Starting phenix.real_space_refine on Wed Sep 25 01:15:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/09_2024/6rdn_4824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/09_2024/6rdn_4824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/09_2024/6rdn_4824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/09_2024/6rdn_4824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/09_2024/6rdn_4824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rdn_4824/09_2024/6rdn_4824.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34297 2.51 5 N 9112 2.21 5 O 10171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 390 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53748 Number of models: 1 Model: "" Number of chains: 37 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4087 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 513} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 23.60, per 1000 atoms: 0.44 Number of scatterers: 53748 At special positions: 0 Unit cell: (209.547, 134.784, 260.091, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 149 16.00 P 13 15.00 Mg 5 11.99 O 10171 8.00 N 9112 7.00 C 34297 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.58 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13086 Finding SS restraints... Secondary structure from input PDB file: 309 helices and 0 sheets defined 58.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.902A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 3 through 8' Processing helix chain '0' and resid 17 through 31 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.575A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 72 Processing helix chain '1' and resid 77 through 81 removed outlier: 3.624A pdb=" N LYS 1 80 " --> pdb=" O PRO 1 77 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN 1 81 " --> pdb=" O LEU 1 78 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 77 through 81' Processing helix chain '1' and resid 96 through 100 removed outlier: 3.550A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.807A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 4.432A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 3.521A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 208 No H-bonds generated for 'chain '1' and resid 206 through 208' Processing helix chain '1' and resid 209 through 224 removed outlier: 4.030A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 Processing helix chain '1' and resid 272 through 277 removed outlier: 3.788A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 278 through 282 removed outlier: 3.717A pdb=" N PHE 1 282 " --> pdb=" O LEU 1 279 " (cutoff:3.500A) Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 317 removed outlier: 3.683A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.580A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 4.116A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.769A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.796A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY 1 421 " --> pdb=" O LYS 1 417 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.928A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 444 Processing helix chain '1' and resid 446 through 460 removed outlier: 3.658A pdb=" N ALA 1 460 " --> pdb=" O LYS 1 456 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 Processing helix chain '1' and resid 479 through 483 removed outlier: 3.620A 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: 3.980A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP 1 504 " --> pdb=" O LEU 1 500 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.672A pdb=" N LEU 1 522 " --> pdb=" O GLU 1 518 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 587 Processing helix chain '1' and resid 588 through 591 Processing helix chain '1' and resid 592 through 606 Processing helix chain '1' and resid 610 through 614 Processing helix chain '2' and resid 7 through 17 removed outlier: 3.547A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 40 Processing helix chain '2' and resid 44 through 58 removed outlier: 4.133A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 77 Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 Processing helix chain '2' and resid 117 through 131 removed outlier: 3.885A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 Processing helix chain '2' and resid 154 through 168 removed outlier: 3.658A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 197 removed outlier: 4.289A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 200 No H-bonds generated for 'chain '2' and resid 198 through 200' Processing helix chain '2' and resid 206 through 220 Processing helix chain '2' and resid 228 through 235 Processing helix chain '2' and resid 240 through 253 removed outlier: 3.819A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.733A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 295 removed outlier: 3.600A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 4.109A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 Processing helix chain '2' and resid 345 through 354 Processing helix chain '2' and resid 396 through 408 removed outlier: 3.937A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 Processing helix chain '3' and resid 78 through 86 Processing helix chain '3' and resid 102 through 113 removed outlier: 3.605A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 128 removed outlier: 3.534A pdb=" N PHE 3 121 " --> pdb=" O SER 3 117 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU 3 126 " --> pdb=" O VAL 3 122 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 Processing helix chain '3' and resid 154 through 168 removed outlier: 3.755A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 187 removed outlier: 4.205A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 205 Processing helix chain '3' and resid 215 through 229 removed outlier: 3.512A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.585A 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 Processing helix chain '3' and resid 253 through 272 removed outlier: 3.644A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 287 removed outlier: 4.029A pdb=" N VAL 3 281 " --> pdb=" O SER 3 277 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 311 removed outlier: 3.677A pdb=" N VAL 3 303 " --> pdb=" O GLU 3 299 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 13 removed outlier: 3.674A pdb=" N LEU 4 12 " --> pdb=" O LYS 4 8 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 13' Processing helix chain '4' and resid 19 through 35 removed outlier: 3.531A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 4.187A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.697A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 removed outlier: 3.502A pdb=" N VAL 4 122 " --> pdb=" O THR 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 150 removed outlier: 3.988A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL 4 141 " --> pdb=" O ALA 4 137 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.981A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 187 removed outlier: 3.735A pdb=" N ILE 4 183 " --> pdb=" O PRO 4 179 " (cutoff:3.500A) Processing helix chain '4' and resid 192 through 234 removed outlier: 3.759A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 258 removed outlier: 3.612A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.561A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 59 removed outlier: 3.500A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU 5 31 " --> pdb=" O ASP 5 27 " (cutoff:3.500A) Proline residue: 5 32 - end of helix removed outlier: 3.640A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 removed outlier: 3.579A pdb=" N PHE 5 81 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 106 removed outlier: 4.040A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 50 through 58 removed outlier: 3.828A pdb=" N ILE 6 54 " --> pdb=" O SER 6 50 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA 6 58 " --> pdb=" O ILE 6 54 " (cutoff:3.500A) Processing helix chain '6' and resid 72 through 94 Processing helix chain '6' and resid 98 through 117 removed outlier: 3.811A pdb=" N VAL 6 107 " --> pdb=" O LEU 6 103 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.090A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 102 removed outlier: 3.733A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 113 removed outlier: 3.790A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 121 removed outlier: 3.623A pdb=" N TYR 7 120 " --> pdb=" O LYS 7 116 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG 7 121 " --> pdb=" O ASP 7 117 " (cutoff:3.500A) Processing helix chain '7' and resid 123 through 145 removed outlier: 3.590A pdb=" N THR 7 145 " --> pdb=" O TYR 7 141 " (cutoff:3.500A) Processing helix chain '7' and resid 149 through 154 Processing helix chain '7' and resid 157 through 166 Processing helix chain '7' and resid 174 through 188 removed outlier: 3.567A pdb=" N SER 7 188 " --> pdb=" O ASN 7 184 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.532A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.578A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 3.755A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 17 Processing helix chain '9' and resid 32 through 55 removed outlier: 4.020A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 3.619A pdb=" N GLU 9 92 " --> pdb=" O GLU 9 88 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 4.684A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.867A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 96 Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.570A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 4.386A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 92 removed outlier: 3.716A