: 0.7190 (tp30) REVERT: 1 441 PHE cc_start: 0.7774 (m-80) cc_final: 0.7540 (m-80) REVERT: 1 453 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7267 (ttp80) REVERT: 1 504 ASP cc_start: 0.7650 (t70) cc_final: 0.7255 (t0) REVERT: 1 586 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7363 (mm-30) REVERT: 2 316 ASP cc_start: 0.7104 (m-30) cc_final: 0.6874 (m-30) REVERT: 4 31 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7072 (pttt) REVERT: 4 178 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7816 (pp) REVERT: 4 232 ARG cc_start: 0.8091 (ttm110) cc_final: 0.7712 (mtp180) REVERT: 5 119 LYS cc_start: 0.7309 (mmtp) cc_final: 0.7008 (mtmt) REVERT: 7 113 MET cc_start: 0.8506 (mtt) cc_final: 0.8211 (mtt) REVERT: 7 142 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7571 (tt0) REVERT: 8 69 LYS cc_start: 0.8310 (mttt) cc_final: 0.6345 (tmtt) REVERT: 9 13 LYS cc_start: 0.7182 (mtmt) cc_final: 0.6817 (mtpp) REVERT: A 61 MET cc_start: 0.6354 (mmt) cc_final: 0.6068 (mmt) REVERT: B 61 MET cc_start: 0.7230 (mtt) cc_final: 0.6944 (mtt) REVERT: C 92 ASN cc_start: 0.8821 (t0) cc_final: 0.8356 (t0) REVERT: F 97 LYS cc_start: 0.8640 (tttt) cc_final: 0.8387 (tttm) REVERT: G 111 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6732 (tt0) REVERT: G 121 VAL cc_start: 0.7935 (t) cc_final: 0.7709 (m) REVERT: I 117 SER cc_start: 0.8376 (m) cc_final: 0.7958 (p) REVERT: J 56 LEU cc_start: 0.6327 (tp) cc_final: 0.5861 (mt) REVERT: J 61 MET cc_start: 0.6153 (tpp) cc_final: 0.5793 (tpp) REVERT: P 128 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6264 (mm-30) REVERT: R 95 ASP cc_start: 0.8685 (m-30) cc_final: 0.8451 (m-30) REVERT: S 121 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7455 (mmtm) REVERT: S 164 ASP cc_start: 0.7785 (m-30) cc_final: 0.7530 (t70) REVERT: S 227 SER cc_start: 0.7768 (t) cc_final: 0.7289 (p) REVERT: S 234 GLU cc_start: 0.7739 (tt0) cc_final: 0.7534 (tt0) REVERT: S 241 ASP cc_start: 0.7788 (m-30) cc_final: 0.7501 (m-30) REVERT: S 291 ASP cc_start: 0.7798 (t0) cc_final: 0.7480 (m-30) REVERT: T 329 LYS cc_start: 0.8509 (mttt) cc_final: 0.8245 (mmmt) REVERT: T 422 ASN cc_start: 0.8359 (t0) cc_final: 0.7366 (t0) REVERT: T 436 PHE cc_start: 0.7932 (t80) cc_final: 0.7646 (t80) REVERT: U 75 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7685 (mtpp) REVERT: U 246 ASN cc_start: 0.7690 (m110) cc_final: 0.7481 (m-40) REVERT: U 282 MET cc_start: 0.7557 (mmm) cc_final: 0.7354 (mmp) REVERT: U 287 MET cc_start: 0.8199 (ttm) cc_final: 0.7937 (ttm) REVERT: U 439 MET cc_start: 0.7768 (tpp) cc_final: 0.7314 (tpp) REVERT: V 112 ASP cc_start: 0.8452 (p0) cc_final: 0.8172 (p0) REVERT: V 414 TYR cc_start: 0.6255 (m-10) cc_final: 0.6013 (m-10) REVERT: V 546 LEU cc_start: 0.6953 (mt) cc_final: 0.6752 (mt) REVERT: X 368 ILE cc_start: 0.9049 (mm) cc_final: 0.8808 (mt) REVERT: X 484 MET cc_start: 0.7219 (tmm) cc_final: 0.6804 (tmm) REVERT: X 498 LYS cc_start: 0.7768 (tttt) cc_final: 0.7503 (ttpt) REVERT: Y 101 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8094 (mmtt) REVERT: Z 44 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8450 (mp) REVERT: Z 91 ASP cc_start: 0.7919 (t70) cc_final: 0.7643 (t0) REVERT: Z 123 ASN cc_start: 0.8884 (p0) cc_final: 0.8539 (p0) REVERT: Z 195 GLU cc_start: 0.7536 (tp30) cc_final: 0.7248 (tp30) REVERT: Z 286 ASN cc_start: 0.8241 (m-40) cc_final: 0.8039 (m-40) outliers start: 120 outliers final: 72 residues processed: 801 average time/residue: 0.6329 time to fit residues: 864.3417 Evaluate side-chains 698 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 624 time to evaluate : 5.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 1 residue 99 THR Chi-restraints excluded: chain 1 residue 155 GLU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 1 residue 510 ILE Chi-restraints excluded: chain 2 residue 125 SER Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 6 residue 147 SER Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain M residue 304 THR Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 278 GLN Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 387 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 298 SER Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 229 GLU Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 