Starting phenix.real_space_refine on Wed Sep 25 00:01:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re8_4845/09_2024/6re8_4845.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re8_4845/09_2024/6re8_4845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re8_4845/09_2024/6re8_4845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re8_4845/09_2024/6re8_4845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re8_4845/09_2024/6re8_4845.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6re8_4845/09_2024/6re8_4845.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34282 2.51 5 N 9107 2.21 5 O 10163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 404 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53720 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3978 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3961 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "Y" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3952 Classifications: {'peptide': 520} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 497} Chain: "Z" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.21, per 1000 atoms: 0.43 Number of scatterers: 53720 At special positions: 0 Unit cell: (214.812, 135.837, 262.197, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10163 8.00 N 9107 7.00 C 34282 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.37 Conformation dependent library (CDL) restraints added in 5.5 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 " 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13076 Finding SS restraints... Secondary structure from input PDB file: 305 helices and 0 sheets defined 58.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.940A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 3 through 8' Processing helix chain '0' and resid 17 through 30 Processing helix chain '0' and resid 43 through 49 Processing helix chain '0' and resid 51 through 56 Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 106 through 142 removed outlier: 3.547A pdb=" N GLU 1 136 " --> pdb=" O GLY 1 132 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.911A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 3.615A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 224 removed outlier: 4.120A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.859A pdb=" N ARG 1 267 " --> pdb=" O LEU 1 263 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.729A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 286 removed outlier: 3.772A pdb=" N LEU 1 286 " --> pdb=" O ASP 1 283 " (cutoff:3.500A) Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 removed outlier: 3.884A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 4.105A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.883A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR 1 388 " --> pdb=" O THR 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.998A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.595A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER 1 432 " --> pdb=" O HIS 1 428 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 445 Processing helix chain '1' and resid 446 through 460 Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 removed outlier: 3.757A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.559A pdb=" N SER 1 494 " --> pdb=" O TYR 1 490 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 4.039A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 removed outlier: 3.574A 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 removed outlier: 3.651A pdb=" N MET 1 574 " --> pdb=" O THR 1 570 " (cutoff:3.500A) Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 Processing helix chain '2' and resid 7 through 20 removed outlier: 3.779A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '2' and resid 44 through 58 removed outlier: 4.091A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 Processing helix chain '2' and resid 80 through 87 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 95 through 98 removed outlier: 3.670A pdb=" N LEU 2 98 " --> pdb=" O LEU 2 95 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 95 through 98' Processing helix chain '2' and resid 99 through 113 removed outlier: 3.731A pdb=" N ALA 2 113 " --> pdb=" O ALA 2 109 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 Processing helix chain '2' and resid 136 through 149 Processing helix chain '2' and resid 155 through 168 removed outlier: 3.800A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 3.616A pdb=" N LYS 2 198 " --> pdb=" O ASP 2 194 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 221 removed outlier: 3.887A pdb=" N ALA 2 210 " --> pdb=" O SER 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 228 through 235 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.810A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 267 Processing helix chain '2' and resid 269 through 276 Processing helix chain '2' and resid 281 through 295 removed outlier: 3.868A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 4.029A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 341 Processing helix chain '2' and resid 345 through 356 Processing helix chain '2' and resid 396 through 408 removed outlier: 4.068A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 removed outlier: 3.787A pdb=" N GLU 2 422 " --> pdb=" O ALA 2 418 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 418 through 422' Processing helix chain '2' and resid 426 through 442 removed outlier: 4.158A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 89 Processing helix chain '3' and resid 91 through 96 Processing helix chain '3' and resid 102 through 113 removed outlier: 3.990A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 128 removed outlier: 3.888A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 129 through 135 removed outlier: 4.045A pdb=" N VAL 3 132 " --> pdb=" O LYS 3 129 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ALA 3 133 " --> pdb=" O PRO 3 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU 3 135 " --> pdb=" O VAL 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 removed outlier: 3.766A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.636A 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: 4.023A 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: 3.983A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 removed outlier: 3.548A pdb=" N LYS 3 251 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 254 through 272 Processing helix chain '3' and resid 277 through 287 removed outlier: 4.220A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL 3 287 " --> pdb=" O GLY 3 283 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 removed outlier: 3.504A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.702A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 20 through 35 Processing helix chain '4' and resid 47 through 68 removed outlier: 3.743A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.900A 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 removed outlier: 3.565A pdb=" N THR 4 113 " --> pdb=" O PHE 4 109 " (cutoff:3.500A) Processing helix chain '4' and resid 118 through 126 Processing helix chain '4' and resid 131 through 150 removed outlier: 3.721A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 176 removed outlier: 3.970A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 Processing helix chain '4' and resid 192 through 234 removed outlier: 4.321A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.875A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.674A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '4' and resid 286 through 289 removed outlier: 3.760A pdb=" N GLY 4 289 " --> pdb=" O PRO 4 286 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 286 through 289' Processing helix chain '5' and resid 7 through 59 removed outlier: 5.140A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.962A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 68 removed outlier: 3.887A pdb=" N SER 5 67 " --> pdb=" O ASP 5 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 5 68 " --> pdb=" O ARG 5 64 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 63 through 68' Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 87 through 106 removed outlier: 4.217A pdb=" N HIS 5 91 " --> pdb=" O ALA 5 87 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 removed outlier: 3.655A pdb=" N GLY 6 34 " --> pdb=" O ASN 6 30 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 58 Processing helix chain '6' and resid 72 through 93 Processing helix chain '6' and resid 98 through 120 removed outlier: 3.990A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE 6 120 " --> pdb=" O PHE 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.165A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 67 removed outlier: 3.795A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 67' Processing helix chain '7' and resid 83 through 102 Processing helix chain '7' and resid 110 through 114 Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 removed outlier: 3.676A 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: 4.012A pdb=" N GLN 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.978A 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 removed outlier: 3.589A pdb=" N ALA 7 178 " --> pdb=" O GLY 7 174 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 Processing helix chain '8' and resid 31 through 39 removed outlier: 3.763A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 6.820A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 32 through 55 removed outlier: 3.729A pdb=" N TYR 9 36 " --> pdb=" O SER 9 32 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 80 removed outlier: 3.533A pdb=" N GLN 9 80 " --> pdb=" O TRP 9 77 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 94 removed outlier: 3.611A pdb=" N ALA 9 86 " --> pdb=" O ASP 9 82 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.580A pdb=" N ALA A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.699A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 127 removed outlier: 3.728A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 67 Processing helix chain 'B' and resid 69 through 92 removed outlier: 3.658A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 Processing helix chain 'B' and resid 111 through 126 removed outlier: 4.032A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.965A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.250A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 3.908A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.998A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.332A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.940A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 67 removed outlier: 3.964A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.013A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 127 removed outlier: 3.790A pdb=" N VAL E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE E 126 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 3.645A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.240A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 96 Processing helix chain 'F' and resid 97 through 127 removed outlier: 4.146A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 4.943A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 90 removed outlier: 4.323A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 94 No H-bonds generated for 'chain 'G' and resid 92 through 94' Processing helix chain 'G' and resid 95 through 126 removed outlier: 4.410A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 66 removed outlier: 3.898A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.329A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 127 removed outlier: 4.236A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 68 removed outlier: 3.693A pdb=" N VAL I 62 " --> pdb=" O ALA I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.254A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 4.290A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU I 118 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.589A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 92 removed outlier: 4.324A pdb=" N VAL J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 96 Processing helix chain 'J' and resid 97 through 