pdb=" N VAL B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 124 removed outlier: 4.374A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 68 removed outlier: 3.786A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 90 removed outlier: 3.969A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.883A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 removed outlier: 4.206A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 92 removed outlier: 3.943A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 127 removed outlier: 3.921A pdb=" N GLY D 101 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.751A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 90 removed outlier: 4.138A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 110 through 126 removed outlier: 3.880A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 69 through 92 removed outlier: 3.985A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 124 removed outlier: 3.914A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 removed outlier: 4.442A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS G 66 " --> pdb=" O VAL G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 70 through 92 removed outlier: 3.818A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 127 removed outlier: 4.311A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU G 125 " --> pdb=" O VAL G 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.855A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 92 removed outlier: 4.072A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN H 87 " --> pdb=" O GLY H 83 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.665A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 126 removed outlier: 4.221A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.829A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 3.726A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 96 removed outlier: 3.526A pdb=" N ALA I 96 " --> pdb=" O PRO I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 96' Processing helix chain 'I' and resid 97 through 127 removed outlier: 3.698A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.209A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 90 removed outlier: 3.975A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 96 removed outlier: 3.583A pdb=" N ILE J 95 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 96 " --> pdb=" O PRO J 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 92 through 96' Processing helix chain 'J' and resid 97 through 109 removed outlier: 3.646A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 126 removed outlier: 3.601A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 143 Processing helix chain 'M' and resid 147 through 166 removed outlier: 3.962A pdb=" N GLY M 166 " --> pdb=" O CYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 201 removed outlier: 3.526A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR M 200 " --> pdb=" O GLY M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 258 removed outlier: 4.512A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.699A pdb=" N PHE M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 309 removed outlier: 3.820A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 60 removed outlier: 3.704A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU P 56 " --> pdb=" O GLN P 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN P 59 " --> pdb=" O THR P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 3.506A pdb=" N GLN P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE P 77 " --> pdb=" O GLU P 73 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 removed outlier: 3.533A pdb=" N ARG P 88 " --> pdb=" O HIS P 84 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU P 90 " --> pdb=" O GLU P 86 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 105 removed outlier: 3.849A pdb=" N ILE P 105 " --> pdb=" O ARG P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 125 removed outlier: 3.748A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 132 removed outlier: 4.544A 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 147 removed outlier: 3.559A pdb=" N ALA P 147 " --> pdb=" O GLU P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 Processing helix chain 'P' and resid 210 through 226 Processing helix chain 'Q' and resid 15 through 29 removed outlier: 3.561A pdb=" N TYR Q 19 " --> pdb=" O SER Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 4.211A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 44 removed outlier: 3.865A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 41 removed outlier: 4.364A pdb=" N LYS R 39 " --> pdb=" O GLU R 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 40 " --> pdb=" O VAL R 36 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 removed outlier: 3.726A pdb=" N TYR R 54 " --> pdb=" O PRO R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 158 through 168 removed outlier: 4.125A pdb=" N ALA R 166 " --> pdb=" O SER R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 Processing helix chain 'S' and resid 40 through 70 removed outlier: 3.842A pdb=" N LYS S 44 " --> pdb=" O ASN S 40 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 79 removed outlier: 3.575A pdb=" N SER S 78 " --> pdb=" O ALA S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 90 removed outlier: 4.342A pdb=" N PHE S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 128 removed outlier: 3.617A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 148 removed outlier: 3.644A pdb=" N ARG S 147 " --> pdb=" O GLY S 143 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER S 148 " --> pdb=" O ASP S 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 143 through 148' Processing helix chain 'S' and resid 171 through 182 Processing helix chain 'S' and resid 227 through 231 removed outlier: 3.730A pdb=" N ALA S 230 " --> pdb=" O SER S 227 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 313 removed outlier: 3.650A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU S 248 " --> pdb=" O ARG S 244 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN S 263 " --> pdb=" O MET S 259 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN S 276 " --> pdb=" O SER S 272 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 76 removed outlier: 3.665A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Proline residue: T 68 - end of helix removed outlier: 3.522A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 4.101A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE T 138 " --> pdb=" O ASP T 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 134 through 138' Processing helix chain 'T' and resid 156 through 160 Processing helix chain 'T' and resid 206 through 213 removed outlier: 3.708A pdb=" N LEU T 212 " --> pdb=" O ALA T 208 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.536A pdb=" N GLN T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU T 247 " --> pdb=" O LYS T 243 " (cutoff:3.500A) Processing helix chain 'T' and resid 265 through 280 Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 3.610A pdb=" N TYR T 312 " --> pdb=" O ALA T 308 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 removed outlier: 3.525A pdb=" N MET T 337 " --> pdb=" O ALA T 333 " (cutoff:3.500A) Processing helix chain 'T' and resid 353 through 363 removed outlier: 3.734A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 removed outlier: 3.525A pdb=" N TYR T 414 " --> pdb=" O THR T 410 " (cutoff:3.500A) Processing helix chain 'T' and resid 430 through 434 removed outlier: 3.865A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.774A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 460 removed outlier: 3.824A pdb=" N GLN T 452 " --> pdb=" O LEU T 448 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG T 454 " --> pdb=" O LEU T 450 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA T 458 " --> pdb=" O ARG T 454 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE T 459 " --> pdb=" O GLU T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 469 through 484 removed outlier: 3.950A pdb=" N ALA T 478 " --> pdb=" O LEU T 474 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG T 479 " --> pdb=" O GLU T 475 " (cutoff:3.500A) Processing helix chain 'T' and resid 494 through 506 removed outlier: 3.562A 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 527 removed outlier: 4.929A pdb=" N GLU T 522 " --> pdb=" O VAL T 518 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA T 523 " --> pdb=" O ALA T 519 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 540 removed outlier: 3.807A pdb=" N ILE T 535 " --> pdb=" O ALA T 531 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU T 536 " --> pdb=" O VAL T 532 " (cutoff:3.500A) Processing helix chain 'T' and resid 543 through 554 removed outlier: 3.921A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA T 552 " --> pdb=" O ALA T 548 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 47 removed outlier: 3.726A pdb=" N GLU U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 64 removed outlier: 3.573A pdb=" N VAL U 62 " --> pdb=" O LEU U 58 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 72 Processing helix chain 'U' and resid 134 through 138 removed outlier: 3.874A pdb=" N VAL U 137 " --> pdb=" O ASN U 134 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 160 removed outlier: 3.826A pdb=" N THR U 159 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.621A pdb=" N VAL U 234 " --> pdb=" O GLY U 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 279 Processing helix chain 'U' and resid 280 through 284 Processing helix chain 'U' and resid 295 through 316 Proline residue: U 303 - end of helix removed outlier: 3.603A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN U 330 " --> pdb=" O ASP U 