3.9990 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 303 optimal weight: 0.8980 chunk 426 optimal weight: 3.9990 chunk 637 optimal weight: 8.9990 chunk 674 optimal weight: 0.9990 chunk 332 optimal weight: 5.9990 chunk 603 optimal weight: 0.1980 chunk 181 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 52 GLN 9 35 GLN ** R 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 529 ASN U 539 ASN V 549 HIS X 132 GLN Y 286 ASN Z 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54694 Z= 0.164 Angle : 0.527 10.827 74172 Z= 0.272 Chirality : 0.041 0.274 8690 Planarity : 0.004 0.052 9512 Dihedral : 5.631 88.177 7678 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 2.40 % Allowed : 13.39 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 7039 helix: 0.29 (0.09), residues: 3873 sheet: -0.85 (0.21), residues: 570 loop : -0.93 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 73 HIS 0.005 0.001 HIS Y 144 PHE 0.033 0.001 PHE G 107 TYR 0.028 0.001 TYR 4 211 ARG 0.007 0.000 ARG T 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 708 time to evaluate : 6.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 61 MET cc_start: 0.8352 (mtp) cc_final: 0.8030 (mtp) REVERT: 1 79 LEU cc_start: 0.8814 (mt) cc_final: 0.8589 (mp) REVERT: 1 378 GLU cc_start: 0.7516 (tp30) cc_final: 0.7160 (tp30) REVERT: 1 441 PHE cc_start: 0.7645 (m-80) cc_final: 0.7408 (m-80) REVERT: 1 453 ARG cc_start: 0.7612 (ttp80) cc_final: 0.7303 (ttp80) REVERT: 1 504 ASP cc_start: 0.7596 (t70) cc_final: 0.7227 (t0) REVERT: 1 586 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7317 (mm-30) REVERT: 2 205 GLU cc_start: 0.4972 (OUTLIER) cc_final: 0.4283 (pm20) REVERT: 2 209 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5827 (m-30) REVERT: 2 428 LYS cc_start: 0.7870 (mppt) cc_final: 0.7545 (ttmt) REVERT: 4 232 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7713 (mtp180) REVERT: 4 260 LYS cc_start: 0.8006 (pttm) cc_final: 0.7717 (mttm) REVERT: 5 119 LYS cc_start: 0.7095 (mmtp) cc_final: 0.6818 (mtmt) REVERT: 6 108 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8367 (tt) REVERT: 7 113 MET cc_start: 0.8504 (mtt) cc_final: 0.8184 (mtt) REVERT: 7 142 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7547 (tt0) REVERT: 8 69 LYS cc_start: 0.8305 (mttt) cc_final: 0.6338 (tmtt) REVERT: 9 13 LYS cc_start: 0.7376 (mtmt) cc_final: 0.6976 (mtpp) REVERT: C 92 ASN cc_start: 0.8839 (t0) cc_final: 0.8405 (t0) REVERT: F 81 MET cc_start: 0.8694 (ttp) cc_final: 0.8249 (ttp) REVERT: F 92 ASN cc_start: 0.8660 (p0) cc_final: 0.8387 (p0) REVERT: F 97 LYS cc_start: 0.8574 (tttt) cc_final: 0.8303 (tttm) REVERT: G 111 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6686 (tt0) REVERT: H 92 ASN cc_start: 0.8353 (p0) cc_final: 0.8143 (p0) REVERT: I 117 SER cc_start: 0.8258 (m) cc_final: 0.7881 (p) REVERT: J 56 LEU cc_start: 0.6243 (tp) cc_final: 0.5863 (mt) REVERT: J 61 MET cc_start: 0.6060 (tpp) cc_final: 0.5581 (tpp) REVERT: P 76 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: R 95 ASP cc_start: 0.8643 (m-30) cc_final: 0.8434 (m-30) REVERT: R 178 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8148 (pt0) REVERT: S 121 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7448 (mmtm) REVERT: S 164 ASP cc_start: 0.7793 (m-30) cc_final: 0.7584 (t70) REVERT: S 227 SER cc_start: 0.7802 (t) cc_final: 0.7364 (p) REVERT: S 241 ASP cc_start: 0.7579 (m-30) cc_final: 0.7331 (m-30) REVERT: S 291 ASP cc_start: 0.7746 (t0) cc_final: 0.7394 (m-30) REVERT: T 329 LYS cc_start: 0.8423 (mttt) cc_final: 0.8165 (mmmt) REVERT: T 436 PHE cc_start: 0.7874 (t80) cc_final: 0.7613 (t80) REVERT: U 75 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7693 (mtpp) REVERT: U 246 ASN cc_start: 0.7659 (m110) cc_final: 0.7457 (m-40) REVERT: U 287 MET cc_start: 0.8227 (ttm) cc_final: 0.7887 (ttm) REVERT: U 439 MET cc_start: 0.7688 (tpp) cc_final: 0.7273 (tpp) REVERT: V 414 TYR cc_start: 0.6159 (m-10) cc_final: 0.5919 (m-10) REVERT: X 368 ILE cc_start: 0.9051 (mm) cc_final: 0.8814 (mt) REVERT: X 414 GLN cc_start: 0.7129 (mt0) cc_final: 0.6855 (mt0) REVERT: X 488 MET cc_start: 0.7129 (mmm) cc_final: 0.6798 (mmm) REVERT: X 498 LYS cc_start: 0.7735 (tttt) cc_final: 0.7054 (tttm) REVERT: Y 101 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8115 (mmtt) REVERT: Z 91 ASP cc_start: 0.7984 (t70) cc_final: 0.7714 (t0) REVERT: Z 195 GLU cc_start: 0.7572 (tp30) cc_final: 0.7242 (tp30) outliers start: 135 outliers final: 78 residues processed: 796 average time/residue: 0.6317 time to fit residues: 862.1497 Evaluate side-chains 700 residues out of total 5637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 617 time to evaluate : 6.