126 removed outlier: 3.585A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 120 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 165 Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.633A pdb=" N ALA M 181 " --> pdb=" O GLY M 177 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 230 removed outlier: 3.920A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 258 removed outlier: 3.699A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 265 Processing helix chain 'M' and resid 270 through 309 removed outlier: 4.001A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.620A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 84 removed outlier: 3.634A pdb=" N HIS P 84 " --> pdb=" O LEU P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 4.110A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP P 93 " --> pdb=" O ARG P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 109 Processing helix chain 'P' and resid 115 through 128 removed outlier: 3.736A pdb=" N GLU P 128 " --> pdb=" O ALA P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.437A pdb=" N SER P 132 " --> pdb=" O GLY P 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 129 through 132' Processing helix chain 'P' and resid 133 through 149 removed outlier: 4.105A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN P 140 " --> pdb=" O GLU P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 4.126A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 178 No H-bonds generated for 'chain 'P' and resid 176 through 178' Processing helix chain 'P' and resid 210 through 227 removed outlier: 3.678A pdb=" N ASN P 223 " --> pdb=" O ASN P 219 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU P 225 " --> pdb=" O PHE P 221 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.624A pdb=" N ASN Q 29 " --> pdb=" O ASP Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 42 removed outlier: 3.815A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS Q 38 " --> pdb=" O PRO Q 34 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 39 removed outlier: 4.298A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 170 removed outlier: 3.762A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 3.771A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N SER R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 79 removed outlier: 3.632A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA S 74 " --> pdb=" O ASN S 70 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLN S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 89 removed outlier: 4.270A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 131 removed outlier: 3.511A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR S 129 " --> pdb=" O ALA S 125 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU S 131 " --> pdb=" O LEU S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 145 through 151 removed outlier: 4.138A pdb=" N GLN S 149 " --> pdb=" O LYS S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 184 removed outlier: 3.536A pdb=" N ALA S 175 " --> pdb=" O THR S 171 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 221 removed outlier: 5.713A pdb=" N LYS S 218 " --> pdb=" O ASP S 214 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN S 219 " --> pdb=" O LEU S 215 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.520A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU S 275 " --> pdb=" O MET S 271 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR S 278 " --> pdb=" O MET S 274 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 76 removed outlier: 3.547A pdb=" N LYS T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 4.130A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.956A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 206 through 213 Processing helix chain 'T' and resid 230 through 247 removed outlier: 4.105A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 279 Processing helix chain 'T' and resid 280 through 283 Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.264A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 326 through 340 Processing helix chain 'T' and resid 346 through 350 removed outlier: 3.517A pdb=" N ALA T 349 " --> pdb=" O GLY T 346 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.538A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU T 363 " --> pdb=" O SER T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 414 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.587A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 Processing helix chain 'T' and resid 443 through 458 Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.649A pdb=" N VAL T 473 " --> pdb=" O ALA T 469 " (cutoff:3.500A) Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.664A pdb=" N ALA T 500 " --> pdb=" O ARG T 496 " (cutoff:3.500A) Processing helix chain 'T' and resid 513 through 515 No H-bonds generated for 'chain 'T' and resid 513 through 515' Processing helix chain 'T' and resid 516 through 528 removed outlier: 4.170A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) Processing helix chain 'T' and resid 529 through 540 removed outlier: 3.773A pdb=" N PHE T 533 " --> pdb=" O ASN T 529 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 556 removed outlier: 3.787A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 49 removed outlier: 3.728A pdb=" N LEU U 48 " --> pdb=" O LEU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 72 removed outlier: 3.612A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.680A 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: 3.660A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 Processing helix chain 'U' and resid 281 through 284 Processing helix chain 'U' and resid 295 through 317 Proline residue: U 303 - end of helix removed outlier: 4.096A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG U 314 " --> pdb=" O ALA U 310 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR U 316 " --> pdb=" O TYR U 312 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY U 317 " --> pdb=" O PHE U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 353 through 363 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.543A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR U 453 " --> pdb=" O GLU U 449 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU U 455 " --> pdb=" O ALA U 451 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL U 456 " --> pdb=" O GLN U 452 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE U 459 " --> pdb=" O GLU U 455 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA U 460 " --> pdb=" O VAL U 456 " (cutoff:3.500A) Processing helix chain 'U' and resid 467 through 485 removed outlier: 3.694A pdb=" N TYR U 472 " --> pdb=" O ALA U 468 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL U 473 " --> pdb=" O ALA U 469 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.897A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.707A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.504A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE U 535 " --> pdb=" O ALA U 531 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 556 removed outlier: 3.710A pdb=" N ARG U 555 " --> pdb=" O LYS U 551 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS U 556 " --> pdb=" O ALA U 552 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.564A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.976A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE V 138 " --> pdb=" O ASP V 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 134 through 138' Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.683A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 211 removed outlier: 3.830A pdb=" N ALA V 211 " --> pdb=" O LYS V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.895A pdb=" N GLN V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 4.261A 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 removed outlier: 3.611A pdb=" N VAL V 269 " --> pdb=" O LYS V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 280 through 283 removed outlier: 4.145A pdb=" N ARG V 283 " --> pdb=" O GLY V 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 280 through 283' Processing helix chain 'V' and resid 295 through 315 Proline residue: V 303 - end of helix removed outlier: 3.907A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG V 314 " --> pdb=" O ALA V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 340 Processing helix chain 'V' and resid 346 through 350 Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.591A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.605A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 removed outlier: 3.723A pdb=" N THR V 396 " --> pdb=" O ALA V 392 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 434 removed outlier: 3.885A pdb=" N ALA V 434 " --> pdb=" O GLY V 431 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.828A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU V 455 " --> pdb=" O ALA V 451 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 484 removed outlier: 3.507A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.530A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 516 through 528 removed outlier: 4.266A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL V 528 " --> pdb=" O VAL V 524 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.812A pdb=" N ALA V 538 " --> pdb=" O LYS V 534 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY V 540 " --> pdb=" O LEU V 536 " (cutoff:3.500A) Processing helix chain 'V' and resid 548 through 554 removed outlier: 3.630A pdb=" N ALA V 552 " --> pdb=" O ALA V 548 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.748A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU X 118 " --> pdb=" O ARG X 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 114 through 118' Processing helix chain 'X' and resid 149 through 153 removed outlier: 3.547A pdb=" N GLN X 153 " --> pdb=" O PHE X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 188 through 204 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.077A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 removed outlier: 3.914A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 286 through 301 removed outlier: 3.686A pdb=" N PHE X 290 " --> pdb=" O ASN X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 314 through 323 Processing helix chain 'X' and resid 341 through 345 removed outlier: 3.707A pdb=" N ASP X 344 " --> pdb=" O VAL X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 365 through 371 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 413 removed outlier: 3.883A pdb=" N VAL X 399 " --> pdb=" O GLU X 395 " (cutoff:3.500A) Processing helix chain 'X' and resid 413 through 421 removed outlier: 3.940A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 removed outlier: 3.556A pdb=" N LEU X 431 " --> pdb=" O GLU X 427 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 462 through 476 removed outlier: 3.741A pdb=" N SER X 468 " --> pdb=" O ALA X 464 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 509 removed outlier: 4.268A pdb=" N LYS X 496 " --> pdb=" O ILE X 492 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE X 506 " --> pdb=" O MET X 502 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA X 507 " --> pdb=" O ALA X 503 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 534 removed outlier: 3.615A pdb=" N SER X 532 " --> pdb=" O ASP X 528 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE X 534 " --> pdb=" O LEU X 530 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 removed outlier: 3.682A pdb=" N THR Y 117 " --> pdb=" O GLY Y 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 231 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 4.113A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 259 removed outlier: 3.582A pdb=" N ALA Y 259 " --> pdb=" O PRO Y 255 " (cutoff:3.500A) Processing helix chain 'Y' and resid 260 through 275 removed outlier: 3.610A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 298 removed outlier: 3.719A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.759A pdb=" N THR Y 354 " --> pdb=" O ALA Y 350 " (cutoff:3.500A) Processing helix chain 'Y' and resid 356 through 358 No H-bonds generated for 'chain 'Y' and resid 356 through 358' Processing helix chain 'Y' and resid 365 through 370 Processing helix