326 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL U 332 " --> pdb=" O SER U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.797A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 400 removed outlier: 3.524A pdb=" N SER U 400 " --> pdb=" O THR U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.839A pdb=" N LYS U 415 " --> pdb=" O GLU U 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 460 removed outlier: 4.001A pdb=" N GLY U 444 " --> pdb=" O LYS U 440 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N THR U 445 " --> pdb=" O GLN U 441 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU U 446 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing helix chain 'U' and resid 469 through 485 removed outlier: 3.786A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 506 removed outlier: 3.570A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA U 504 " --> pdb=" O ALA U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 516 through 528 removed outlier: 3.664A pdb=" N GLU U 522 " --> pdb=" O VAL U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.809A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 Processing helix chain 'V' and resid 45 through 49 Processing helix chain 'V' and resid 58 through 67 removed outlier: 3.972A pdb=" N GLN V 64 " --> pdb=" O GLN V 60 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.944A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 246 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 316 Proline residue: V 303 - end of helix removed outlier: 3.733A pdb=" N TYR V 312 " --> pdb=" O ALA V 308 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 341 removed outlier: 3.528A pdb=" N GLN V 330 " --> pdb=" O ASP V 326 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.583A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.598A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 402 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.997A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 435 removed outlier: 4.050A pdb=" N ALA V 433 " --> pdb=" O VAL V 430 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN V 435 " --> pdb=" O SER V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 456 removed outlier: 3.632A pdb=" N VAL V 442 " --> pdb=" O GLY V 438 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU V 448 " --> pdb=" O GLY V 444 " (cutoff:3.500A) Processing helix chain 'V' and resid 469 through 482 removed outlier: 4.030A pdb=" N VAL V 473 " --> pdb=" O ALA V 469 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU V 482 " --> pdb=" O ALA V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 526 removed outlier: 4.228A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.609A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 543 through 554 removed outlier: 4.169A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 removed outlier: 3.528A pdb=" N THR X 117 " --> pdb=" O GLY X 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 171 Processing helix chain 'X' and resid 188 through 204 removed outlier: 4.679A pdb=" N LYS X 202 " --> pdb=" O ASN X 198 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA X 203 " --> pdb=" O ASN X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 3.733A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 275 removed outlier: 3.528A pdb=" N ARG X 260 " --> pdb=" O GLY X 256 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA X 262 " --> pdb=" O ARG X 258 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU X 263 " --> pdb=" O ALA X 259 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE X 272 " --> pdb=" O VAL X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 287 through 300 removed outlier: 3.846A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA X 299 " --> pdb=" O SER X 295 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU X 300 " --> pdb=" O GLU X 296 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 348 through 355 Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 371 removed outlier: 3.548A pdb=" N LEU X 371 " --> pdb=" O SER X 367 " (cutoff:3.500A) Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 421 removed outlier: 4.548A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 426 through 443 Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 Processing helix chain 'X' and resid 491 through 505 Processing helix chain 'X' and resid 526 through 533 removed outlier: 4.052A pdb=" N GLU X 533 " --> pdb=" O LYS X 529 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 201 Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.787A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 3.615A pdb=" N ARG Y 260 " --> pdb=" O GLY Y 256 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 297 removed outlier: 3.789A pdb=" N THR Y 291 " --> pdb=" O ILE Y 287 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL Y 297 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 Processing helix chain 'Y' and resid 313 through 323 Processing helix chain 'Y' and resid 348 through 355 removed outlier: 3.707A 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 371 Processing helix chain 'Y' and resid 388 through 393 Processing helix chain 'Y' and resid 393 through 418 removed outlier: 3.903A pdb=" N VAL Y 399 " --> pdb=" O GLU Y 395 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 411 " --> pdb=" O LEU Y 407 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP Y 415 " --> pdb=" O LYS Y 411 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ILE Y 416 " --> pdb=" O ASN Y 412 " (cutoff:3.500A) Processing helix chain 'Y' and resid 428 through 443 Processing helix chain 'Y' and resid 462 through 475 Processing helix chain 'Y' and resid 482 through 487 Processing helix chain 'Y' and resid 491 through 507 removed outlier: 3.894A pdb=" N LYS Y 501 " --> pdb=" O GLU Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 526 through 533 Processing helix chain 'Y' and resid 544 through 555 Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 164 through 170 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 4.114A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG Z 239 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 3.510A pdb=" N ARG Z 260 " --> pdb=" O GLY Z 256 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 301 Processing helix chain 'Z' and resid 313 through 323 removed outlier: 4.080A pdb=" N LEU Z 321 " --> pdb=" O ASP Z 317 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 355 Processing helix chain 'Z' and resid 365 through 370 Processing helix chain 'Z' and resid 392 through 412 removed outlier: 4.283A pdb=" N HIS Z 396 " --> pdb=" O ILE Z 392 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 421 removed outlier: 4.079A pdb=" N ILE Z 419 " --> pdb=" O ASP Z 415 " (cutoff:3.500A) Processing helix chain 'Z' and resid 426 through 443 Processing helix chain 'Z' and resid 447 through 449 No H-bonds generated for 'chain 'Z' and resid 447 through 449' Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.615A pdb=" N GLY Z 472 " --> pdb=" O SER Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 487 removed outlier: 3.787A pdb=" N TYR Z 487 " --> pdb=" O MET Z 484 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 508 removed outlier: 3.683A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU Z 497 " --> pdb=" O LYS Z 493 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA Z 507 " --> pdb=" O ALA Z 503 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 532 2562 hydrogen bonds defined for protein. 7509 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: 16.90 Time building geometry restraints manager: 11.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12615 1.33 - 1.45: 11629 1.45 - 1.58: 30167 1.58 - 1.70: 21 1.70 - 1.82: 254 Bond restraints: 54686 Sorted by residual: bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.95e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.452 -0.064 1.00e-02 1.00e+04 4.07e+01 bond pdb=" C5 ATP V1001 " pdb=" C6 ATP V1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.47e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.468 -0.059 1.00e-02 1.00e+04 3.46e+01 ... (remaining 54681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 73447 3.81 - 7.62: 641 7.62 - 11.44: 62 11.44 - 15.25: 8 15.25 - 19.06: 3 Bond angle restraints: 74161 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 120.81 19.06 1.00e+00 1.00e+00 3.63e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 122.01 17.86 1.00e+00 1.00e+00 3.19e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 121.70 15.13 1.00e+00 1.00e+00 2.29e+02 angle pdb=" PA ATP U1001 " pdb=" O3A ATP U1001 " pdb=" PB ATP U1001 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 ... (remaining 74156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.29: 31080 23.29 - 46.57: 1719 46.57 - 69.86: 172 69.86 - 93.15: 52 93.15 - 116.44: 2 Dihedral angle restraints: 33025 sinusoidal: 12667 harmonic: 20358 Sorted by residual: dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -119.20 -60.80 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -120.33 -59.67 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -123.12 -56.88 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 33022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 7786 0.098 - 0.196: 850 0.196 - 0.294: 49 0.294 - 0.392: 2 0.392 - 0.490: 2 Chirality restraints: 8689 Sorted by residual: chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.99e+00 chirality pdb=" CB ILE P 157 " pdb=" CA ILE P 157 " pdb=" CG1 ILE P 157 " pdb=" CG2 ILE P 157 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB VAL U 180 " pdb=" CA VAL U 180 " pdb=" CG1 VAL U 180 " pdb=" CG2 VAL U 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 8686 not shown) Planarity restraints: 