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 40 VAL Chi-restraints excluded: chain 1 residue 99 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 155 GLU Chi-restraints excluded: chain 1 residue 204 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 247 LYS Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 486 ASP Chi-restraints excluded: chain 1 residue 510 ILE Chi-restraints excluded: chain 2 residue 125 SER Chi-restraints excluded: chain 2 residue 205 GLU Chi-restraints excluded: chain 2 residue 209 ASP Chi-restraints excluded: chain 2 residue 229 VAL Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 371 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 79 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain P residue 76 GLN Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 186 MET Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 178 GLN Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 183 ILE Chi-restraints excluded: chain S residue 206 THR Chi-restraints excluded: chain S residue 223 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 255 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 436 PHE Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 226 GLU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 443 LEU Chi-restraints excluded: chain Y residue 162 THR Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 327 THR Chi-restraints excluded: chain Y residue 344 ASP Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Y residue 456 THR Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 226 GLU Chi-restraints excluded: chain Z residue 229 GLU Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 280 VAL Chi-restraints excluded: chain Z residue 383 THR Chi-restraints excluded: chain Z residue 440 GLN Chi-restraints excluded: chain Z residue 538 VAL Chi-restraints excluded: chain Z residue 558 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2241 > 50: distance: 4 - 9: 27.949 distance: 9 - 10: 41.697 distance: 10 - 11: 17.400 distance: 10 - 13: 45.171 distance: 11 - 12: 60.094 distance: 11 - 16: 44.516 distance: 13 - 14: 53.444 distance: 13 - 15: 32.434 distance: 16 - 17: 49.205 distance: 17 - 18: 14.450 distance: 17 - 20: 37.268 distance: 18 - 19: 23.760 distance: 18 - 25: 41.346 distance: 20 - 21: 37.353 distance: 21 - 22: 48.370 distance: 22 - 23: 45.371 distance: 22 - 24: 20.404 distance: 25 - 26: 31.029 distance: 26 - 27: 47.962 distance: 26 - 29: 44.176 distance: 27 - 28: 39.184 distance: 27 - 34: 51.938 distance: 29 - 30: 18.653 distance: 30 - 31: 29.704 distance: 31 - 32: 14.399 distance: 31 - 33: 23.609 distance: 34 - 35: 47.820 distance: 35 - 36: 57.815 distance: 35 - 38: 31.535 distance: 36 - 37: 64.653 distance: 36 - 42: 43.949 distance: 38 - 39: 39.783 distance: 38 - 40: 46.304 distance: 39 - 41: 26.335 distance: 42 - 43: 42.426 distance: 43 - 44: 55.451 distance: 43 - 46: 55.103 distance: 44 - 45: 61.684 distance: 44 - 49: 41.110 distance: 46 - 47: 35.749 distance: 46 - 48: 33.259 distance: 49 - 50: 49.516 distance: 50 - 53: 39.615 distance: 51 - 52: 55.709 distance: 51 - 54: 40.645 distance: 54 - 55: 45.316 distance: 54 - 60: 32.187 distance: 55 - 56: 39.115 distance: 55 - 58: 39.567 distance: 56 - 57: 27.260 distance: 56 - 61: 27.475 distance: 58 - 59: 47.750 distance: 59 - 60: 58.301 distance: 61 - 62: 57.354 distance: 62 - 63: 67.891 distance: 62 - 65: 68.394 distance: 63 - 70: 56.934 distance: 65 - 66: 49.317 distance: 66 - 67: 25.116 distance: 67 - 68: 36.135 distance: 68 - 69: 36.391 distance: 70 - 71: 58.297 distance: 71 - 72: 45.131 distance: 71 - 74: 39.410 distance: 72 - 73: 48.475 distance: 72 - 77: 64.121 distance: 74 - 75: 50.588 distance: 74 - 76: 58.028 distance: 77 - 78: 41.768 distance: 78 - 79: 41.197 distance: 78 - 81: 41.388 distance: 79 - 80: 68.251 distance: 79 - 82: 35.861