chain 'Y' and resid 393 through 413 removed outlier: 3.804A pdb=" N LEU Y 413 " --> pdb=" O ASP Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 Processing helix chain 'Y' and resid 421 through 425 removed outlier: 3.996A pdb=" N GLU Y 424 " --> pdb=" O GLY Y 421 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU Y 425 " --> pdb=" O MET Y 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 421 through 425' Processing helix chain 'Y' and resid 428 through 444 removed outlier: 3.873A pdb=" N ALA Y 434 " --> pdb=" O LYS Y 430 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Y 444 " --> pdb=" O GLN Y 440 " (cutoff:3.500A) Processing helix chain 'Y' and resid 450 through 455 removed outlier: 3.513A pdb=" N GLY Y 455 " --> pdb=" O GLU Y 451 " (cutoff:3.500A) Processing helix chain 'Y' and resid 462 through 476 Processing helix chain 'Y' and resid 482 through 486 Processing helix chain 'Y' and resid 491 through 505 removed outlier: 4.020A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) Processing helix chain 'Y' and resid 511 through 515 removed outlier: 4.317A pdb=" N ASN Y 514 " --> pdb=" O GLU Y 511 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS Y 515 " --> pdb=" O ALA Y 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 511 through 515' Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Z' and resid 114 through 118 removed outlier: 3.560A pdb=" N LEU Z 118 " --> pdb=" O ARG Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 188 through 198 Processing helix chain 'Z' and resid 216 through 230 removed outlier: 3.622A pdb=" N GLY Z 220 " --> pdb=" O ARG Z 216 " (cutoff:3.500A) Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.098A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.547A pdb=" N ARG Z 258 " --> pdb=" O PRO Z 254 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 298 removed outlier: 3.865A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) Processing helix chain 'Z' and resid 314 through 323 Processing helix chain 'Z' and resid 342 through 345 Processing helix chain 'Z' and resid 348 through 354 removed outlier: 3.795A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.604A pdb=" N ALA Z 369 " --> pdb=" O SER Z 365 " (cutoff:3.500A) Processing helix chain 'Z' and resid 384 through 387 removed outlier: 3.550A pdb=" N LEU Z 387 " --> pdb=" O SER Z 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 384 through 387' Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 418 removed outlier: 4.353A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP Z 415 " --> pdb=" O LYS Z 411 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N ILE Z 416 " --> pdb=" O ASN Z 412 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Z 418 " --> pdb=" O GLN Z 414 " (cutoff:3.500A) Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.539A pdb=" N VAL Z 433 " --> pdb=" O ASP Z 429 " (cutoff:3.500A) Processing helix chain 'Z' and resid 448 through 452 removed outlier: 3.944A pdb=" N GLU Z 451 " --> pdb=" O GLN Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 462 through 475 Processing helix chain 'Z' and resid 483 through 487 Processing helix chain 'Z' and resid 491 through 509 removed outlier: 3.521A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS Z 501 " --> pdb=" O GLU Z 497 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER Z 508 " --> pdb=" O LYS Z 504 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG Z 509 " --> pdb=" O ASP Z 505 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 534 removed outlier: 3.525A pdb=" N LEU Z 530 " --> pdb=" O SER Z 526 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE Z 534 " --> pdb=" O LEU Z 530 " (cutoff:3.500A) 2586 hydrogen bonds defined for protein. 7611 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: 15.26 Time building geometry restraints manager: 11.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16513 1.34 - 1.46: 8101 1.46 - 1.57: 29769 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54658 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C5 ATP T1001 " pdb=" C6 ATP T1001 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.43e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 ... (remaining 54653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 73775 4.20 - 8.40: 316 8.40 - 12.61: 23 12.61 - 16.81: 3 16.81 - 21.01: 4 Bond angle restraints: 74121 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 118.86 21.01 1.00e+00 1.00e+00 4.41e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 119.84 20.03 1.00e+00 1.00e+00 4.01e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 117.80 19.03 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 119.16 17.67 1.00e+00 1.00e+00 3.12e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 124.43 15.44 1.00e+00 1.00e+00 2.38e+02 ... (remaining 74116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 30882 22.60 - 45.21: 1860 45.21 - 67.81: 196 67.81 - 90.42: 65 90.42 - 113.02: 2 Dihedral angle restraints: 33005 sinusoidal: 12661 harmonic: 20344 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -127.06 -52.94 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -131.19 -48.81 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA LYS 5 119 " pdb=" C LYS 5 119 " pdb=" N PRO 5 120 " pdb=" CA PRO 5 120 " ideal model delta harmonic sigma weight residual -180.00 -148.29 -31.71 0 5.00e+00 4.00e-02 4.02e+01 ... (remaining 33002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 7580 0.078 - 0.157: 1041 0.157 - 0.235: 50 0.235 - 0.313: 10 0.313 - 0.392: 2 Chirality restraints: 8683 Sorted by residual: chirality pdb=" CB VAL 2 357 " pdb=" CA VAL 2 357 " pdb=" CG1 VAL 2 357 " pdb=" CG2 VAL 2 357 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CB VAL 2 41 " pdb=" CA VAL 2 41 " pdb=" CG1 VAL 2 41 " pdb=" CG2 VAL 2 41 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB ILE Z 524 " pdb=" CA ILE Z 524 " pdb=" CG1 ILE Z 524 " pdb=" CG2 ILE Z 524 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 8680 not shown) Planarity restraints: 9504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 503 " 0.031 2.00e-02 2.50e+03 6.11e-02 3.73e+01 pdb=" C ALA Y 503 " -0.106 2.00e-02 2.50e+03 pdb=" O ALA Y 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Y 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.031 2.00e-02 2.50e+03 6.04e-02 3.65e+01 pdb=" C ALA Z 503 " -0.105 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.039 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU Q 33 " -0.051 5.00e-02 4.00e+02 7.66e-02 9.38e+00 pdb=" N PRO Q 34 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO Q 34 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 34 " -0.043 5.00e-02 4.00e+02 ... (remaining 9501 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 501 2.57 - 3.15: 41397 3.15 - 3.73: 86189 3.73 - 4.32: 118652 4.32 - 4.90: 196406 Nonbonded interactions: 443145 Sorted by model distance: nonbonded pdb=" O ASN Z 514 " pdb=" CG2 VAL Z 517 " model vdw 1.985 3.460 nonbonded pdb=" O2B ATP V1001 " pdb="MG MG V1002 " model vdw 2.054 2.170 nonbonded pdb=" O1B ATP U1001 " pdb="MG MG U1002 " model vdw 2.058 2.170 nonbonded pdb=" OG1 THR Y 190 " pdb="MG MG Y 602 " model vdw 2.068 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.090 2.170 ... (remaining 443140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 562 or resid 1001 through 1002)) selection = chain 'V' } ncs_group { reference = (chain 'X' and resid 37 through 552) selection = (chain 'Y' and resid 37 through 552) selection = (chain 'Z' and resid 37 through 552) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.450 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: 0.050 Extract box with map and model: 1.560 Check model and map are aligned: 0.340 Set scattering table: 0.380 Process input model: 97.840 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 54658 Z= 0.365 Angle : 0.864 21.011 74121 Z= 0.504 Chirality : 0.053 0.392 8683 Planarity : 0.007 0.077 9504 Dihedral : 14.608 113.020 19929 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.32 % Favored : 95.51 % Rotamer: Outliers : 0.21 % Allowed : 8.49 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.08), residues: 7034 helix: -2.83 (0.06), residues: 3769 sheet: -2.38 (0.20), residues: 550 loop : -2.38 (0.10), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 4 206 HIS 0.011 0.001 HIS R 66 PHE 0.026 0.002 PHE 3 115 TYR 0.026 0.002 TYR 7 119 ARG 0.006 0.001 ARG T 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1244 time to evaluate : 4.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 69 ASP cc_start: 0.8348 (t0) cc_final: 0.8045 (t0) REVERT: 1 172 ASP cc_start: 0.7979 (m-30) cc_final: 0.7529 (t0) REVERT: 1 223 GLU cc_start: 0.6348 (mt-10) cc_final: 0.5940 (mt-10) REVERT: 2 345 TYR cc_start: 0.7877 (m-80) cc_final: 0.7386 (m-10) REVERT: 3 176 GLN cc_start: 0.8456 (mt0) cc_final: 0.8161 (mt0) REVERT: 3 185 ASP cc_start: 0.8695 (t70) cc_final: 0.8206 (t0) REVERT: 3 269 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7004 (tm-30) REVERT: 4 58 LEU cc_start: 0.9059 (tp) cc_final: 0.8744 (tt) REVERT: 4 64 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7232 (mm-30) REVERT: 5 27 ASP cc_start: 0.8889 (t0) cc_final: 0.8297 (t0) REVERT: 5 63 ASP cc_start: 0.8724 (p0) cc_final: 0.8459 (p0) REVERT: 5 74 ASN cc_start: 0.8848 (t0) cc_final: 0.8573 (t0) REVERT: 5 104 ASP cc_start: 0.8168 (m-30) cc_final: 0.7517 (t0) REVERT: 5 111 LYS cc_start: 0.8529 (mmmt) cc_final: 0.7835 (pttt) REVERT: 6 46 ASN cc_start: 0.7312 (p0) cc_final: 0.6994 (p0) REVERT: 7 37 LEU cc_start: 0.7249 (tp) cc_final: 0.6996 (tp) REVERT: 7 101 TYR cc_start: 0.9086 (t80) cc_final: 0.8840 (t80) REVERT: 7 164 ARG cc_start: 0.8510 (mtp85) cc_final: 0.8260 (ttm-80) REVERT: 7 166 ARG cc_start: 0.8301 (ttp-110) cc_final: 0.7744 (ttm110) REVERT: 9 13 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7398 (mtmt) REVERT: 9 56 ASN cc_start: 0.8281 (p0) cc_final: 0.8049 (p0) REVERT: 9 74 GLU cc_start: 0.7368 (tp30) cc_final: 0.7143 (tp30) REVERT: A 81 MET cc_start: 0.7233 (ppp) cc_final: 0.7008 (ttp) REVERT: A 119 LEU cc_start: 0.5766 (tt) cc_final: 0.5045 (mt) REVERT: B 60 LYS cc_start: 0.7445 (mtpp) cc_final: 0.7203 (ttpt) REVERT: B 69 ILE cc_start: 0.8052 (mt) cc_final: 0.7811 (mt) REVERT: D 82 PHE cc_start: 0.7750 (m-80) cc_final: 0.7381 (m-80) REVERT: D 87 ASN cc_start: 0.8076 (t0) cc_final: 0.7831 (t0) REVERT: D 115 LEU cc_start: 0.7310 (pp) cc_final: 0.6691 (mt) REVERT: E 60 LYS cc_start: 0.7888 (ptpt) cc_final: 0.7628 (pttm) REVERT: E 85 LEU cc_start: 0.8307 (tp) cc_final: 0.8018 (tp) REVERT: G 102 TYR cc_start: 0.6684 (m-80) cc_final: 0.6356 (m-10) REVERT: H 56 LEU cc_start: 0.7384 (mp) cc_final: 0.7174 (mp) REVERT: I 115 LEU cc_start: 0.7783 (tt) cc_final: 0.7391 (mp) REVERT: J 95 ILE cc_start: 0.5338 (OUTLIER) cc_final: 0.5054 (mt) REVERT: M 99 ASP cc_start: 0.8520 (t0) cc_final: 0.8110 (t0) REVERT: M 160 ILE cc_start: 0.9547 (tt) cc_final: 0.9337 (tt) REVERT: M 178 LEU cc_start: 0.8240 (tp) cc_final: 0.7989 (tp) REVERT: M 227 ILE cc_start: 0.8424 (mm) cc_final: 0.8173 (tp) REVERT: M 311 ASN cc_start: 0.8365 (t0) cc_final: 0.8097 (t0) REVERT: P 142 GLU cc_start: 0.7467 (mt-10) cc_final: 0.6996 (mt-10) REVERT: P 151 GLU cc_start: 0.7647 (pt0) cc_final: 0.7327 (pt0) REVERT: P 200 ILE cc_start: 0.9010 (mm) cc_final: 0.8641 (mt) REVERT: R 86 LYS cc_start: 0.7883 (mmtt) cc_final: 0.7604 (mptt) REVERT: S 60 MET cc_start: 0.8095 (ttm) cc_final: 0.7557 (mtp) REVERT: S 68 MET cc_start: 0.7248 (ttp) cc_final: 0.6892 (ttt) REVERT: S 274 MET cc_start: 0.8204 (mmp) cc_final: 0.7938 (mmt) REVERT: T 284 TYR cc_start: 0.8682 (m-80) cc_final: 0.8371 (m-80) REVERT: T 342 ARG cc_start: 0.8384 (mmm160) cc_final: 0.8101 (mmt-90) REVERT: U 151 VAL cc_start: 0.8408 (t) cc_final: 0.8151 (t) REVERT: U 236 ILE cc_start: 0.9320 (mm) cc_final: 0.9000 (mt) REVERT: U 240 ILE cc_start: 0.9227 (mm) cc_final: 0.9016 (mt) REVERT: U 307 CYS cc_start: 0.8333 (t) cc_final: 0.8122 (t) REVERT: U 448 LEU cc_start: 0.8571 (mt) cc_final: 0.7964 (mt) REVERT: U 551 LYS cc_start: 0.7252 (mttt) cc_final: 0.7028 (ttpp) REVERT: U 558 LYS cc_start: 0.5987 (tmtt) cc_final: 0.5524 (mmmt) REVERT: V 325 ASP cc_start: 0.8809 (t0) cc_final: 0.8403 (t0) REVERT: V 479 ARG cc_start: 0.8170 (mmt-90) cc_final: 0.7597 (tpp-160) REVERT: V 497 GLN cc_start: 0.7939 (mt0) cc_final: 0.7685 (mt0) REVERT: X 198 ASN cc_start: 0.7816 (t0) cc_final: 0.7437 (m-40) REVERT: X 317 ASP cc_start: 0.7440 (t0) cc_final: 0.7093 (m-30) REVERT: X 386 MET cc_start: 0.7862 (mmm) cc_final: 0.7629 (mmt) REVERT: X 430 LYS cc_start: 0.6954 (mttp) cc_final: 0.6505 (mttm) REVERT: X 497 GLU cc_start: 0.7403 (pp20) cc_final: 0.6953 (pp20) REVERT: Y 195 GLU cc_start: 0.6534 (tp30) cc_final: 0.6308 (tp30) REVERT: Y 221 ASN cc_start: 0.8964 (t0) cc_final: 0.8704 (t0) REVERT: Y 416 ILE cc_start: 0.8268 (mt) cc_final: 0.7981 (mt) REVERT: Y 439 ILE cc_start: 0.8878 (pt) cc_final: 0.8524 (mt) REVERT: Z 401 ARG cc_start: 0.7160 (tpt-90) cc_final: 0.6354 (ptp-170) REVERT: Z 498 LYS cc_start: 0.5792 (tttt) cc_final: 0.5589 (ttmm) REVERT: Z 502 MET cc_start: 0.7007 (mtp) cc_final: 0.6503 (mtm) REVERT: Z 535 LYS cc_start: 0.7284 (pttp) cc_final: 0.7072 (mmmt) outliers start: 12 outliers final: 4 residues processed: 1254 average time/residue: 0.6068 time to fit residues: 1265.8286 Evaluate side-chains 773 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 768 time to evaluate : 4.