9510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.030 2.00e-02 2.50e+03 5.88e-02 3.45e+01 pdb=" C ALA Z 503 " -0.102 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.038 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA U 296 " 0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO U 297 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO U 297 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO U 297 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 348 " 0.055 5.00e-02 4.00e+02 8.42e-02 1.13e+01 pdb=" N PRO X 349 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO X 349 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO X 349 " 0.046 5.00e-02 4.00e+02 ... (remaining 9507 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 544 2.60 - 3.17: 44405 3.17 - 3.75: 86749 3.75 - 4.32: 125407 4.32 - 4.90: 204044 Nonbonded interactions: 461149 Sorted by model distance: nonbonded pdb=" OG1 THR V 232 " pdb="MG MG V1002 " model vdw 2.023 2.170 nonbonded pdb=" O2B ATP U1001 " pdb="MG MG U1002 " model vdw 2.063 2.170 nonbonded pdb=" OG1 THR U 232 " pdb="MG MG U1002 " model vdw 2.105 2.170 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.114 2.170 nonbonded pdb=" O3G ATP V1001 " pdb="MG MG V1002 " model vdw 2.120 2.170 ... (remaining 461144 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 37 through 556) selection = (chain 'Y' and resid 37 through 556) selection = (chain 'Z' and resid 37 through 556) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.600 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 101.370 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.123 54686 Z= 0.691 Angle : 1.021 19.062 74161 Z= 0.577 Chirality : 0.062 0.490 8689 Planarity : 0.008 0.087 9510 Dihedral : 14.485 116.437 19939 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.19 % Favored : 94.61 % Rotamer: Outliers : 0.41 % Allowed : 6.64 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.34 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.08), residues: 7038 helix: -2.91 (0.06), residues: 3828 sheet: -1.33 (0.20), residues: 647 loop : -2.04 (0.11), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP Z 141 HIS 0.013 0.002 HIS S 250 PHE 0.043 0.003 PHE E 122 TYR 0.031 0.003 TYR 4 211 ARG 0.010 0.001 ARG U 217 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1112 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.8130 (tptp) cc_final: 0.7692 (ttpp) REVERT: 0 41 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6626 (pm20) REVERT: 1 191 GLU cc_start: 0.6531 (mm-30) cc_final: 0.6260 (tp30) REVERT: 1 572 ASP cc_start: 0.7938 (m-30) cc_final: 0.7642 (m-30) REVERT: 5 57 LYS cc_start: 0.8647 (mttt) cc_final: 0.8431 (mtpp) REVERT: 6 98 GLU cc_start: 0.7518 (mp0) cc_final: 0.7224 (mp0) REVERT: 7 179 ASP cc_start: 0.7870 (m-30) cc_final: 0.7665 (m-30) REVERT: 7 184 ASN cc_start: 0.8675 (t0) cc_final: 0.8353 (t0) REVERT: 8 69 LYS cc_start: 0.9026 (mttt) cc_final: 0.7114 (tmtt) REVERT: 8 81 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8178 (mttm) REVERT: 9 3 VAL cc_start: 0.7548 (m) cc_final: 0.7268 (p) REVERT: 9 9 LYS cc_start: 0.6820 (ttpt) cc_final: 0.6289 (tttm) REVERT: 9 80 GLN cc_start: 0.8200 (tp40) cc_final: 0.7947 (tp-100) REVERT: 9 89 MET cc_start: 0.8882 (mtp) cc_final: 0.8597 (mtp) REVERT: B 81 MET cc_start: 0.7057 (ttp) cc_final: 0.6687 (ttp) REVERT: D 98 GLN cc_start: 0.7095 (tp-100) cc_final: 0.6865 (tt0) REVERT: M 127 HIS cc_start: 0.7528 (t70) cc_final: 0.7322 (t-90) REVERT: P 88 ARG cc_start: 0.8118 (ptp90) cc_final: 0.7619 (ptp90) REVERT: P 151 GLU cc_start: 0.7761 (mp0) cc_final: 0.7506 (mm-30) REVERT: P 160 GLU cc_start: 0.7811 (pm20) cc_final: 0.7587 (pm20) REVERT: P 183 LYS cc_start: 0.8588 (tttt) cc_final: 0.8255 (ttmm) REVERT: P 189 LYS cc_start: 0.8395 (mtpp) cc_final: 0.8183 (mmtt) REVERT: P 191 ASP cc_start: 0.7738 (t70) cc_final: 0.7345 (t0) REVERT: S 204 LYS cc_start: 0.7041 (ptpp) cc_final: 0.6777 (ttmm) REVERT: S 245 ASP cc_start: 0.7780 (m-30) cc_final: 0.7523 (m-30) REVERT: S 284 MET cc_start: 0.7985 (ttm) cc_final: 0.7734 (ttm) REVERT: S 291 ASP cc_start: 0.7948 (t70) cc_final: 0.7577 (t0) REVERT: T 96 ARG cc_start: 0.8223 (mtt-85) cc_final: 0.7998 (mmt180) REVERT: T 524 VAL cc_start: 0.7702 (t) cc_final: 0.7444 (p) REVERT: T 529 ASN cc_start: 0.7267 (t0) cc_final: 0.6868 (p0) REVERT: U 62 VAL cc_start: 0.7994 (m) cc_final: 0.7779 (p) REVERT: U 96 ARG cc_start: 0.7773 (mtp-110) cc_final: 0.7440 (mtp-110) REVERT: U 471 GLN cc_start: 0.7912 (tp40) cc_final: 0.7551 (tp-100) REVERT: U 474 LEU cc_start: 0.7991 (mt) cc_final: 0.7730 (tp) REVERT: V 55 SER cc_start: 0.8550 (t) cc_final: 0.8134 (p) REVERT: X 317 ASP cc_start: 0.6756 (m-30) cc_final: 0.6533 (m-30) REVERT: Y 382 SER cc_start: 0.8873 (m) cc_final: 0.8421 (p) REVERT: Z 103 VAL cc_start: 0.8838 (t) cc_final: 0.8550 (m) REVERT: Z 227 MET cc_start: 0.8539 (mtt) cc_final: 0.8232 (mtt) outliers start: 23 outliers final: 11 residues processed: 1128 average time/residue: 0.5563 time to fit residues: 1020.6079 Evaluate side-chains 692 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 681 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain Y residue 200 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 8.9990 chunk 529 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 chunk 356 optimal weight: 0.9990 chunk 282 optimal weight: 0.9980 chunk 547 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 332 optimal weight: 4.9990 chunk 407 optimal weight: 1.9990 chunk 633 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 29 ASN 0 48 ASN 0 60 GLN 1 257 HIS 1 285 GLN 1 313 GLN 1 316 ASN 1 346 GLN 1 365 GLN 1 423 ASN 1 482 ASN 1 587 ASN 1 590 HIS 2 40 GLN 2 68 ASN 2 243 GLN 2 289 HIS 3 97 ASN 3 179 GLN 3 206 ASN 4 38 GLN 4 124 ASN 4 135 ASN 4 240 GLN 5 29 GLN ** 5 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 40 ASN 6 74 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 86 HIS 7 98 ASN 7 123 HIS ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 190 GLN 8 26 HIS 9 35 GLN D 94 ASN G 87 ASN M 108 ASN M 163 ASN P 220 ASN P 223 ASN Q 21 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 73 ASN R 85 GLN S 70 ASN S 174 GLN S 293 ASN S 297 GLN T 64 GLN T 104 GLN T 126 HIS T 134 ASN T 241 HIS T 497 GLN T 529 ASN U 152 ASN U 241 HIS U 242 GLN U 244 ASN U 248 GLN U 253 GLN U 319 HIS U 386 GLN ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 461 GLN U 471 GLN U 497 GLN U 529 ASN V 60 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 139 HIS V 149 GLN V 241 HIS V 386 GLN V 422 ASN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 497 GLN ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 199 ASN X 408 GLN Y 68 HIS Y 132 GLN Y 322 GLN Y 440 GLN Z 132 GLN Z 199 ASN Z 278 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 ASN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 54686 Z= 0.194 Angle : 0.586 9.394 74161 Z= 0.308 Chirality : 0.042 0.178 8689 Planarity : 0.005 0.063 9510 Dihedral : 6.519 94.745 7683 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.85 % Favored : 95.96 % Rotamer: Outliers : 1.79 % Allowed : 11.24 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.09), residues: 7038 helix: -1.06 (0.08), residues: 3887 sheet: -0.98 (0.21), residues: 584 loop : -1.42 (0.12), residues: 2567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 9 73 HIS 0.008 0.001 HIS T 549 PHE 0.032 0.001 PHE Y 549 TYR 0.025 0.001 TYR 4 211 ARG 0.007 0.000 ARG 1 609 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 809 time to evaluate : 4.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 41 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6641 (pm20) REVERT: 1 24 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8181 (pp) REVERT: 1 194 LYS cc_start: 0.7225 (ptmm) cc_final: 0.6922 (ttmt) REVERT: 1 572 ASP cc_start: 0.7975 (m-30) cc_final: 0.7673 (m-30) REVERT: 5 57 LYS cc_start: 0.8603 (mttt) cc_final: 0.8385 (mtpp) REVERT: 5 112 ARG cc_start: 0.8233 (mtm180) cc_final: 0.7984 (ptm-80) REVERT: 7 184 ASN cc_start: 0.8541 (t0) cc_final: 0.8029 (t0) REVERT: 8 62 ASP cc_start: 0.8173 (m-30) cc_final: 0.7946 (m-30) REVERT: 8 69 LYS cc_start: 0.8989 (mttt) cc_final: 0.7176 (tmtt) REVERT: 9 9 LYS cc_start: 0.6807 (ttpt) cc_final: 0.6284 (tttm) REVERT: E 60 LYS cc_start: 0.6826 (ptpp) cc_final: 0.6303 (mtpt) REVERT: H 119 LEU cc_start: 0.5318 (OUTLIER) cc_final: 0.4963 (pt) REVERT: P 116 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7119 (tp30) REVERT: P 160 GLU cc_start: 0.7893 (pm20) cc_final: 0.7608 (pm20) REVERT: P 183 LYS cc_start: 0.8648 (tttt) cc_final: 0.8145 (ttmm) REVERT: P 191 ASP cc_start: 0.7706 (t70) cc_final: 0.7410 (t0) REVERT: Q 19 TYR cc_start: 0.8515 (t80) cc_final: 0.8313 (t80) REVERT: S 220 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7541 (mm) REVERT: S 240 SER cc_start: 0.8790 (t) cc_final: 0.8563 (p) REVERT: S 256 TYR cc_start: 0.8360 (t80) cc_final: 0.8064 (t80) REVERT: S 284 MET cc_start: 0.7757 (ttm) cc_final: 0.7527 (ttm) REVERT: U 77 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7703 (m-80) REVERT: U 96 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7598 (mtp-110) REVERT: U 441 GLN cc_start: 0.7097 (mt0) cc_final: 0.6877 (mt0) REVERT: V 47 GLU cc_start: 0.7635 (mp0) cc_final: 0.7314 (pm20) REVERT: V 55 SER cc_start: 0.8497 (t) cc_final: 0.8093 (p) REVERT: X 49 ASP cc_start: 0.7724 (m-30) cc_final: 0.7464 (m-30) REVERT: X 82 ASP cc_start: 0.7754 (t0) cc_final: 0.7542 (t70) REVERT: X 316 THR cc_start: 0.8692 (m) cc_final: 0.8389 (p) REVERT: Y 382 SER cc_start: 0.8755 (m) cc_final: 0.8320 (p) REVERT: Z 103 VAL cc_start: 0.9064 (t) cc_final: 0.8821 (m) REVERT: Z 227 MET cc_start: 0.8551 (mtt) cc_final: 0.8270 (mtt) outliers start: 101 outliers final: 55 residues processed: 876 average time/residue: 0.5112 time to fit residues: 749.2954 Evaluate side-chains 702 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 643 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 373 ASP Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 510 ILE Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain M residue 280 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 285 THR Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 77 TYR Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain U residue 529 ASN Chi-restraints excluded: chain U residue 557 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 528 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 528 ASP Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 489 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 0.0000 chunk 196 optimal weight: 4.9990 chunk 527 optimal weight: 0.9990 chunk 431 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 635 optimal weight: 6.9990 chunk 685 optimal weight: 5.9990 chunk 565 optimal weight: 2.9990 chunk 629 optimal weight: 1.9990 chunk 216 optimal weight: 0.2980 chunk 509 optimal weight: 4.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 189 HIS 4 124 ASN 5 107 ASN ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 98 GLN P 59 GLN Q 40 GLN R 38 ASN R 137 HIS ** S 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 244 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN ** U 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 322 GLN Y 337 GLN Z 132 GLN Z 198 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 471 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54686 Z= 0.194 Angle : 0.558 12.299 74161 Z= 0.289 Chirality : 0.042 0.201 8689 Planarity : 0.004 0.058 9510 Dihedral : 6.092 84.323 7679 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.18 % Favored : 95.69 % Rotamer: Outliers : 2.27 % Allowed : 13.41 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.10), residues: 7038 helix: -0.22 (0.08), residues: 3912 sheet: -0.83 (0.22), residues: 583 loop : -1.09 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 4 206 HIS 0.008 0.001 HIS U 549 PHE 0.022 0.001 PHE Y 549 TYR 0.025 0.001 TYR 4 211 ARG 0.006 0.000 ARG X 441 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 724 time to evaluate : 4.455 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 41 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6537 (pm20) REVERT: 1 24 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8275 (pp) REVERT: 1 194 LYS cc_start: 0.7506 (ptmm) cc_final: 0.7016 (ttmt) REVERT: 1 572 ASP cc_start: 0.7996 (m-30) cc_final: 0.7686 (m-30) REVERT: 2 197 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6777 (mm) REVERT: 4 121 ASP cc_start: 0.7684 (t0) cc_final: 0.7406 (t70) REVERT: 5 1 MET cc_start: 0.6884 (ptp) cc_final: 0.6644 (ptp) REVERT: 5 51 TYR cc_start: 0.9127 (t80) cc_final: 0.8895 (t80) REVERT: 5 57 LYS cc_start: 0.8569 (mttt) cc_final: 0.8361 (mtpp) REVERT: 5 112 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7987 (ptm-80) REVERT: 8 62 ASP cc_start: 0.8133 (m-30) cc_final: 0.7886 (m-30) REVERT: 8 69 LYS cc_start: 0.8921 (mttt) cc_final: 0.7163 (tmtt) REVERT: 8 81 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7536 (ttmt) REVERT: 9 9 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6403 (tttm) REVERT: B 97 LYS cc_start: 0.7477 (mmtt) cc_final: 0.6044 (mttt) REVERT: E 60 LYS cc_start: 0.6845 (ptpp) cc_final: 0.6334 (mtpt) REVERT: P 116 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7170 (tp30) REVERT: P 191 ASP cc_start: 0.7707 (t70) cc_final: 0.7505 (t0) REVERT: S 122 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.5984 (m-10) REVERT: S 124 ARG cc_start: 0.6652 (ptm-80) cc_final: 0.5936 (ptm-80) REVERT: S 220 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7587 (mm) REVERT: S 240 SER cc_start: 0.8776 (t) cc_final: 0.8529 (p) REVERT: S 256 TYR cc_start: 0.8387 (t80) cc_final: 0.8092 (t80) REVERT: S 284 MET cc_start: 0.7747 (ttm) cc_final: 0.7466 (ttm) REVERT: T 121 ASN cc_start: 0.8503 (p0) cc_final: 0.8228 (p0) REVERT: T 245 CYS cc_start: 0.7004 (m) cc_final: 0.6424 (t) REVERT: U 96 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.7655 (mtp-110) REVERT: V 47 GLU cc_start: 0.7586 (mp0) cc_final: 0.7315 (pm20) REVERT: V 55 SER cc_start: 0.8498 (t) cc_final: 0.8091 (p) REVERT: X 229 GLU cc_start: 0.7379 (tp30) cc_final: 0.7120 (mm-30) REVERT: X 459 LYS cc_start: 0.7306 (mmmt) cc_final: 0.6997 (mmtm) REVERT: Y 195 GLU cc_start: 0.7398 (tp30) cc_final: 0.6824 (tp30) REVERT: Y 382 SER cc_start: 0.8774 (m) cc_final: 0.8544 (m) REVERT: Y 388 ASN cc_start: 0.7705 (t0) cc_final: 0.7458 (t0) REVERT: Z 103 VAL cc_start: 0.9133 (t) cc_final: 0.8904 (m) REVERT: Z 227 MET cc_start: 0.8574 (mtt) cc_final: 0.8242 (mtt) REVERT: Z 483 GLU cc_start: 0.6183 (pm20) cc_final: 0.5811 (pt0) REVERT: Z 527 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6273 (mp) outliers start: 128 outliers final: 80 residues processed: 811 average time/residue: 0.5154 time to fit residues: 708.3743 Evaluate side-chains 710 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 624 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 383 ILE Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 197 LEU Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain R residue 65 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 269 VAL Chi-restraints excluded: chain T residue 285 THR Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 492 ILE Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 120 LEU Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain X residue 245 THR Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 528 ASP Chi-restraints excluded: chain Y residue 94 ASP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 489 VAL Chi-restraints excluded: chain Z residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 8.9990 chunk 477 optimal weight: 9.9990 chunk 329 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 426 optimal weight: 5.9990 chunk 637 optimal weight: 9.9990 chunk 674 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 603 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 562 ASN 4 68 HIS 4 124 ASN 4 240 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN P 59 GLN Q 21 ASN R 38 ASN R 78 HIS R 104 HIS ** R 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 116 ASN S 262 ASN T 529 ASN U 152 ASN U 228 GLN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 471 GLN U 497 GLN ** V 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 440 GLN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 414 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 54686 Z= 0.438 Angle : 0.676 10.038 74161 Z= 0.348 Chirality : 0.047 0.205 8689 Planarity : 0.005 0.066 9510 Dihedral : 6.572 91.391 7679 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.07 % Favored : 94.74 % Rotamer: Outliers : 3.13 % Allowed : 14.74 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.10), residues: 7038 helix: -0.19 (0.08), residues: 3895 sheet: -1.02 (0.21), residues: 607 loop : -1.08 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 3 109 HIS 0.008 0.001 HIS T 319 PHE 0.026 0.002 PHE G 107 TYR 0.026 0.002 TYR Q 19 ARG 0.007 0.001 ARG X 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 655 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7511 (ttpp) REVERT: 1 194 LYS cc_start: 0.7549 (ptmm) cc_final: 0.7150 (ttmt) REVERT: 1 572 ASP cc_start: 0.7970 (m-30) cc_final: 0.7716 (m-30) REVERT: 2 197 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6774 (mm) REVERT: 4 121 ASP cc_start: 0.7856 (t0) cc_final: 0.7540 (t70) REVERT: 5 1 MET cc_start: 0.7042 (ptp) cc_final: 0.6820 (ptp) REVERT: 7 184 ASN cc_start: 0.8674 (t0) cc_final: 0.8242 (t0) REVERT: 8 69 LYS cc_start: 0.8961 (mttt) cc_final: 0.7060 (tmtt) REVERT: 8 81 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7691 (ttmt) REVERT: 9 1 MET cc_start: 0.4103 (OUTLIER) cc_final: -0.0640 (mpp) REVERT: 9 9 LYS cc_start: 0.6953 (ttpt) cc_final: 0.6291 (tttm) REVERT: 9 26 LEU cc_start: 0.8903 (mt) cc_final: 0.8645 (mp) REVERT: A 81 MET cc_start: 0.6876 (ttp) cc_final: 0.6646 (ttp) REVERT: B 97 LYS cc_start: 0.7552 (mmtt) cc_final: 0.6013 (mttp) REVERT: D 95 ILE cc_start: 0.5644 (OUTLIER) cc_final: 0.5256 (mm) REVERT: E 60 LYS cc_start: 0.6523 (ptpp) cc_final: 0.6074 (mtpt) REVERT: F 81 MET cc_start: 0.6799 (ttp) cc_final: 0.6378 (ttp) REVERT: J 109 LEU cc_start: 0.7645 (mm) cc_final: 0.7164 (mt) REVERT: M 110 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8818 (mm) REVERT: P 116 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7512 (mm-30) REVERT: P 191 ASP cc_start: 0.7858 (t70) cc_final: 0.7576 (t0) REVERT: Q 26 LEU cc_start: 0.8523 (mm) cc_final: 0.8291 (mp) REVERT: R 175 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4327 (pm20) REVERT: S 122 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: S 188 GLN cc_start: 0.7046 (mp10) cc_final: 0.6646 (mt0) REVERT: S 220 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7329 (mm) REVERT: S 240 SER cc_start: 0.8823 (t) cc_final: 0.8591 (p) REVERT: S 284 MET cc_start: 0.7926 (ttm) cc_final: 0.7566 (ttm) REVERT: T 121 ASN cc_start: 0.8721 (p0) cc_final: 0.8451 (p0) REVERT: T 496 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.6871 (mtp-110) REVERT: V 55 SER cc_start: 0.8614 (t) cc_final: 0.8216 (p) REVERT: V 84 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8506 (mp) REVERT: V 322 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8669 (tp) REVERT: V 418 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7828 (mtt90) REVERT: V 452 GLN cc_start: 0.7863 (mt0) cc_final: 0.7645 (mt0) REVERT: V 472 TYR cc_start: 0.6975 (t80) cc_final: 0.6759 (t80) REVERT: V 516 ASP cc_start: 0.5713 (OUTLIER) cc_final: 0.5068 (p0) REVERT: X 229 GLU cc_start: 0.7550 (tp30) cc_final: 0.7291 (mm-30) REVERT: Y 382 SER cc_start: 0.8683 (m) cc_final: 0.8382 (p) REVERT: Y 388 ASN cc_start: 0.7853 (t0) cc_final: 0.7651 (t0) REVERT: Y 440 GLN cc_start: 0.8341 (mt0) cc_final: 0.8103 (mt0) REVERT: Y 531 VAL cc_start: 0.7530 (m) cc_final: 0.7289 (t) outliers start: 176 outliers final: 115 residues processed: 781 average time/residue: 0.5508 time to fit residues: 733.6678 Evaluate side-chains 712 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 587 time to evaluate : 4.