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain P residue 187 GLN Chi-restraints excluded: chain X residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 588 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 chunk 293 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 356 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 546 optimal weight: 0.4980 chunk 211 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 406 optimal weight: 0.7980 chunk 632 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 0 44 ASN 1 285 GLN 1 316 ASN 1 394 GLN 1 535 HIS 1 590 HIS 2 68 ASN 2 74 ASN 2 153 ASN 2 243 GLN 2 289 HIS 3 87 ASN 3 309 ASN 4 38 GLN 4 124 ASN 4 240 GLN 5 107 ASN 5 109 GLN 6 40 ASN 6 97 HIS ** 6 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 GLN 7 86 HIS 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 97 ASN A 94 ASN C 87 ASN D 98 GLN G 94 ASN M 108 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 HIS P 220 ASN R 85 GLN R 154 GLN S 70 ASN S 174 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 452 GLN U 104 GLN U 123 GLN ** U 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 241 HIS U 248 GLN U 264 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 319 HIS ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 527 GLN U 539 ASN V 60 GLN V 139 HIS V 242 GLN V 244 ASN V 264 GLN V 278 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 386 GLN V 497 GLN V 549 HIS X 78 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 144 HIS X 157 GLN X 199 ASN X 278 GLN X 337 GLN X 404 GLN X 414 GLN X 448 GLN Y 174 GLN Y 199 ASN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 408 GLN Z 174 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54658 Z= 0.211 Angle : 0.602 13.092 74121 Z= 0.310 Chirality : 0.042 0.226 8683 Planarity : 0.005 0.062 9504 Dihedral : 6.139 93.134 7672 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 1.83 % Allowed : 14.98 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.09), residues: 7034 helix: -1.02 (0.08), residues: 3851 sheet: -2.11 (0.20), residues: 565 loop : -1.85 (0.11), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 5 21 HIS 0.010 0.001 HIS 7 86 PHE 0.023 0.001 PHE 0 12 TYR 0.031 0.001 TYR C 102 ARG 0.005 0.000 ARG Z 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 889 time to evaluate : 4.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8700 (tp) cc_final: 0.8338 (tp) REVERT: 1 69 ASP cc_start: 0.8242 (t0) cc_final: 0.7927 (t0) REVERT: 1 556 ILE cc_start: 0.9215 (mt) cc_final: 0.8936 (mt) REVERT: 1 609 ARG cc_start: 0.7398 (mtm180) cc_final: 0.7180 (ttp-170) REVERT: 2 5 GLU cc_start: 0.5641 (tt0) cc_final: 0.3280 (pm20) REVERT: 2 316 ASP cc_start: 0.7740 (t70) cc_final: 0.7441 (t70) REVERT: 2 345 TYR cc_start: 0.8076 (m-80) cc_final: 0.7646 (m-10) REVERT: 3 269 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7173 (tm-30) REVERT: 4 52 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8509 (mm-40) REVERT: 5 27 ASP cc_start: 0.8812 (t0) cc_final: 0.8604 (t0) REVERT: 5 104 ASP cc_start: 0.7920 (m-30) cc_final: 0.7367 (t0) REVERT: 5 111 LYS cc_start: 0.8521 (mmmt) cc_final: 0.7782 (pttt) REVERT: 6 46 ASN cc_start: 0.7217 (p0) cc_final: 0.6912 (p0) REVERT: 7 37 LEU cc_start: 0.7154 (tp) cc_final: 0.6775 (tp) REVERT: 7 101 TYR cc_start: 0.9027 (t80) cc_final: 0.8767 (t80) REVERT: 9 12 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7789 (tm-30) REVERT: 9 56 ASN cc_start: 0.8320 (p0) cc_final: 0.7991 (p0) REVERT: 9 74 GLU cc_start: 0.7427 (tp30) cc_final: 0.7113 (tp30) REVERT: 9 77 TRP cc_start: 0.8092 (p-90) cc_final: 0.7880 (p-90) REVERT: A 119 LEU cc_start: 0.6173 (tt) cc_final: 0.5292 (mt) REVERT: C 119 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4564 (mt) REVERT: E 60 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7565 (pttm) REVERT: E 82 PHE cc_start: 0.8746 (m-80) cc_final: 0.8545 (m-80) REVERT: G 102 TYR cc_start: 0.6632 (m-80) cc_final: 0.6244 (m-10) REVERT: I 81 MET cc_start: 0.8627 (tmm) cc_final: 0.8414 (tmm) REVERT: I 109 LEU cc_start: 0.8951 (mt) cc_final: 0.8628 (tp) REVERT: J 78 LEU cc_start: 0.7659 (tp) cc_final: 0.7326 (tt) REVERT: M 99 ASP cc_start: 0.8689 (t0) cc_final: 0.8360 (t0) REVERT: M 133 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6634 (tmm160) REVERT: M 167 LEU cc_start: 0.9025 (mt) cc_final: 0.8809 (mm) REVERT: M 311 ASN cc_start: 0.8552 (t0) cc_final: 0.8099 (t0) REVERT: P 142 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7030 (mt-10) REVERT: P 151 GLU cc_start: 0.7676 (pt0) cc_final: 0.7309 (pt0) REVERT: R 86 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7632 (mptt) REVERT: R 97 TYR cc_start: 0.8066 (m-80) cc_final: 0.7688 (m-80) REVERT: R 126 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8038 (mttt) REVERT: R 176 PHE cc_start: 0.4187 (t80) cc_final: 0.3984 (t80) REVERT: S 60 MET cc_start: 0.8085 (ttm) cc_final: 0.7449 (mtp) REVERT: S 68 MET cc_start: 0.7185 (ttp) cc_final: 0.6982 (ttt) REVERT: S 147 ARG cc_start: 0.6529 (pmt-80) cc_final: 0.6203 (pmt-80) REVERT: S 216 LEU cc_start: 0.7851 (mt) cc_final: 0.7233 (mp) REVERT: S 249 PHE cc_start: 0.8865 (t80) cc_final: 0.8656 (t80) REVERT: T 342 ARG cc_start: 0.8507 (mmm160) cc_final: 0.8206 (mmt-90) REVERT: T 441 GLN cc_start: 0.6100 (pp30) cc_final: 0.5780 (tm-30) REVERT: U 307 CYS cc_start: 0.8423 (t) cc_final: 0.8111 (t) REVERT: U 495 GLU cc_start: 0.7866 (pm20) cc_final: 0.7584 (pm20) REVERT: U 551 LYS cc_start: 0.7398 (mttt) cc_final: 0.7176 (ttpp) REVERT: U 558 LYS cc_start: 0.6108 (tmtt) cc_final: 0.5609 (mmmt) REVERT: V 90 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8671 (t) REVERT: V 210 ASP cc_start: 0.8066 (m-30) cc_final: 0.7798 (m-30) REVERT: V 304 TYR cc_start: 0.9096 (m-80) cc_final: 0.8874 (m-80) REVERT: V 479 ARG cc_start: 0.8041 (mmt-90) cc_final: 0.7715 (tpp-160) REVERT: X 198 ASN cc_start: 0.7902 (t0) cc_final: 0.7533 (m-40) REVERT: X 430 LYS cc_start: 0.6459 (mttp) cc_final: 0.6001 (mttm) REVERT: X 497 GLU cc_start: 0.7081 (pp20) cc_final: 0.6822 (pp20) REVERT: Y 195 GLU cc_start: 0.6736 (tp30) cc_final: 0.6470 (tp30) REVERT: Y 251 MET cc_start: 0.9261 (ptp) cc_final: 0.8842 (ptm) REVERT: Y 266 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8816 (mm) REVERT: Y 439 ILE cc_start: 0.8871 (pt) cc_final: 0.8597 (mt) REVERT: Z 227 MET cc_start: 0.8302 (mtp) cc_final: 0.7972 (mtp) REVERT: Z 401 ARG cc_start: 0.6976 (tpt-90) cc_final: 0.6450 (ptp-170) REVERT: Z 502 MET cc_start: 0.7062 (mtp) cc_final: 0.6535 (mtm) outliers start: 103 outliers final: 55 residues processed: 948 average time/residue: 0.5391 time to fit residues: 868.3818 Evaluate side-chains 806 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 747 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 CYS Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 318 SER Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 414 GLN Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 351 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 526 optimal weight: 2.9990 chunk 431 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 chunk 634 optimal weight: 0.3980 chunk 685 optimal weight: 0.7980 chunk 564 optimal weight: 0.3980 chunk 628 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 508 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 1 531 HIS 4 124 ASN 6 97 HIS 6 109 GLN 7 170 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 195 ASN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 435 GLN U 264 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS V 271 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 337 GLN Z 562 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 54658 Z= 0.155 Angle : 0.549 11.580 74121 Z= 0.280 Chirality : 0.041 0.294 8683 Planarity : 0.004 0.054 9504 Dihedral : 5.697 83.963 7666 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.55 % Rotamer: Outliers : 1.97 % Allowed : 16.63 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 7034 helix: -0.15 (0.08), residues: 3828 sheet: -1.85 (0.21), residues: 551 loop : -1.44 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 5 21 HIS 0.006 0.001 HIS R 66 PHE 0.030 0.001 PHE 3 115 TYR 0.046 0.001 TYR C 102 ARG 0.007 0.000 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 887 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8652 (tp) cc_final: 0.8294 (tp) REVERT: 1 69 ASP cc_start: 0.8191 (t0) cc_final: 0.7916 (t0) REVERT: 1 556 ILE cc_start: 0.9096 (mt) cc_final: 0.8832 (mt) REVERT: 1 609 ARG cc_start: 0.7374 (mtm180) cc_final: 0.7122 (ttp-170) REVERT: 2 345 TYR cc_start: 0.8074 (m-80) cc_final: 0.7621 (m-10) REVERT: 3 269 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7212 (tm-30) REVERT: 4 52 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8503 (mm-40) REVERT: 5 104 ASP cc_start: 0.7985 (m-30) cc_final: 0.7292 (t0) REVERT: 5 111 LYS cc_start: 0.8510 (mmmt) cc_final: 0.7745 (ptpp) REVERT: 6 46 ASN cc_start: 0.7143 (p0) cc_final: 0.6914 (p0) REVERT: 7 37 LEU cc_start: 0.6895 (tp) cc_final: 0.6543 (tp) REVERT: 7 101 TYR cc_start: 0.8921 (t80) cc_final: 0.8560 (t80) REVERT: 9 56 ASN cc_start: 0.8315 (p0) cc_final: 0.8071 (p0) REVERT: 9 74 GLU cc_start: 0.7358 (tp30) cc_final: 0.7103 (tp30) REVERT: A 109 LEU cc_start: 0.8189 (tp) cc_final: 0.7946 (tp) REVERT: A 119 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5188 (mt) REVERT: C 119 LEU cc_start: 0.4889 (OUTLIER) cc_final: 0.4676 (mt) REVERT: E 60 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7628 (pttm) REVERT: F 61 MET cc_start: 0.7042 (mmt) cc_final: 0.6752 (mmt) REVERT: F 109 LEU cc_start: 0.7867 (mt) cc_final: 0.7490 (mt) REVERT: G 102 TYR cc_start: 0.6447 (m-80) cc_final: 0.6177 (m-10) REVERT: H 116 PHE cc_start: 0.6443 (m-10) cc_final: 0.6160 (m-80) REVERT: J 81 MET cc_start: 0.7506 (tmm) cc_final: 0.7221 (tmm) REVERT: M 99 ASP cc_start: 0.8687 (t0) cc_final: 0.8405 (t0) REVERT: M 178 LEU cc_start: 0.8292 (tp) cc_final: 0.8004 (tp) REVERT: M 257 MET cc_start: 0.8145 (mmt) cc_final: 0.7593 (mmp) REVERT: M 301 ILE cc_start: 0.8966 (mm) cc_final: 0.8316 (mt) REVERT: M 311 ASN cc_start: 0.8569 (t0) cc_final: 0.8156 (t0) REVERT: P 142 GLU cc_start: 0.7459 (mt-10) cc_final: 0.7081 (mt-10) REVERT: P 151 GLU cc_start: 0.7625 (pt0) cc_final: 0.7293 (pt0) REVERT: R 86 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7604 (mptt) REVERT: S 60 MET cc_start: 0.7926 (ttm) cc_final: 0.7266 (mtp) REVERT: S 68 MET cc_start: 0.7159 (ttp) cc_final: 0.6944 (ttt) REVERT: S 188 GLN cc_start: 0.7304 (mm110) cc_final: 0.6871 (tp-100) REVERT: S 216 LEU cc_start: 0.7976 (mt) cc_final: 0.7384 (mp) REVERT: S 249 PHE cc_start: 0.8838 (t80) cc_final: 0.8607 (t80) REVERT: S 303 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: T 271 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: T 304 TYR cc_start: 0.8759 (m-80) cc_final: 0.8515 (m-80) REVERT: T 342 ARG cc_start: 0.8444 (mmm160) cc_final: 0.8191 (mmt-90) REVERT: T 502 TYR cc_start: 0.7877 (t80) cc_final: 0.7469 (t80) REVERT: T 550 LEU cc_start: 0.8259 (tp) cc_final: 0.8020 (tt) REVERT: U 307 CYS cc_start: 0.8313 (t) cc_final: 0.8083 (t) REVERT: U 551 LYS cc_start: 0.7446 (mttt) cc_final: 0.7157 (ttpp) REVERT: U 557 VAL cc_start: 0.7919 (m) cc_final: 0.7655 (m) REVERT: U 558 LYS cc_start: 0.6046 (tmtt) cc_final: 0.5575 (mmmt) REVERT: U 559 LEU cc_start: 0.7213 (mp) cc_final: 0.6570 (tp) REVERT: V 304 TYR cc_start: 0.9027 (m-80) cc_final: 0.8808 (m-80) REVERT: V 479 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7693 (tpp-160) REVERT: X 198 ASN cc_start: 0.7830 (t0) cc_final: 0.7436 (m-40) REVERT: X 215 GLU cc_start: 0.7152 (tp30) cc_final: 0.6904 (tp30) REVERT: Y 39 TYR cc_start: 0.7401 (p90) cc_final: 0.7069 (p90) REVERT: Y 195 GLU cc_start: 0.6602 (tp30) cc_final: 0.6320 (tp30) REVERT: Y 251 MET cc_start: 0.9230 (ptp) cc_final: 0.8847 (ptm) REVERT: Y 266 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8695 (mm) REVERT: Y 311 GLN cc_start: 0.8618 (pm20) cc_final: 0.8408 (pm20) REVERT: Y 439 ILE cc_start: 0.8859 (pt) cc_final: 0.8645 (mt) REVERT: Z 195 GLU cc_start: 0.6370 (tp30) cc_final: 0.6120 (tp30) REVERT: Z 316 THR cc_start: 0.8654 (m) cc_final: 0.8398 (m) REVERT: Z 359 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7213 (t0) REVERT: Z 401 ARG cc_start: 0.6878 (tpt-90) cc_final: 0.6419 (ptp-170) REVERT: Z 414 GLN cc_start: 0.4582 (tt0) cc_final: 0.4354 (mt0) REVERT: Z 502 MET cc_start: 0.7021 (mtp) cc_final: 0.6551 (mtm) REVERT: Z 562 ASN cc_start: 0.7696 (OUTLIER) cc_final: 0.7075 (m110) outliers start: 111 outliers final: 58 residues processed: 958 average time/residue: 0.5163 time to fit residues: 844.8202 Evaluate side-chains 811 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 746 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 359 ASP Chi-restraints excluded: chain Z residue 562 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 626 optimal weight: 3.9990 chunk 476 optimal weight: 10.0000 chunk 329 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 425 optimal weight: 1.9990 chunk 636 optimal weight: 6.9990 chunk 673 optimal weight: 8.9990 chunk 332 optimal weight: 3.9990 chunk 603 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 GLN 1 535 HIS 2 380 GLN 4 124 ASN 5 107 ASN ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 109 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN H 87 ASN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 GLN P 140 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 264 GLN T 271 GLN ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 HIS ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 294 ASN ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 68 HIS Z 204 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 54658 Z= 0.306 Angle : 0.613 10.535 74121 Z= 0.312 Chirality : 0.044 0.294 8683 Planarity : 0.004 0.057 9504 Dihedral : 5.784 79.910 7664 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 3.48 % Allowed : 17.40 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 7034 helix: 0.09 (0.08), residues: 3841 sheet: -1.96 (0.21), residues: 578 loop : -1.29 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 9 77 HIS 0.020 0.001 HIS 6 97 PHE 0.030 0.002 PHE I 107 TYR 0.030 0.002 TYR C 102 ARG 0.005 0.000 ARG Y 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 767 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8680 (tp) cc_final: 0.8315 (tp) REVERT: 1 69 ASP cc_start: 0.8206 (t0) cc_final: 0.7959 (t0) REVERT: 1 609 ARG cc_start: 0.7447 (mtm180) cc_final: 0.7184 (ttp-170) REVERT: 2 5 GLU cc_start: 0.5604 (tt0) cc_final: 0.3329 (pm20) REVERT: 2 198 LYS cc_start: 0.8271 (ptpt) cc_final: 0.8045 (pttt) REVERT: 2 345 TYR cc_start: 0.8244 (m-80) cc_final: 0.7836 (m-10) REVERT: 2 378 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8179 (tt) REVERT: 2 380 GLN cc_start: 0.7373 (mm110) cc_final: 0.7159 (mm-40) REVERT: 3 197 ASP cc_start: 0.7985 (m-30) cc_final: 0.7781 (m-30) REVERT: 3 269 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7323 (tm-30) REVERT: 5 104 ASP cc_start: 0.7966 (m-30) cc_final: 0.7315 (t0) REVERT: 5 111 LYS cc_start: 0.8534 (mmmt) cc_final: 0.7717 (ptpp) REVERT: 7 37 LEU cc_start: 0.7043 (tp) cc_final: 0.6684 (tp) REVERT: 8 66 ASP cc_start: 0.7455 (t70) cc_final: 0.6986 (t70) REVERT: 9 56 ASN cc_start: 0.8425 (p0) cc_final: 0.8031 (p0) REVERT: 9 74 GLU cc_start: 0.7379 (tp30) cc_final: 0.7143 (tp30) REVERT: A 107 PHE cc_start: 0.7653 (t80) cc_final: 0.7429 (t80) REVERT: A 119 LEU cc_start: 0.6070 (OUTLIER) cc_final: 0.5253 (mt) REVERT: C 119 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4735 (mt) REVERT: E 60 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7554 (pttm) REVERT: E 107 PHE cc_start: 0.5927 (t80) cc_final: 0.5636 (t80) REVERT: G 102 TYR cc_start: 0.6525 (m-80) cc_final: 0.6187 (m-10) REVERT: H 85 LEU cc_start: 0.8896 (tp) cc_final: 0.8657 (tt) REVERT: J 81 MET cc_start: 0.7436 (tmm) cc_final: 0.7195 (tmm) REVERT: M 99 ASP cc_start: 0.8699 (t0) cc_final: 0.8392 (t0) REVERT: M 133 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6844 (tmm160) REVERT: M 178 LEU cc_start: 0.8471 (tp) cc_final: 0.8178 (tp) REVERT: M 243 ASN cc_start: 0.8411 (t0) cc_final: 0.7800 (t0) REVERT: M 257 MET cc_start: 0.8196 (mmt) cc_final: 0.7619 (mmp) REVERT: M 301 ILE cc_start: 0.8985 (mm) cc_final: 0.8381 (mt) REVERT: M 311 ASN cc_start: 0.8652 (t0) cc_final: 0.8308 (t0) REVERT: P 142 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7158 (mt-10) REVERT: P 151 GLU cc_start: 0.7759 (pt0) cc_final: 0.7370 (pt0) REVERT: R 83 GLN cc_start: 0.7017 (mm-40) cc_final: 0.6783 (tt0) REVERT: R 86 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7366 (mptt) REVERT: R 97 TYR cc_start: 0.8133 (m-80) cc_final: 0.7807 (m-80) REVERT: S 60 MET cc_start: 0.8023 (ttm) cc_final: 0.7419 (mtp) REVERT: S 68 MET cc_start: 0.7320 (ttp) cc_final: 0.7026 (ttt) REVERT: S 303 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: T 271 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: T 342 ARG cc_start: 0.8527 (mmm160) cc_final: 0.8276 (mmt-90) REVERT: U 307 CYS cc_start: 0.8337 (t) cc_final: 0.8084 (t) REVERT: U 558 LYS cc_start: 0.6157 (tmtt) cc_final: 0.5732 (mmmt) REVERT: V 452 GLN cc_start: 0.6438 (tp-100) cc_final: 0.6117 (tp-100) REVERT: V 479 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7693 (tpp-160) REVERT: X 198 ASN cc_start: 0.7934 (t0) cc_final: 0.7543 (m-40) REVERT: Y 195 GLU cc_start: 0.6866 (tp30) cc_final: 0.6590 (tp30) REVERT: Y 251 MET cc_start: 0.9327 (ptp) cc_final: 0.9037 (ptm) REVERT: Y 439 ILE cc_start: 0.8910 (pt) cc_final: 0.8670 (mt) REVERT: Z 401 ARG cc_start: 0.6966 (tpt-90) cc_final: 0.6376 (ptp-170) REVERT: Z 441 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7378 (mmm160) REVERT: Z 502 MET cc_start: 0.7194 (mtp) cc_final: 0.6658 (mtm) outliers start: 196 outliers final: 136 residues processed: 898 average time/residue: 0.5446 time to fit residues: 846.7389 Evaluate side-chains 862 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 720 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 CYS Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 170 VAL Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 1 residue 524 THR Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 378 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 180 ILE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 124 ASN Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 5 residue 14 THR Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 5 residue 107 ASN Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 8 residue 56 THR Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 47 VAL Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 55 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 238 GLU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 303 GLU Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 513 ARG Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 498 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 450 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 561 optimal weight: 0.6980 chunk 382 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 501 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 574 optimal weight: 0.4980 chunk 465 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 604 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 97 HIS 6 109 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 140 ASN P 220 ASN ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 54658 Z= 0.175 Angle : 0.558 9.514 74121 Z= 0.283 Chirality : 0.042 0.310 8683 Planarity : 0.004 0.052 9504 Dihedral : 5.574 82.996 7664 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 2.79 % Allowed : 18.96 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.10), residues: 7034 helix: 0.45 (0.09), residues: 3825 sheet: -1.82 (0.21), residues: 582 loop : -1.14 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP 9 77 HIS 0.025 0.001 HIS 6 97 PHE 0.032 0.001 PHE 3 115 TYR 0.045 0.001 TYR C 102 ARG 0.005 0.000 ARG Y 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 800 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 78 PRO cc_start: 0.8371 (Cg_endo) cc_final: 0.8169 (Cg_exo) REVERT: 1 46 LEU cc_start: 0.8667 (tp) cc_final: 0.8288 (tp) REVERT: 1 69 ASP cc_start: 0.8168 (t0) cc_final: 0.7926 (t0) REVERT: 1 289 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8013 (mttm) REVERT: 1 366 MET cc_start: 0.7668 (mmm) cc_final: 0.7375 (tpp) REVERT: 1 416 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7944 (mt) REVERT: 1 427 LYS cc_start: 0.7815 (tptp) cc_final: 0.7562 (ptpp) REVERT: 2 5 GLU cc_start: 0.5676 (tt0) cc_final: 0.3387 (pm20) REVERT: 2 319 ARG cc_start: 0.8403 (ttt90) cc_final: 0.8171 (ttt90) REVERT: 2 345 TYR cc_start: 0.8259 (m-80) cc_final: 0.7765 (m-10) REVERT: 2 380 GLN cc_start: 0.7368 (mm110) cc_final: 0.7138 (mm110) REVERT: 3 185 ASP cc_start: 0.8671 (t70) cc_final: 0.8424 (t0) REVERT: 3 269 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7276 (tm-30) REVERT: 4 178 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8561 (pp) REVERT: 5 35 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8118 (mmm) REVERT: 5 104 ASP cc_start: 0.7965 (m-30) cc_final: 0.7340 (t0) REVERT: 5 111 LYS cc_start: 0.8456 (mmmt) cc_final: 0.7695 (pttt) REVERT: 7 37 LEU cc_start: 0.6917 (tp) cc_final: 0.6533 (tp) REVERT: 7 101 TYR cc_start: 0.8908 (t80) cc_final: 0.8531 (t80) REVERT: 9 56 ASN cc_start: 0.8392 (p0) cc_final: 0.8051 (p0) REVERT: A 119 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5213 (mt) REVERT: C 119 LEU cc_start: 0.4988 (OUTLIER) cc_final: 0.4731 (mt) REVERT: E 60 LYS cc_start: 0.7900 (ptpt) cc_final: 0.7567 (pttm) REVERT: G 102 TYR cc_start: 0.6443 (m-80) cc_final: 0.6185 (m-10) REVERT: J 81 MET cc_start: 0.7370 (tmm) cc_final: 0.7138 (tmm) REVERT: M 99 ASP cc_start: 0.8675 (t0) cc_final: 0.8428 (t0) REVERT: M 133 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.6942 (tmm160) REVERT: M 178 LEU cc_start: 0.8354 (tp) cc_final: 0.8126 (tp) REVERT: M 243 ASN cc_start: 0.8280 (t0) cc_final: 0.7725 (t0) REVERT: M 257 MET cc_start: 0.8163 (mmt) cc_final: 0.7558 (mmp) REVERT: M 301 ILE cc_start: 0.8964 (mm) cc_final: 0.8361 (mt) REVERT: M 311 ASN cc_start: 0.8611 (t0) cc_final: 0.8276 (t0) REVERT: P 142 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7186 (mt-10) REVERT: P 151 GLU cc_start: 0.7767 (pt0) cc_final: 0.7341 (pt0) REVERT: P 163 ASP cc_start: 0.6304 (t0) cc_final: 0.5871 (t0) REVERT: R 97 TYR cc_start: 0.8103 (m-80) cc_final: 0.7775 (m-80) REVERT: S 60 MET cc_start: 0.8001 (ttm) cc_final: 0.7314 (mtp) REVERT: S 68 MET cc_start: 0.7282 (ttp) cc_final: 0.7013 (ttt) REVERT: S 87 ARG cc_start: 0.7079 (ttp-110) cc_final: 0.6830 (mtp180) REVERT: S 186 ASN cc_start: 0.7504 (t0) cc_final: 0.7257 (t0) REVERT: T 271 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: T 304 TYR cc_start: 0.8892 (m-80) cc_final: 0.8636 (m-80) REVERT: T 342 ARG cc_start: 0.8513 (mmm160) cc_final: 0.8239 (mmt-90) REVERT: T 508 PHE cc_start: 0.7644 (m-80) cc_final: 0.7285 (m-80) REVERT: U 246 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7759 (t0) REVERT: U 307 CYS cc_start: 0.8303 (t) cc_final: 0.7963 (t) REVERT: U 558 LYS cc_start: 0.6185 (tmtt) cc_final: 0.5717 (mmmt) REVERT: U 559 LEU cc_start: 0.7346 (mp) cc_final: 0.6704 (tp) REVERT: V 304 TYR cc_start: 0.9056 (m-80) cc_final: 0.8794 (m-80) REVERT: V 452 GLN cc_start: 0.6353 (tp-100) cc_final: 0.6079 (tp-100) REVERT: V 479 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.7758 (tpp-160) REVERT: X 198 ASN cc_start: 0.7867 (t0) cc_final: 0.7452 (m-40) REVERT: X 471 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7217 (tm-30) REVERT: Y 195 GLU cc_start: 0.6780 (tp30) cc_final: 0.6511 (tp30) REVERT: Y 251 MET cc_start: 0.9251 (ptp) cc_final: 0.8907 (ptm) REVERT: Y 266 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8572 (mm) REVERT: Z 401 ARG cc_start: 0.6879 (tpt-90) cc_final: 0.6406 (ptp-170) REVERT: Z 404 GLN cc_start: 0.7428 (mt0) cc_final: 0.7179 (mt0) REVERT: Z 441 ARG cc_start: 0.7660 (mmm-85) cc_final: 0.7418 (mmm160) REVERT: Z 502 MET cc_start: 0.7131 (mtp) cc_final: 0.6612 (mtm) outliers start: 157 outliers final: 109 residues processed: 902 average time/residue: 0.5316 time to fit residues: 831.3505 Evaluate side-chains 837 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 719 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 416 LEU Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 8 LEU Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 61 MET Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain P residue 45 GLN Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 255 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 421 LEU Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 246 ASN Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 226 optimal weight: 6.9990 chunk 606 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 395 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 674 optimal weight: 4.9990 chunk 559 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 59 GLN 6 97 HIS 6 109 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN J 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 66 GLN S 77 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 54658 Z= 0.240 Angle : 0.584 10.546 74121 Z= 0.296 Chirality : 0.043 0.312 8683 Planarity : 0.004 0.061 9504 Dihedral : 5.562 81.777 7664 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.74 % Rotamer: Outliers : 3.39 % Allowed : 19.83 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 7034 helix: 0.58 (0.09), residues: 3827 sheet: -1.81 (0.21), residues: 590 loop : -1.08 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP 9 77 HIS 0.012 0.001 HIS 6 97 PHE 0.032 0.001 PHE E 107 TYR 0.039 0.001 TYR C 102 ARG 0.006 0.000 ARG 2 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 746 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8676 (tp) cc_final: 0.8319 (tp) REVERT: 1 69 ASP cc_start: 0.8176 (t0) cc_final: 0.7963 (t0) REVERT: 1 289 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8044 (mttm) REVERT: 1 366 MET cc_start: 0.7688 (mmm) cc_final: 0.7453 (tpp) REVERT: 1 427 LYS cc_start: 0.7804 (tptp) cc_final: 0.7593 (ptpp) REVERT: 2 5 GLU cc_start: 0.5694 (tt0) cc_final: 0.3404 (pm20) REVERT: 2 198 LYS cc_start: 0.8280 (ptpt) cc_final: 0.8058 (pttt) REVERT: 2 319 ARG cc_start: 0.8385 (ttt90) cc_final: 0.8180 (ttt90) REVERT: 2 345 TYR cc_start: 0.8303 (m-80) cc_final: 0.7753 (m-10) REVERT: 3 185 ASP cc_start: 0.8693 (t70) cc_final: 0.8452 (t0) REVERT: 3 269 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7321 (tm-30) REVERT: 4 178 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8537 (pp) REVERT: 5 35 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8191 (mmm) REVERT: 5 104 ASP cc_start: 0.7983 (m-30) cc_final: 0.7354 (t0) REVERT: 5 111 LYS cc_start: 0.8499 (mmmt) cc_final: 0.7606 (ptpp) REVERT: 7 37 LEU cc_start: 0.7041 (tp) cc_final: 0.6624 (tp) REVERT: 7 101 TYR cc_start: 0.8965 (t80) cc_final: 0.8558 (t80) REVERT: 8 66 ASP cc_start: 0.7427 (t70) cc_final: 0.6988 (t70) REVERT: 9 56 ASN cc_start: 0.8425 (p0) cc_final: 0.8013 (p0) REVERT: 9 77 TRP cc_start: 0.7656 (OUTLIER) cc_final: 0.7432 (p-90) REVERT: A 119 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.4972 (mt) REVERT: C 119 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4777 (mt) REVERT: E 60 LYS cc_start: 0.7745 (ptpt) cc_final: 0.7374 (pttm) REVERT: E 107 PHE cc_start: 0.5796 (t80) cc_final: 0.5578 (t80) REVERT: F 61 MET cc_start: 0.7294 (mmt) cc_final: 0.6911 (mmp) REVERT: G 102 TYR cc_start: 0.6482 (m-80) cc_final: 0.6225 (m-10) REVERT: J 81 MET cc_start: 0.7390 (tmm) cc_final: 0.7137 (tmm) REVERT: M 99 ASP cc_start: 0.8694 (t0) cc_final: 0.8411 (t0) REVERT: M 133 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.6975 (tmm160) REVERT: M 178 LEU cc_start: 0.8378 (tp) cc_final: 0.8132 (tp) REVERT: M 243 ASN cc_start: 0.8323 (t0) cc_final: 0.7948 (t0) REVERT: M 257 MET cc_start: 0.8191 (mmt) cc_final: 0.7578 (mmp) REVERT: M 301 ILE cc_start: 0.9006 (mm) cc_final: 0.8402 (mt) REVERT: M 311 ASN cc_start: 0.8631 (t0) cc_final: 0.8315 (t0) REVERT: P 142 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7243 (mt-10) REVERT: P 151 GLU cc_start: 0.7799 (pt0) cc_final: 0.7342 (pt0) REVERT: R 86 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7428 (mptt) REVERT: R 135 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: S 60 MET cc_start: 0.8031 (ttm) cc_final: 0.7366 (mtp) REVERT: S 68 MET cc_start: 0.7368 (ttp) cc_final: 0.7109 (ttt) REVERT: S 186 ASN cc_start: 0.7463 (t0) cc_final: 0.7196 (t0) REVERT: T 284 TYR cc_start: 0.8579 (m-80) cc_final: 0.8289 (m-80) REVERT: T 342 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8280 (mmt-90) REVERT: T 508 PHE cc_start: 0.7670 (m-80) cc_final: 0.7396 (m-80) REVERT: U 307 CYS cc_start: 0.8324 (t) cc_final: 0.8016 (t) REVERT: U 558 LYS cc_start: 0.6157 (tmtt) cc_final: 0.5698 (mmmt) REVERT: U 559 LEU cc_start: 0.7428 (mp) cc_final: 0.6759 (tp) REVERT: V 210 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7813 (t0) REVERT: V 452 GLN cc_start: 0.6436 (tp-100) cc_final: 0.6187 (tp-100) REVERT: V 479 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.7692 (tpp-160) REVERT: X 198 ASN cc_start: 0.7870 (t0) cc_final: 0.7451 (m-40) REVERT: X 471 GLN cc_start: 0.7808 (tp-100) cc_final: 0.7217 (tm-30) REVERT: Y 195 GLU cc_start: 0.6862 (tp30) cc_final: 0.6583 (tp30) REVERT: Z 401 ARG cc_start: 0.6936 (tpt-90) cc_final: 0.6339 (ptp-170) REVERT: Z 441 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7398 (mmm160) REVERT: Z 502 MET cc_start: 0.7160 (mtp) cc_final: 0.6646 (mtm) outliers start: 191 outliers final: 146 residues processed: 875 average time/residue: 0.4965 time to fit residues: 750.0004 Evaluate side-chains 866 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 712 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 31 CYS Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 384 THR Chi-restraints excluded: chain 1 residue 424 VAL Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 47 VAL Chi-restraints excluded: chain 9 residue 77 TRP Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain P residue 52 GLN Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 185 HIS Chi-restraints excluded: chain S residue 255 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 357 LEU Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 167 LEU Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 421 LEU Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 169 LEU Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 489 VAL Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 650 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 384 optimal weight: 0.8980 chunk 492 optimal weight: 4.9990 chunk 381 optimal weight: 0.8980 chunk 567 optimal weight: 0.5980 chunk 376 optimal weight: 1.9990 chunk 671 optimal weight: 0.2980 chunk 420 optimal weight: 6.9990 chunk 409 optimal weight: 0.7980 chunk 310 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 124 ASN 6 97 HIS 6 109 GLN ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 278 GLN Z 157 GLN Z 404 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 54658 Z= 0.161 Angle : 0.563 11.721 74121 Z= 0.284 Chirality : 0.042 0.336 8683 Planarity : 0.004 0.052 9504 Dihedral : 5.387 83.809 7664 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 2.91 % Allowed : 20.45 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.10), residues: 7034 helix: 0.77 (0.09), residues: 3832 sheet: -1.61 (0.21), residues: 578 loop : -0.99 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP 9 77 HIS 0.022 0.001 HIS 6 97 PHE 0.052 0.001 PHE 3 115 TYR 0.045 0.001 TYR C 102 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 791 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8602 (tp) cc_final: 0.8235 (tp) REVERT: 1 69 ASP cc_start: 0.8146 (t0) cc_final: 0.7929 (t0) REVERT: 1 289 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8015 (mttm) REVERT: 1 366 MET cc_start: 0.7647 (mmm) cc_final: 0.7378 (tpp) REVERT: 2 5 GLU cc_start: 0.5678 (tt0) cc_final: 0.3394 (pm20) REVERT: 2 282 VAL cc_start: 0.8805 (m) cc_final: 0.8304 (t) REVERT: 2 345 TYR cc_start: 0.8221 (m-80) cc_final: 0.7718 (m-10) REVERT: 2 378 LEU cc_start: 0.8145 (tt) cc_final: 0.7935 (tt) REVERT: 3 179 GLN cc_start: 0.7685 (mt0) cc_final: 0.7259 (mt0) REVERT: 3 269 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7237 (tm-30) REVERT: 4 178 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8635 (pp) REVERT: 5 27 ASP cc_start: 0.8779 (t0) cc_final: 0.8232 (t0) REVERT: 5 35 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8173 (mmm) REVERT: 5 104 ASP cc_start: 0.8060 (m-30) cc_final: 0.7356 (t0) REVERT: 5 107 ASN cc_start: 0.7878 (t0) cc_final: 0.7413 (t0) REVERT: 5 111 LYS cc_start: 0.8461 (mmmt) cc_final: 0.7578 (ptpp) REVERT: 7 101 TYR cc_start: 0.8824 (t80) cc_final: 0.8432 (t80) REVERT: 9 56 ASN cc_start: 0.8379 (p0) cc_final: 0.7983 (p0) REVERT: A 105 LEU cc_start: 0.7109 (tt) cc_final: 0.6086 (mm) REVERT: A 119 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5280 (mt) REVERT: E 60 LYS cc_start: 0.7534 (ptpt) cc_final: 0.7226 (pttm) REVERT: F 61 MET cc_start: 0.6953 (mmt) cc_final: 0.6571 (mmp) REVERT: G 102 TYR cc_start: 0.6376 (m-80) cc_final: 0.6117 (m-10) REVERT: J 81 MET cc_start: 0.7311 (tmm) cc_final: 0.7089 (tmm) REVERT: J 107 PHE cc_start: 0.6182 (t80) cc_final: 0.5879 (t80) REVERT: M 99 ASP cc_start: 0.8676 (t0) cc_final: 0.8470 (t0) REVERT: M 133 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7019 (tmm160) REVERT: M 243 ASN cc_start: 0.8184 (t0) cc_final: 0.7793 (t0) REVERT: M 257 MET cc_start: 0.8181 (mmt) cc_final: 0.7561 (mmp) REVERT: M 301 ILE cc_start: 0.8986 (mm) cc_final: 0.8393 (mt) REVERT: M 311 ASN cc_start: 0.8581 (t0) cc_final: 0.8258 (t0) REVERT: P 142 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7153 (mt-10) REVERT: P 151 GLU cc_start: 0.7761 (pt0) cc_final: 0.7306 (pt0) REVERT: P 163 ASP cc_start: 0.6220 (t0) cc_final: 0.5739 (t0) REVERT: R 86 LYS cc_start: 0.7794 (mmtt) cc_final: 0.7407 (mptt) REVERT: S 60 MET cc_start: 0.7962 (ttm) cc_final: 0.7258 (mtp) REVERT: S 68 MET cc_start: 0.7262 (ttp) cc_final: 0.6983 (ttt) REVERT: S 133 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.3631 (pp20) REVERT: S 186 ASN cc_start: 0.7462 (t0) cc_final: 0.7229 (t0) REVERT: T 284 TYR cc_start: 0.8587 (m-80) cc_final: 0.8295 (m-80) REVERT: T 304 TYR cc_start: 0.8831 (m-80) cc_final: 0.8612 (m-80) REVERT: T 342 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8258 (mmt-90) REVERT: U 307 CYS cc_start: 0.8279 (t) cc_final: 0.7902 (t) REVERT: U 558 LYS cc_start: 0.6088 (tmtt) cc_final: 0.5655 (mmmt) REVERT: U 559 LEU cc_start: 0.7274 (mp) cc_final: 0.6828 (tp) REVERT: V 210 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7585 (t0) REVERT: V 304 TYR cc_start: 0.9053 (m-80) cc_final: 0.8749 (m-80) REVERT: V 452 GLN cc_start: 0.6490 (tp-100) cc_final: 0.6233 (tp-100) REVERT: V 474 LEU cc_start: 0.8227 (tt) cc_final: 0.7808 (tp) REVERT: V 497 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: X 198 ASN cc_start: 0.7817 (t0) cc_final: 0.7428 (m-40) REVERT: X 471 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7165 (tm-30) REVERT: Y 194 MET cc_start: 0.8176 (mmt) cc_final: 0.7554 (mpp) REVERT: Y 195 GLU cc_start: 0.6573 (tp30) cc_final: 0.6339 (tp30) REVERT: Y 266 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8456 (mm) REVERT: Z 386 MET cc_start: 0.7374 (mmm) cc_final: 0.6943 (ttm) REVERT: Z 401 ARG cc_start: 0.6873 (tpt-90) cc_final: 0.6372 (ptp-170) REVERT: Z 441 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7350 (mmm160) REVERT: Z 502 MET cc_start: 0.7090 (mtp) cc_final: 0.6604 (mtm) outliers start: 164 outliers final: 124 residues processed: 896 average time/residue: 0.5025 time to fit residues: 778.2543 Evaluate side-chains 853 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 721 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 