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 197 LEU Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 119 LYS Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 8 residue 52 THR Chi-restraints excluded: chain 9 residue 1 MET Chi-restraints excluded: chain 9 residue 29 PHE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 69 ILE Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 175 GLU Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 236 ILE Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 269 VAL Chi-restraints excluded: chain T residue 285 THR Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 474 LEU Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 425 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 322 ILE Chi-restraints excluded: chain V residue 429 ARG Chi-restraints excluded: chain V residue 481 THR Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 230 SER Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 316 THR Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain X residue 528 ASP Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 431 LEU Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 321 LEU Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 489 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.9980 chunk 382 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 502 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 575 optimal weight: 7.9990 chunk 466 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 344 optimal weight: 2.9990 chunk 605 optimal weight: 10.0000 chunk 170 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 3 94 ASN 4 124 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 94 ASN R 38 ASN S 116 ASN T 196 GLN T 358 HIS T 441 GLN T 529 ASN T 539 ASN U 152 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 61 HIS ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54686 Z= 0.176 Angle : 0.546 9.733 74161 Z= 0.280 Chirality : 0.041 0.164 8689 Planarity : 0.004 0.060 9510 Dihedral : 5.894 88.568 7679 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 2.13 % Allowed : 16.02 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 7038 helix: 0.29 (0.09), residues: 3894 sheet: -0.86 (0.22), residues: 591 loop : -0.86 (0.13), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 4 206 HIS 0.004 0.001 HIS 4 233 PHE 0.024 0.001 PHE A 116 TYR 0.023 0.001 TYR 4 211 ARG 0.006 0.000 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 696 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 24 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8274 (pp) REVERT: 1 194 LYS cc_start: 0.7560 (ptmm) cc_final: 0.7161 (ttmt) REVERT: 1 572 ASP cc_start: 0.7974 (m-30) cc_final: 0.7753 (m-30) REVERT: 2 197 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6696 (mm) REVERT: 4 54 GLU cc_start: 0.7934 (tt0) cc_final: 0.7654 (tt0) REVERT: 4 121 ASP cc_start: 0.7756 (t0) cc_final: 0.7428 (t70) REVERT: 5 1 MET cc_start: 0.7161 (ptp) cc_final: 0.6834 (ptp) REVERT: 5 51 TYR cc_start: 0.9141 (t80) cc_final: 0.8829 (t80) REVERT: 5 112 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8020 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8204 (t80) REVERT: 8 62 ASP cc_start: 0.8090 (m-30) cc_final: 0.7886 (m-30) REVERT: 8 69 LYS cc_start: 0.8909 (mttt) cc_final: 0.7164 (tmtt) REVERT: 8 81 LYS cc_start: 0.8153 (mtpt) cc_final: 0.7577 (ttmt) REVERT: 9 1 MET cc_start: 0.3260 (ttp) cc_final: -0.0288 (mpp) REVERT: 9 9 LYS cc_start: 0.6657 (ttpt) cc_final: 0.6174 (tttm) REVERT: 9 13 LYS cc_start: 0.8078 (mptt) cc_final: 0.7799 (mmtt) REVERT: 9 26 LEU cc_start: 0.8870 (mt) cc_final: 0.8600 (mp) REVERT: B 97 LYS cc_start: 0.7286 (mmtt) cc_final: 0.6023 (mttp) REVERT: E 60 LYS cc_start: 0.6185 (ptpp) cc_final: 0.5706 (mtpt) REVERT: H 119 LEU cc_start: 0.5708 (OUTLIER) cc_final: 0.5438 (pp) REVERT: P 84 HIS cc_start: 0.7860 (m90) cc_final: 0.7625 (m-70) REVERT: P 116 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7077 (tp30) REVERT: P 191 ASP cc_start: 0.7907 (t70) cc_final: 0.7679 (t0) REVERT: R 148 GLU cc_start: 0.5852 (tp30) cc_final: 0.5542 (tp30) REVERT: S 122 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.5872 (m-10) REVERT: S 124 ARG cc_start: 0.6647 (ptm-80) cc_final: 0.5920 (ptm-80) REVERT: S 188 GLN cc_start: 0.6945 (mp10) cc_final: 0.6625 (mt0) REVERT: S 220 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7233 (mm) REVERT: S 240 SER cc_start: 0.8784 (t) cc_final: 0.8538 (p) REVERT: S 256 TYR cc_start: 0.8468 (t80) cc_final: 0.8199 (t80) REVERT: S 284 MET cc_start: 0.7798 (ttm) cc_final: 0.7520 (ttm) REVERT: T 496 ARG cc_start: 0.7139 (mtp-110) cc_final: 0.6764 (mtp-110) REVERT: U 96 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7685 (mtp-110) REVERT: U 246 ASN cc_start: 0.6913 (m-40) cc_final: 0.6577 (m-40) REVERT: U 441 GLN cc_start: 0.7134 (mt0) cc_final: 0.6868 (mt0) REVERT: V 55 SER cc_start: 0.8550 (t) cc_final: 0.8144 (p) REVERT: V 414 TYR cc_start: 0.6832 (m-80) cc_final: 0.6630 (m-80) REVERT: V 516 ASP cc_start: 0.5482 (OUTLIER) cc_final: 0.4893 (p0) REVERT: X 229 GLU cc_start: 0.7449 (tp30) cc_final: 0.7225 (mm-30) REVERT: X 459 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6997 (mmtm) REVERT: Y 195 GLU cc_start: 0.7467 (tp30) cc_final: 0.6864 (tp30) REVERT: Y 382 SER cc_start: 0.8612 (m) cc_final: 0.8411 (m) REVERT: Y 388 ASN cc_start: 0.7826 (t0) cc_final: 0.7608 (t0) REVERT: Y 440 GLN cc_start: 0.8379 (mt0) cc_final: 0.8145 (mt0) REVERT: Y 531 VAL cc_start: 0.7376 (m) cc_final: 0.7156 (t) REVERT: Z 387 LEU cc_start: 0.9178 (tp) cc_final: 0.8958 (tp) outliers start: 120 outliers final: 80 residues processed: 778 average time/residue: 0.5116 time to fit residues: 676.0523 Evaluate side-chains 709 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 621 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 197 LEU Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 206 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain U residue 60 GLN Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 152 ASN Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 358 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 6.9990 chunk 607 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 396 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 675 optimal weight: 0.8980 chunk 560 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 354 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN 4 124 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN P 84 HIS Q 21 ASN R 181 ASN S 116 ASN T 121 ASN T 529 ASN U 152 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 471 GLN ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 204 HIS ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 54686 Z= 0.253 Angle : 0.577 9.153 74161 Z= 0.295 Chirality : 0.043 0.168 8689 Planarity : 0.004 0.061 9510 Dihedral : 5.841 86.960 7679 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 2.66 % Allowed : 16.20 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 7038 helix: 0.39 (0.09), residues: 3896 sheet: -0.86 (0.22), residues: 577 loop : -0.85 (0.13), residues: 2565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP V 73 HIS 0.005 0.001 HIS 4 233 PHE 0.028 0.001 PHE G 107 TYR 0.022 0.002 TYR 4 211 ARG 0.006 0.000 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 645 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8736 (ttpt) cc_final: 0.7882 (mptt) REVERT: 0 41 GLU cc_start: 0.4956 (pm20) cc_final: 0.4743 (pm20) REVERT: 1 24 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8373 (pp) REVERT: 1 194 LYS cc_start: 0.7599 (ptmm) cc_final: 0.7198 (ttmt) REVERT: 1 572 ASP cc_start: 0.7994 (m-30) cc_final: 0.7711 (m-30) REVERT: 4 121 ASP cc_start: 0.7775 (t0) cc_final: 0.7446 (t70) REVERT: 5 1 MET cc_start: 0.7078 (ptp) cc_final: 0.6830 (ptp) REVERT: 5 112 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7974 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8196 (t80) REVERT: 8 62 ASP cc_start: 0.8124 (m-30) cc_final: 0.7901 (m-30) REVERT: 8 69 LYS cc_start: 0.8925 (mttt) cc_final: 0.7154 (tmtt) REVERT: 8 81 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7895 (ttmt) REVERT: 9 1 MET cc_start: 0.3305 (ttp) cc_final: -0.0217 (mpp) REVERT: 9 9 LYS cc_start: 0.6768 (ttpt) cc_final: 0.6314 (ttpp) REVERT: 9 26 LEU cc_start: 0.8970 (mt) cc_final: 0.8647 (mp) REVERT: B 97 LYS cc_start: 0.7205 (mmtt) cc_final: 0.5996 (mttp) REVERT: D 60 LYS cc_start: 0.6636 (tppp) cc_final: 0.6412 (tptp) REVERT: D 95 ILE cc_start: 0.5590 (OUTLIER) cc_final: 0.5235 (mm) REVERT: E 60 LYS cc_start: 0.6240 (ptpp) cc_final: 0.5775 (mtpt) REVERT: F 81 MET cc_start: 0.6804 (ttp) cc_final: 0.6369 (ttp) REVERT: P 116 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6948 (tp30) REVERT: P 191 ASP cc_start: 0.7928 (t70) cc_final: 0.7704 (t0) REVERT: R 148 GLU cc_start: 0.5886 (tp30) cc_final: 0.5648 (tp30) REVERT: S 122 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.5970 (m-10) REVERT: S 188 GLN cc_start: 0.6977 (mp10) cc_final: 0.6709 (mt0) REVERT: S 220 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7180 (mm) REVERT: S 240 SER cc_start: 0.8794 (t) cc_final: 0.8537 (p) REVERT: S 284 MET cc_start: 0.7833 (ttm) cc_final: 0.7524 (ttm) REVERT: T 475 GLU cc_start: 0.7774 (tp30) cc_final: 0.7481 (tp30) REVERT: T 496 ARG cc_start: 0.7240 (mtp-110) cc_final: 0.6805 (mtp-110) REVERT: U 441 GLN cc_start: 0.7130 (mt0) cc_final: 0.6822 (mt0) REVERT: V 55 SER cc_start: 0.8489 (t) cc_final: 0.8080 (p) REVERT: V 414 TYR cc_start: 0.6886 (m-80) cc_final: 0.6679 (m-80) REVERT: V 516 ASP cc_start: 0.5515 (OUTLIER) cc_final: 0.4956 (p0) REVERT: X 229 GLU cc_start: 0.7520 (tp30) cc_final: 0.7268 (mm-30) REVERT: X 278 GLN cc_start: 0.6533 (pp30) cc_final: 0.6179 (pp30) REVERT: X 459 LYS cc_start: 0.7185 (mmtm) cc_final: 0.6943 (mmtm) REVERT: Y 388 ASN cc_start: 0.7867 (t0) cc_final: 0.7654 (t0) REVERT: Y 440 GLN cc_start: 0.8371 (mt0) cc_final: 0.8077 (mt0) REVERT: Z 387 LEU cc_start: 0.9163 (tp) cc_final: 0.8935 (tp) outliers start: 150 outliers final: 110 residues processed: 746 average time/residue: 0.5027 time to fit residues: 636.6910 Evaluate side-chains 731 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 614 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 119 LYS Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 236 ILE Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 439 MET Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain T residue 529 ASN Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 125 ASP Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 429 ARG Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain V residue 559 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 194 MET Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 422 MET Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 383 THR Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 358 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 384 optimal weight: 3.9990 chunk 493 optimal weight: 0.9980 chunk 382 optimal weight: 2.9990 chunk 568 optimal weight: 5.9990 chunk 377 optimal weight: 0.6980 chunk 672 optimal weight: 0.8980 chunk 421 optimal weight: 0.9990 chunk 410 optimal weight: 0.7980 chunk 310 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 346 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS E 98 GLN P 52 GLN Q 21 ASN T 121 ASN T 529 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 337 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54686 Z= 0.167 Angle : 0.539 9.176 74161 Z= 0.276 Chirality : 0.041 0.185 8689 Planarity : 0.004 0.059 9510 Dihedral : 5.464 80.049 7679 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.98 % Rotamer: Outliers : 2.34 % Allowed : 16.55 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.10), residues: 7038 helix: 0.65 (0.09), residues: 3898 sheet: -0.67 (0.23), residues: 576 loop : -0.72 (0.13), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP V 73 HIS 0.004 0.001 HIS 4 233 PHE 0.030 0.001 PHE D 116 TYR 0.033 0.001 TYR I 102 ARG 0.005 0.000 ARG 4 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 681 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8696 (ttpt) cc_final: 0.7852 (mptt) REVERT: 1 24 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8222 (pp) REVERT: 1 194 LYS cc_start: 0.7585 (ptmm) cc_final: 0.7247 (ttmt) REVERT: 1 572 ASP cc_start: 0.7949 (m-30) cc_final: 0.7711 (m-30) REVERT: 2 197 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6644 (mm) REVERT: 4 121 ASP cc_start: 0.7716 (t0) cc_final: 0.7224 (t0) REVERT: 4 146 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6514 (tp30) REVERT: 5 1 MET cc_start: 0.7325 (ptp) cc_final: 0.7067 (ptp) REVERT: 5 51 TYR cc_start: 0.9153 (t80) cc_final: 0.8787 (t80) REVERT: 5 112 ARG cc_start: 0.8322 (mtm180) cc_final: 0.8020 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9086 (OUTLIER) cc_final: 0.8186 (t80) REVERT: 8 69 LYS cc_start: 0.8878 (mttt) cc_final: 0.7111 (tmtt) REVERT: 8 81 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7962 (ttmm) REVERT: 9 1 MET cc_start: 0.2769 (ttp) cc_final: 0.0142 (mpp) REVERT: 9 9 LYS cc_start: 0.6717 (ttpt) cc_final: 0.6254 (tttm) REVERT: 9 13 LYS cc_start: 0.8093 (mptt) cc_final: 0.7869 (mmtt) REVERT: 9 26 LEU cc_start: 0.8942 (mt) cc_final: 0.8631 (mp) REVERT: B 97 LYS cc_start: 0.7003 (mmtt) cc_final: 0.5998 (mttp) REVERT: C 123 LEU cc_start: 0.7267 (mt) cc_final: 0.7051 (mt) REVERT: D 95 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5406 (mm) REVERT: E 60 LYS cc_start: 0.6197 (ptpp) cc_final: 0.5768 (ttpp) REVERT: E 115 LEU cc_start: 0.6007 (mm) cc_final: 0.5671 (tp) REVERT: F 81 MET cc_start: 0.6721 (ttp) cc_final: 0.6268 (ttp) REVERT: I 102 TYR cc_start: 0.5708 (OUTLIER) cc_final: 0.5046 (t80) REVERT: M 110 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8730 (mm) REVERT: P 52 GLN cc_start: 0.8011 (mt0) cc_final: 0.7712 (mt0) REVERT: P 83 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7007 (mt0) REVERT: P 116 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6801 (tp30) REVERT: P 136 GLU cc_start: 0.7218 (mp0) cc_final: 0.6887 (mp0) REVERT: S 122 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.5888 (m-10) REVERT: S 124 ARG cc_start: 0.6877 (ptm-80) cc_final: 0.6155 (ptm-80) REVERT: S 188 GLN cc_start: 0.6904 (mp10) cc_final: 0.6628 (mt0) REVERT: S 220 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7196 (mm) REVERT: S 240 SER cc_start: 0.8745 (t) cc_final: 0.8482 (p) REVERT: S 256 TYR cc_start: 0.8457 (t80) cc_final: 0.8134 (t80) REVERT: T 287 MET cc_start: 0.7605 (ttm) cc_final: 0.7324 (ttm) REVERT: U 246 ASN cc_start: 0.6728 (m-40) cc_final: 0.6268 (m-40) REVERT: U 441 GLN cc_start: 0.7149 (mt0) cc_final: 0.6804 (mt0) REVERT: V 55 SER cc_start: 0.8435 (t) cc_final: 0.8053 (p) REVERT: V 516 ASP cc_start: 0.5419 (OUTLIER) cc_final: 0.4891 (p0) REVERT: V 549 HIS cc_start: 0.7628 (m-70) cc_final: 0.7406 (t-90) REVERT: X 82 ASP cc_start: 0.7813 (t70) cc_final: 0.7440 (t0) REVERT: X 229 GLU cc_start: 0.7441 (tp30) cc_final: 0.7207 (mm-30) REVERT: X 278 GLN cc_start: 0.6228 (pp30) cc_final: 0.5972 (pp30) REVERT: Y 83 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7823 (t0) REVERT: Y 195 GLU cc_start: 0.7350 (tp30) cc_final: 0.6748 (tp30) REVERT: Y 422 MET cc_start: 0.4885 (mtp) cc_final: 0.4651 (mtm) REVERT: Y 440 GLN cc_start: 0.8375 (mt0) cc_final: 0.8103 (mt0) REVERT: Z 387 LEU cc_start: 0.9132 (tp) cc_final: 0.8900 (tp) outliers start: 132 outliers final: 93 residues processed: 773 average time/residue: 0.5018 time to fit residues: 657.4615 Evaluate side-chains 725 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 620 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 197 LEU Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 146 GLU Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 5 residue 119 LYS Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 122 PHE Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 203 PHE Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain U residue 517 ILE Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 358 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 130 optimal weight: 0.0050 chunk 427 optimal weight: 6.9990 chunk 458 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 528 optimal weight: 0.6980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 346 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS T 121 ASN T 529 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 322 GLN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54686 Z= 0.216 Angle : 0.564 9.238 74161 Z= 0.288 Chirality : 0.042 0.184 8689 Planarity : 0.004 0.060 9510 Dihedral : 5.451 75.145 7677 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 2.45 % Allowed : 17.24 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.10), residues: 7038 helix: 0.72 (0.09), residues: 3892 sheet: -0.70 (0.23), residues: 576 loop : -0.72 (0.13), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP V 73 HIS 0.005 0.001 HIS 4 233 PHE 0.034 0.001 PHE G 107 TYR 0.029 0.001 TYR I 102 ARG 0.008 0.000 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 642 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8705 (ttpt) cc_final: 0.7868 (mptt) REVERT: 1 24 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8312 (pp) REVERT: 1 194 LYS cc_start: 0.7591 (ptmm) cc_final: 0.7262 (ttmt) REVERT: 1 572 ASP cc_start: 0.7960 (m-30) cc_final: 0.7666 (m-30) REVERT: 4 121 ASP cc_start: 0.7664 (t0) cc_final: 0.7177 (t0) REVERT: 4 146 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: 5 1 MET cc_start: 0.7224 (ptp) cc_final: 0.6944 (ptp) REVERT: 5 51 TYR cc_start: 0.9209 (t80) cc_final: 0.8876 (t80) REVERT: 5 112 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8060 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8225 (t80) REVERT: 8 69 LYS cc_start: 0.8903 (mttt) cc_final: 0.7117 (tmtt) REVERT: 8 81 LYS cc_start: 0.8396 (mtpt) cc_final: 0.8017 (ttmm) REVERT: 9 1 MET cc_start: 0.2648 (ttp) cc_final: 0.0130 (mpp) REVERT: 9 9 LYS cc_start: 0.6790 (ttpt) cc_final: 0.6283 (ttpp) REVERT: 9 13 LYS cc_start: 0.8177 (mptt) cc_final: 0.7934 (mmtt) REVERT: 9 26 LEU cc_start: 0.8951 (mt) cc_final: 0.8645 (mp) REVERT: B 97 LYS cc_start: 0.7101 (mmtt) cc_final: 0.6123 (mttp) REVERT: D 95 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5218 (mm) REVERT: E 60 LYS cc_start: 0.6188 (ptpp) cc_final: 0.5774 (mtpt) REVERT: E 115 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5584 (tp) REVERT: F 81 MET cc_start: 0.6741 (ttp) cc_final: 0.6287 (ttp) REVERT: I 98 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7146 (tp40) REVERT: I 102 TYR cc_start: 0.5874 (OUTLIER) cc_final: 0.4949 (t80) REVERT: M 110 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8747 (mm) REVERT: P 52 GLN cc_start: 0.8039 (mt0) cc_final: 0.7751 (mt0) REVERT: P 83 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7095 (mt0) REVERT: P 116 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6830 (tp30) REVERT: P 136 GLU cc_start: 0.7239 (mp0) cc_final: 0.6984 (mp0) REVERT: S 122 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.5918 (m-10) REVERT: S 188 GLN cc_start: 0.6976 (mp10) cc_final: 0.6670 (mt0) REVERT: S 220 