PHE Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 7 SER Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 9 residue 47 VAL Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 255 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 103 VAL Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 497 GLN Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 505 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 415 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 401 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 427 optimal weight: 1.9990 chunk 457 optimal weight: 7.9990 chunk 332 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 528 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 206 ASN ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 26 HIS 8 78 HIS D 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 220 ASN ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 54658 Z= 0.283 Angle : 0.620 13.766 74121 Z= 0.312 Chirality : 0.044 0.415 8683 Planarity : 0.004 0.051 9504 Dihedral : 5.527 80.134 7664 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.18 % Allowed : 21.00 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.10), residues: 7034 helix: 0.73 (0.09), residues: 3830 sheet: -1.71 (0.21), residues: 589 loop : -1.01 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP 9 77 HIS 0.017 0.001 HIS 6 97 PHE 0.041 0.002 PHE E 107 TYR 0.039 0.002 TYR C 102 ARG 0.006 0.000 ARG Y 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 721 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8644 (tp) cc_final: 0.8272 (tp) REVERT: 1 69 ASP cc_start: 0.8136 (t0) cc_final: 0.7911 (t0) REVERT: 1 289 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8085 (mttp) REVERT: 1 366 MET cc_start: 0.7672 (mmm) cc_final: 0.7438 (tpp) REVERT: 2 5 GLU cc_start: 0.5742 (tt0) cc_final: 0.3404 (pm20) REVERT: 2 198 LYS cc_start: 0.8290 (ptpt) cc_final: 0.8045 (pttt) REVERT: 2 319 ARG cc_start: 0.8337 (ttt90) cc_final: 0.8129 (ttt90) REVERT: 2 345 TYR cc_start: 0.8289 (m-80) cc_final: 0.7756 (m-10) REVERT: 3 196 ASP cc_start: 0.7965 (t0) cc_final: 0.7695 (t0) REVERT: 3 269 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7523 (tm-30) REVERT: 4 178 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8573 (pp) REVERT: 5 35 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8137 (mmm) REVERT: 5 104 ASP cc_start: 0.8029 (m-30) cc_final: 0.7368 (t0) REVERT: 5 107 ASN cc_start: 0.7993 (t0) cc_final: 0.7546 (t0) REVERT: 5 111 LYS cc_start: 0.8587 (mmmt) cc_final: 0.7659 (ptpp) REVERT: 7 37 LEU cc_start: 0.7051 (tp) cc_final: 0.6573 (tp) REVERT: 8 66 ASP cc_start: 0.7434 (t70) cc_final: 0.6995 (t70) REVERT: 9 12 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 119 LEU cc_start: 0.5756 (OUTLIER) cc_final: 0.4988 (mt) REVERT: E 60 LYS cc_start: 0.7447 (ptpt) cc_final: 0.7160 (pttm) REVERT: G 102 TYR cc_start: 0.6471 (m-80) cc_final: 0.6217 (m-10) REVERT: J 95 ILE cc_start: 0.5502 (OUTLIER) cc_final: 0.5277 (tp) REVERT: M 99 ASP cc_start: 0.8712 (t0) cc_final: 0.8430 (t0) REVERT: M 133 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.6996 (tmm160) REVERT: M 243 ASN cc_start: 0.8424 (t0) cc_final: 0.8036 (t0) REVERT: M 275 PHE cc_start: 0.6643 (m-80) cc_final: 0.6309 (m-10) REVERT: M 301 ILE cc_start: 0.9027 (mm) cc_final: 0.8434 (mt) REVERT: M 311 ASN cc_start: 0.8623 (t0) cc_final: 0.8312 (t0) REVERT: P 142 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7217 (mt-10) REVERT: P 151 GLU cc_start: 0.7821 (pt0) cc_final: 0.7421 (pt0) REVERT: P 163 ASP cc_start: 0.6388 (t0) cc_final: 0.5923 (t0) REVERT: R 86 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7590 (mptt) REVERT: R 135 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: S 60 MET cc_start: 0.8011 (ttm) cc_final: 0.7326 (mtp) REVERT: S 68 MET cc_start: 0.7360 (ttp) cc_final: 0.7073 (ttt) REVERT: S 133 GLU cc_start: 0.5370 (OUTLIER) cc_final: 0.3991 (pp20) REVERT: S 186 ASN cc_start: 0.7551 (t0) cc_final: 0.7299 (t0) REVERT: T 342 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8284 (mmt-90) REVERT: T 508 PHE cc_start: 0.7682 (m-80) cc_final: 0.7350 (m-80) REVERT: U 307 CYS cc_start: 0.8297 (t) cc_final: 0.7995 (t) REVERT: U 558 LYS cc_start: 0.6136 (tmtt) cc_final: 0.5737 (mmmt) REVERT: U 559 LEU cc_start: 0.7443 (mp) cc_final: 0.6942 (tp) REVERT: V 210 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7691 (t0) REVERT: V 439 MET cc_start: 0.8634 (tpp) cc_final: 0.8414 (tpp) REVERT: V 452 GLN cc_start: 0.6440 (tp-100) cc_final: 0.6219 (tp-100) REVERT: V 474 LEU cc_start: 0.8245 (tt) cc_final: 0.7894 (tp) REVERT: V 497 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: X 198 ASN cc_start: 0.7876 (t0) cc_final: 0.7502 (m-40) REVERT: X 471 GLN cc_start: 0.7807 (tp-100) cc_final: 0.7200 (tm-30) REVERT: Y 195 GLU cc_start: 0.6644 (tp30) cc_final: 0.6387 (tp30) REVERT: Z 195 GLU cc_start: 0.6466 (tp30) cc_final: 0.5854 (tp30) REVERT: Z 386 MET cc_start: 0.7531 (mmm) cc_final: 0.7083 (ttm) REVERT: Z 401 ARG cc_start: 0.6946 (tpt-90) cc_final: 0.6357 (ptp-170) REVERT: Z 502 MET cc_start: 0.7192 (mtp) cc_final: 0.6676 (mtm) outliers start: 179 outliers final: 148 residues processed: 837 average time/residue: 0.5710 time to fit residues: 836.8439 Evaluate side-chains 857 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 700 time to evaluate : 4.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 PHE Chi-restraints excluded: chain 0 residue 31 CYS Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 384 THR Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 198 VAL Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 7 SER Chi-restraints excluded: chain 5 residue 14 THR Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 117 SER Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 47 VAL Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 104 ILE Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 255 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 164 THR Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 497 GLN Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 66 GLU Chi-restraints excluded: chain X residue 97 VAL Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 127 GLU Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain X residue 568 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 611 optimal weight: 0.7980 chunk 643 optimal weight: 8.9990 chunk 587 optimal weight: 1.9990 chunk 626 optimal weight: 0.9990 chunk 376 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 491 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 565 optimal weight: 0.9990 chunk 592 optimal weight: 0.9990 chunk 623 optimal weight: 0.3980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 124 ASN 6 97 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS D 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 271 GLN ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 196 GLN ** V 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 54658 Z= 0.167 Angle : 0.572 13.528 74121 Z= 0.287 Chirality : 0.042 0.306 8683 Planarity : 0.004 0.052 9504 Dihedral : 5.353 82.014 7664 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.41 % Favored : 96.52 % Rotamer: Outliers : 2.68 % Allowed : 21.78 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.10), residues: 7034 helix: 0.91 (0.09), residues: 3837 sheet: -1.54 (0.22), residues: 572 loop : -0.91 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP 9 77 HIS 0.013 0.001 HIS 8 78 PHE 0.035 0.001 PHE E 107 TYR 0.042 0.001 TYR C 102 ARG 0.006 0.000 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 766 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 34 ARG cc_start: 0.6604 (tpt170) cc_final: 0.6354 (mmt180) REVERT: 1 46 LEU cc_start: 0.8568 (tp) cc_final: 0.8212 (tp) REVERT: 1 69 ASP cc_start: 0.8096 (t0) cc_final: 0.7891 (t0) REVERT: 1 289 LYS cc_start: 0.8281 (mmtt) cc_final: 0.8003 (mttm) REVERT: 1 366 MET cc_start: 0.7645 (mmm) cc_final: 0.7401 (tpp) REVERT: 1 553 ILE cc_start: 0.8938 (mm) cc_final: 0.8733 (mm) REVERT: 2 5 GLU cc_start: 0.5648 (tt0) cc_final: 0.3379 (pm20) REVERT: 2 194 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: 2 345 TYR cc_start: 0.8166 (m-80) cc_final: 0.7693 (m-10) REVERT: 3 179 GLN cc_start: 0.7699 (mt0) cc_final: 0.7279 (mt0) REVERT: 3 196 ASP cc_start: 0.7990 (t0) cc_final: 0.7665 (t0) REVERT: 3 269 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7468 (tm-30) REVERT: 4 178 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8603 (pp) REVERT: 5 27 ASP cc_start: 0.8801 (t0) cc_final: 0.8214 (t0) REVERT: 5 35 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: 5 104 ASP cc_start: 0.8068 (m-30) cc_final: 0.7335 (t0) REVERT: 5 111 LYS cc_start: 0.8504 (mmmt) cc_final: 0.7553 (ptpp) REVERT: 6 117 SER cc_start: 0.8858 (p) cc_final: 0.8618 (t) REVERT: 7 101 TYR cc_start: 0.8785 (t80) cc_final: 0.8402 (t80) REVERT: 8 81 LYS cc_start: 0.7239 (mmmm) cc_final: 0.6747 (mtmt) REVERT: 9 56 ASN cc_start: 0.7889 (p0) cc_final: 0.7652 (p0) REVERT: A 105 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.5875 (mm) REVERT: A 119 LEU cc_start: 0.5675 (OUTLIER) cc_final: 0.5028 (mt) REVERT: B 61 MET cc_start: 0.7545 (ppp) cc_final: 0.7343 (ppp) REVERT: G 102 TYR cc_start: 0.6413 (m-80) cc_final: 0.6177 (m-10) REVERT: I 115 LEU cc_start: 0.7741 (tt) cc_final: 0.7474 (mp) REVERT: M 99 ASP cc_start: 0.8704 (t0) cc_final: 0.8481 (t0) REVERT: M 133 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6943 (tmm160) REVERT: M 147 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8272 (p) REVERT: M 243 ASN cc_start: 0.8222 (t0) cc_final: 0.7774 (t0) REVERT: M 275 PHE cc_start: 0.6449 (m-80) cc_final: 0.6171 (m-10) REVERT: M 301 ILE cc_start: 0.8992 (mm) cc_final: 0.8384 (mt) REVERT: M 311 ASN cc_start: 0.8558 (t0) cc_final: 0.8240 (t0) REVERT: P 142 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7189 (mt-10) REVERT: P 151 GLU cc_start: 0.7808 (pt0) cc_final: 0.7382 (pt0) REVERT: R 86 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7477 (mptt) REVERT: R 135 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: S 55 LYS cc_start: 0.7869 (pttt) cc_final: 0.7578 (mmmt) REVERT: S 60 MET cc_start: 0.8007 (ttm) cc_final: 0.7390 (mtp) REVERT: S 68 MET cc_start: 0.7262 (ttp) cc_final: 0.6998 (ttt) REVERT: S 133 GLU cc_start: 0.5251 (OUTLIER) cc_final: 0.3839 (pp20) REVERT: S 186 ASN cc_start: 0.7499 (t0) cc_final: 0.7243 (t0) REVERT: S 201 ILE cc_start: 0.8426 (mm) cc_final: 0.8209 (mm) REVERT: T 284 TYR cc_start: 0.8594 (m-80) cc_final: 0.8342 (m-80) REVERT: T 304 TYR cc_start: 0.8780 (m-80) cc_final: 0.8558 (m-80) REVERT: T 309 MET cc_start: 0.8085 (mtt) cc_final: 0.7798 (mtt) REVERT: T 342 ARG cc_start: 0.8499 (mmm160) cc_final: 0.8236 (mmt-90) REVERT: T 508 PHE cc_start: 0.7790 (m-80) cc_final: 0.7449 (m-80) REVERT: U 307 CYS cc_start: 0.8322 (t) cc_final: 0.7998 (t) REVERT: U 558 LYS cc_start: 0.6007 (tmtt) cc_final: 0.5618 (mmmt) REVERT: U 559 LEU cc_start: 0.7289 (mp) cc_final: 0.6888 (tp) REVERT: V 210 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7499 (t0) REVERT: V 304 TYR cc_start: 0.9048 (m-80) cc_final: 0.8737 (m-80) REVERT: V 474 LEU cc_start: 0.8183 (tt) cc_final: 0.7823 (tp) REVERT: V 497 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: X 82 ASP cc_start: 0.6402 (t70) cc_final: 0.5980 (t70) REVERT: X 198 ASN cc_start: 0.7824 (t0) cc_final: 0.7409 (m-40) REVERT: X 471 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7197 (tm-30) REVERT: Y 194 MET cc_start: 0.8523 (tpp) cc_final: 0.7448 (mpp) REVERT: Y 195 GLU cc_start: 0.6610 (tp30) cc_final: 0.6388 (tp30) REVERT: Y 266 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8444 (mm) REVERT: Z 370 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6358 (mt-10) REVERT: Z 386 MET cc_start: 0.7113 (mmm) cc_final: 0.6819 (ttm) REVERT: Z 401 ARG cc_start: 0.6840 (tpt-90) cc_final: 0.6375 (ptp-170) REVERT: Z 502 MET cc_start: 0.7097 (mtp) cc_final: 0.6622 (mtm) outliers start: 151 outliers final: 121 residues processed: 861 average time/residue: 0.4902 time to fit residues: 727.7758 Evaluate side-chains 846 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 713 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 PHE Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 194 ASP Chi-restraints excluded: chain 2 residue 228 ILE Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 7 SER Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 35 ILE Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 28 VAL Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 7 residue 103 LEU Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 9 residue 47 VAL Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 77 TRP Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 147 SER Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 255 LEU Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 210 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 497 GLN Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 697 random chunks: chunk 411 optimal weight: 1.9990 chunk 661 optimal weight: 7.9990 chunk 404 optimal weight: 3.9990 chunk 314 optimal weight: 7.9990 chunk 460 optimal weight: 0.6980 chunk 694 optimal weight: 8.9990 chunk 639 optimal weight: 0.5980 chunk 552 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 427 optimal weight: 5.9990 chunk 339 optimal weight: 20.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 380 GLN 5 107 ASN ** 5 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 97 HIS ** 7 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 78 HIS D 98 GLN ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 386 GLN ** U 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 GLN X 42 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 54658 Z= 0.289 Angle : 0.632 12.416 74121 Z= 0.319 Chirality : 0.045 0.450 8683 Planarity : 0.004 0.050 9504 Dihedral : 5.501 76.911 7664 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 2.75 % Allowed : 21.96 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7034 helix: 0.78 (0.09), residues: 3845 sheet: -1.65 (0.22), residues: 571 loop : -0.95 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP 9 77 HIS 0.013 0.001 HIS 8 78 PHE 0.039 0.002 PHE T 489 TYR 0.041 0.002 TYR C 102 ARG 0.010 0.000 ARG S 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14068 Ramachandran restraints generated. 7034 Oldfield, 0 Emsley, 7034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 714 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 46 LEU cc_start: 0.8651 (tp) cc_final: 0.8273 (tp) REVERT: 1 69 ASP cc_start: 0.8147 (t0) cc_final: 0.7929 (t0) REVERT: 1 289 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8083 (mttm) REVERT: 1 366 MET cc_start: 0.7688 (mmm) cc_final: 0.7473 (tpp) REVERT: 2 5 GLU cc_start: 0.5589 (tt0) cc_final: 0.3519 (pm20) REVERT: 2 198 LYS cc_start: 0.8433 (ptpt) cc_final: 0.8148 (pttt) REVERT: 2 345 TYR cc_start: 0.8219 (m-80) cc_final: 0.7744 (m-10) REVERT: 2 380 GLN cc_start: 0.7392 (mm110) cc_final: 0.7118 (mm110) REVERT: 3 269 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7567 (tm-30) REVERT: 4 178 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8561 (pp) REVERT: 5 35 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8046 (mmm) REVERT: 5 104 ASP cc_start: 0.8015 (m-30) cc_final: 0.7328 (t0) REVERT: 5 111 LYS cc_start: 0.8454 (mmmt) cc_final: 0.7551 (ptpp) REVERT: 7 37 LEU cc_start: 0.7029 (tp) cc_final: 0.6527 (tp) REVERT: 7 101 TYR cc_start: 0.8970 (t80) cc_final: 0.8615 (t80) REVERT: 8 66 ASP cc_start: 0.7445 (t70) cc_final: 0.7006 (t70) REVERT: 8 81 LYS cc_start: 0.7342 (mmmm) cc_final: 0.6795 (mtmt) REVERT: 9 56 ASN cc_start: 0.8023 (p0) cc_final: 0.7610 (p0) REVERT: A 81 MET cc_start: 0.7561 (tmm) cc_final: 0.7214 (ttp) REVERT: A 105 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.5796 (mt) REVERT: A 119 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5072 (mt) REVERT: D 61 MET cc_start: 0.8214 (mmm) cc_final: 0.7718 (mmm) REVERT: H 85 LEU cc_start: 0.8637 (tp) cc_final: 0.8428 (tt) REVERT: I 115 LEU cc_start: 0.7816 (tt) cc_final: 0.7412 (mp) REVERT: M 99 ASP cc_start: 0.8712 (t0) cc_final: 0.8434 (t0) REVERT: M 133 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7166 (tmm160) REVERT: M 243 ASN cc_start: 0.8425 (t0) cc_final: 0.8027 (t0) REVERT: M 275 PHE cc_start: 0.6585 (m-80) cc_final: 0.6293 (m-10) REVERT: M 301 ILE cc_start: 0.9022 (mm) cc_final: 0.8445 (mt) REVERT: M 311 ASN cc_start: 0.8614 (t0) cc_final: 0.8320 (t0) REVERT: P 142 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7199 (mt-10) REVERT: P 151 GLU cc_start: 0.7774 (pt0) cc_final: 0.7408 (pt0) REVERT: R 86 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7634 (mptt) REVERT: R 135 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: S 60 MET cc_start: 0.7991 (ttm) cc_final: 0.7337 (mtp) REVERT: S 68 MET cc_start: 0.7355 (ttp) cc_final: 0.7087 (ttt) REVERT: S 133 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.3975 (pp20) REVERT: S 186 ASN cc_start: 0.7565 (t0) cc_final: 0.7325 (t0) REVERT: T 342 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8268 (mmt-90) REVERT: T 439 MET cc_start: 0.7923 (tpp) cc_final: 0.7683 (tpp) REVERT: U 307 CYS cc_start: 0.8348 (t) cc_final: 0.7984 (t) REVERT: U 558 LYS cc_start: 0.6139 (tmtt) cc_final: 0.5700 (mmmt) REVERT: V 439 MET cc_start: 0.8691 (tpp) cc_final: 0.8017 (mtt) REVERT: V 497 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: X 82 ASP cc_start: 0.6356 (t70) cc_final: 0.6066 (t70) REVERT: X 198 ASN cc_start: 0.7874 (t0) cc_final: 0.7504 (m-40) REVERT: X 294 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8678 (t0) REVERT: X 471 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7206 (tm-30) REVERT: Y 195 GLU cc_start: 0.6717 (tp30) cc_final: 0.6428 (tp30) REVERT: Z 195 GLU cc_start: 0.6488 (tp30) cc_final: 0.5857 (tp30) REVERT: Z 401 ARG cc_start: 0.6966 (tpt-90) cc_final: 0.6382 (ptp-170) REVERT: Z 441 ARG cc_start: 0.7679 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: Z 502 MET cc_start: 0.7195 (mtp) cc_final: 0.6708 (mtm) outliers start: 155 outliers final: 134 residues processed: 818 average time/residue: 0.4930 time to fit residues: 694.5084 Evaluate side-chains 831 residues out of total 5633 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 688 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 14 PHE Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 74 VAL Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 178 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 249 ILE Chi-restraints excluded: chain 1 residue 384 THR Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 42 LYS Chi-restraints excluded: chain 2 residue 44 ASN Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 53 GLU Chi-restraints excluded: chain 2 residue 120 LEU Chi-restraints excluded: chain 2 residue 168 THR Chi-restraints excluded: chain 2 residue 228 ILE Chi-restraints excluded: chain 2 residue 303 VAL Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 390 THR Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 3 residue 110 LEU Chi-restraints excluded: chain 3 residue 137 THR Chi-restraints excluded: chain 3 residue 259 ASP Chi-restraints excluded: chain 3 residue 265 LEU Chi-restraints excluded: chain 3 residue 281 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 174 VAL Chi-restraints excluded: chain 4 residue 178 LEU Chi-restraints excluded: chain 5 residue 7 SER Chi-restraints excluded: chain 5 residue 31 LEU Chi-restraints excluded: chain 5 residue 35 MET Chi-restraints excluded: chain 5 residue 37 GLU Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 96 VAL Chi-restraints excluded: chain 5 residue 102 VAL Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 97 HIS Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 35 ILE Chi-restraints excluded: chain 8 residue 40 LEU Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 62 ASP Chi-restraints excluded: chain 9 residue 47 VAL Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 89 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 102 TYR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 133 ARG Chi-restraints excluded: chain M residue 226 THR Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 121 LEU Chi-restraints excluded: chain P residue 156 VAL Chi-restraints excluded: chain P residue 184 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 135 PHE Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 141 SER Chi-restraints excluded: chain S residue 153 ILE Chi-restraints excluded: chain S residue 169 ARG Chi-restraints excluded: chain S residue 259 MET Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 139 HIS Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 501 VAL Chi-restraints excluded: chain T residue 539 ASN Chi-restraints excluded: chain T residue 543 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 183 SER Chi-restraints excluded: chain U residue 255 VAL Chi-restraints excluded: chain U residue 305 SER Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 386 GLN Chi-restraints excluded: chain U residue 430 VAL Chi-restraints excluded: chain U residue 546 LEU Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 178 THR Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain V residue 354 VAL Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 492 ILE Chi-restraints excluded: chain V residue 497 GLN Chi-restraints excluded: chain V residue 543 THR Chi-restraints excluded: chain X residue 39 TYR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 136 ASP Chi-restraints excluded: chain X residue 140 ILE Chi-restraints excluded: chain X residue 159 ILE Chi-restraints excluded: chain X residue 190 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ASN Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 317 ASP Chi-restraints excluded: chain X residue 327 THR Chi-restraints excluded: chain X residue 341 VAL Chi-restraints excluded: chain X residue 407 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 454 THR Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 97 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 161 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 318 LEU Chi-restraints excluded: chain Y residue 326 THR Chi-restraints excluded: chain Y residue 347 THR Chi-restraints excluded: chain Y residue 367 SER Chi-restraints excluded: chain Y residue 423 ASP Chi-restraints excluded: chain Y residue 521 LEU Chi-restraints excluded: chain Z residue 166 VAL Chi-restraints excluded: chain Z residue 228 ILE Chi-restraints excluded: chain Z residue 347 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.0788 > 50: distance: 65 - 70: 12.087 distance: 70 - 71: 19.305 distance: 71 - 72: 26.528 distance: 71 - 74: 15.037 distance: 72 - 73: 29.564 distance: 72 - 79: 27.669 distance: 74 - 75: 11.547 distance: 75 - 76: 11.857 distance: 76 - 77: 30.212 distance: 76 - 78: 6.533 distance: 79 - 80: 10.533 distance: 80 - 81: 40.167 distance: 80 - 83: 20.840 distance: 81 - 82: 12.947 distance: 81 - 86: 25.092 distance: 83 - 85: 18.797 distance: 86 - 87: 4.771 distance: 87 - 88: 6.147 distance: 87 - 90: 11.979 distance: 88 - 89: 8.259 distance: 88 - 93: 13.348 distance: 90 - 91: 16.276 distance: 90 - 92: 37.006 distance: 93 - 94: 17.786 distance: 94 - 95: 22.183 distance: 94 - 97: 13.308 distance: 95 - 96: 18.298 distance: 95 - 101: 18.948 distance: 97 - 98: 17.852 distance: 97 - 99: 26.353 distance: 98 - 100: 21.478 distance: 101 - 102: 21.328 distance: 102 - 103: 4.681 distance: 102 - 105: 7.766 distance: 103 - 104: 5.586 distance: 103 - 110: 14.884 distance: 105 - 106: 20.957 distance: 106 - 107: 14.189 distance: 107 - 108: 18.923 distance: 107 - 109: 3.083 distance: 110 - 111: 25.735 distance: 111 - 112: 25.000 distance: 111 - 114: 20.596 distance: 112 - 113: 24.516 distance: 112 - 119: 10.544 distance: 114 - 115: 43.582 distance: 115 - 116: 19.971 distance: 116 - 117: 6.801 distance: 116 - 118: 14.323 distance: 119 - 120: 8.198 distance: 120 - 123: 9.398 distance: 121 - 122: 14.007 distance: 121 - 127: 25.878 distance: 123 - 124: 23.114 distance: 124 - 125: 3.596 distance: 124 - 126: 17.780 distance: 127 - 128: 20.368 distance: 128 - 129: 10.504 distance: 128 - 131: 32.546 distance: 129 - 130: 41.579 distance: 129 - 135: 17.188 distance: 131 - 132: 28.157 distance: 132 - 133: 8.168 distance: 132 - 134: 18.712 distance: 135 - 136: 21.786 distance: 136 - 137: 6.100 distance: 137 - 138: 37.932 distance: 137 - 139: 25.859 distance: 139 - 140: 35.083 distance: 140 - 141: 35.475 distance: 140 - 143: 21.076 distance: 141 - 142: 11.152 distance: 141 - 147: 14.619 distance: 143 - 144: 7.372 distance: 144 - 145: 8.088 distance: 144 - 146: 9.738