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7255 (mm) REVERT: S 240 SER cc_start: 0.8707 (t) cc_final: 0.8480 (p) REVERT: S 256 TYR cc_start: 0.8501 (t80) cc_final: 0.8173 (t80) REVERT: S 284 MET cc_start: 0.7786 (ttm) cc_final: 0.7446 (ttm) REVERT: U 441 GLN cc_start: 0.7125 (mt0) cc_final: 0.6799 (mt0) REVERT: V 55 SER cc_start: 0.8479 (t) cc_final: 0.8084 (p) REVERT: V 516 ASP cc_start: 0.5737 (OUTLIER) cc_final: 0.5150 (p0) REVERT: X 229 GLU cc_start: 0.7445 (tp30) cc_final: 0.7222 (mm-30) REVERT: X 278 GLN cc_start: 0.6300 (pp30) cc_final: 0.6012 (pp30) REVERT: Y 83 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.7865 (t0) REVERT: Y 422 MET cc_start: 0.4897 (mtp) cc_final: 0.4672 (mtm) REVERT: Y 440 GLN cc_start: 0.8411 (mt0) cc_final: 0.8113 (mt0) REVERT: Z 387 LEU cc_start: 0.9138 (tp) cc_final: 0.8916 (tp) outliers start: 138 outliers final: 103 residues processed: 741 average time/residue: 0.5302 time to fit residues: 670.6203 Evaluate side-chains 736 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 620 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 146 GLU Chi-restraints excluded: chain 4 residue 194 ASP Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 112 ARG Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 83 GLN Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 160 GLU Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 121 ASN Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 215 ILE Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 286 ILE Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 442 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 70 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 335 SER Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 141 TRP Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 358 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 0.8980 chunk 644 optimal weight: 1.9990 chunk 588 optimal weight: 0.8980 chunk 626 optimal weight: 1.9990 chunk 377 optimal weight: 0.8980 chunk 273 optimal weight: 8.9990 chunk 492 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 566 optimal weight: 0.9990 chunk 592 optimal weight: 0.5980 chunk 624 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 346 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS T 529 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54686 Z= 0.170 Angle : 0.543 9.189 74161 Z= 0.277 Chirality : 0.041 0.188 8689 Planarity : 0.004 0.059 9510 Dihedral : 5.234 71.890 7675 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.08 % Favored : 95.79 % Rotamer: Outliers : 2.18 % Allowed : 17.71 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.10), residues: 7038 helix: 0.89 (0.09), residues: 3887 sheet: -0.64 (0.22), residues: 606 loop : -0.63 (0.13), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP V 73 HIS 0.004 0.001 HIS 4 233 PHE 0.034 0.001 PHE G 122 TYR 0.029 0.001 TYR I 102 ARG 0.008 0.000 ARG 2 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 655 time to evaluate : 4.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8658 (ttpt) cc_final: 0.7864 (mptt) REVERT: 1 24 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8218 (pp) REVERT: 1 194 LYS cc_start: 0.7562 (ptmm) cc_final: 0.7249 (ttmt) REVERT: 1 572 ASP cc_start: 0.7951 (m-30) cc_final: 0.7713 (m-30) REVERT: 4 121 ASP cc_start: 0.7598 (t0) cc_final: 0.7151 (t0) REVERT: 4 146 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: 5 1 MET cc_start: 0.7322 (ptp) cc_final: 0.6934 (ptp) REVERT: 5 51 TYR cc_start: 0.9144 (t80) cc_final: 0.8753 (t80) REVERT: 5 112 ARG cc_start: 0.8335 (mtm180) cc_final: 0.8049 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8191 (t80) REVERT: 8 69 LYS cc_start: 0.8909 (mttt) cc_final: 0.7123 (tmtt) REVERT: 8 81 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7963 (ttmm) REVERT: 9 1 MET cc_start: 0.2126 (ttp) cc_final: 0.0285 (mpp) REVERT: 9 9 LYS cc_start: 0.6891 (ttpt) cc_final: 0.6633 (ttpp) REVERT: 9 13 LYS cc_start: 0.8176 (mptt) cc_final: 0.7947 (mmtt) REVERT: 9 26 LEU cc_start: 0.8941 (mt) cc_final: 0.8643 (mp) REVERT: B 97 LYS cc_start: 0.7024 (mmtt) cc_final: 0.6183 (mttp) REVERT: C 123 LEU cc_start: 0.7239 (mt) cc_final: 0.7030 (mt) REVERT: D 95 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5288 (mm) REVERT: E 60 LYS cc_start: 0.6234 (ptpp) cc_final: 0.5810 (mtpt) REVERT: E 115 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5467 (tp) REVERT: F 81 MET cc_start: 0.6603 (ttp) cc_final: 0.6220 (ttp) REVERT: I 98 GLN cc_start: 0.7431 (tm-30) cc_final: 0.7166 (tp40) REVERT: I 102 TYR cc_start: 0.5615 (OUTLIER) cc_final: 0.4880 (t80) REVERT: M 110 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8725 (mm) REVERT: P 52 GLN cc_start: 0.8031 (mt0) cc_final: 0.7764 (mt0) REVERT: P 68 ASP cc_start: 0.8272 (m-30) cc_final: 0.8050 (t0) REVERT: P 136 GLU cc_start: 0.7124 (mp0) cc_final: 0.6900 (mp0) REVERT: Q 26 LEU cc_start: 0.8447 (mm) cc_final: 0.8204 (mp) REVERT: Q 48 ARG cc_start: 0.7249 (ptt180) cc_final: 0.6860 (ptt90) REVERT: S 122 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.5950 (m-10) REVERT: S 188 GLN cc_start: 0.6966 (mp10) cc_final: 0.6639 (mt0) REVERT: S 220 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7176 (mm) REVERT: S 240 SER cc_start: 0.8670 (t) cc_final: 0.8437 (p) REVERT: S 256 TYR cc_start: 0.8462 (t80) cc_final: 0.8143 (t80) REVERT: S 284 MET cc_start: 0.7721 (ttm) cc_final: 0.7384 (ttm) REVERT: U 514 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7678 (m) REVERT: V 55 SER cc_start: 0.8453 (t) cc_final: 0.8076 (p) REVERT: V 429 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7475 (mtm-85) REVERT: V 516 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5112 (p0) REVERT: X 229 GLU cc_start: 0.7454 (tp30) cc_final: 0.7230 (mm-30) REVERT: Y 83 ASN cc_start: 0.8389 (OUTLIER) cc_final: 0.7884 (t0) REVERT: Y 422 MET cc_start: 0.4819 (mtp) cc_final: 0.4596 (mtm) REVERT: Y 440 GLN cc_start: 0.8383 (mt0) cc_final: 0.8072 (mt0) REVERT: Y 441 ARG cc_start: 0.7695 (mpt90) cc_final: 0.7463 (mpt90) REVERT: Z 435 ARG cc_start: 0.6855 (ttm-80) cc_final: 0.6512 (ttm-80) outliers start: 123 outliers final: 93 residues processed: 734 average time/residue: 0.5199 time to fit residues: 653.6014 Evaluate side-chains 731 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 625 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 146 GLU Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 83 LEU Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 66 SER Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 206 THR Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 212 LEU Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 429 ARG Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.6980 chunk 662 optimal weight: 8.9990 chunk 404 optimal weight: 0.9990 chunk 314 optimal weight: 4.9990 chunk 460 optimal weight: 0.9990 chunk 695 optimal weight: 0.0470 chunk 640 optimal weight: 9.9990 chunk 553 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 427 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 65 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 198 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54686 Z= 0.163 Angle : 0.550 10.687 74161 Z= 0.280 Chirality : 0.041 0.191 8689 Planarity : 0.004 0.059 9510 Dihedral : 5.086 72.097 7675 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.06 % Favored : 95.81 % Rotamer: Outliers : 1.99 % Allowed : 18.20 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7038 helix: 0.96 (0.09), residues: 3898 sheet: -0.54 (0.23), residues: 586 loop : -0.61 (0.13), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP V 73 HIS 0.004 0.001 HIS U 61 PHE 0.030 0.001 PHE V 489 TYR 0.033 0.001 TYR I 102 ARG 0.008 0.000 ARG 2 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14076 Ramachandran restraints generated. 7038 Oldfield, 0 Emsley, 7038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 662 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8656 (ttpt) cc_final: 0.7907 (mptt) REVERT: 1 24 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8176 (pp) REVERT: 1 194 LYS cc_start: 0.7528 (ptmm) cc_final: 0.7241 (ttmt) REVERT: 1 423 ASN cc_start: 0.7821 (m-40) cc_final: 0.7531 (p0) REVERT: 1 572 ASP cc_start: 0.7954 (m-30) cc_final: 0.7703 (m-30) REVERT: 4 121 ASP cc_start: 0.7616 (t0) cc_final: 0.7209 (t0) REVERT: 4 146 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: 5 1 MET cc_start: 0.7334 (ptp) cc_final: 0.6922 (ptp) REVERT: 5 51 TYR cc_start: 0.9137 (t80) cc_final: 0.8731 (t80) REVERT: 5 112 ARG cc_start: 0.8324 (mtm180) cc_final: 0.8055 (ptm-80) REVERT: 6 146 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8139 (t80) REVERT: 8 69 LYS cc_start: 0.8903 (mttt) cc_final: 0.7139 (tmtt) REVERT: 8 81 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7935 (ttmm) REVERT: 9 1 MET cc_start: 0.2151 (ttp) cc_final: 0.0085 (mpp) REVERT: 9 9 LYS cc_start: 0.6895 (ttpt) cc_final: 0.6643 (ttpp) REVERT: 9 13 LYS cc_start: 0.8195 (mptt) cc_final: 0.7974 (mmtt) REVERT: 9 26 LEU cc_start: 0.8991 (mt) cc_final: 0.8694 (mp) REVERT: B 97 LYS cc_start: 0.6911 (mmtt) cc_final: 0.6106 (mttp) REVERT: D 95 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5335 (mm) REVERT: E 60 LYS cc_start: 0.6273 (ptpp) cc_final: 0.5845 (ttpp) REVERT: E 115 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5492 (tp) REVERT: F 81 MET cc_start: 0.6625 (ttp) cc_final: 0.6300 (ttp) REVERT: G 122 PHE cc_start: 0.6084 (m-80) cc_final: 0.5854 (m-80) REVERT: I 98 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7508 (tm-30) REVERT: I 102 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5090 (t80) REVERT: M 110 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8753 (mm) REVERT: P 52 GLN cc_start: 0.8000 (mt0) cc_final: 0.7740 (mt0) REVERT: P 68 ASP cc_start: 0.8237 (m-30) cc_final: 0.7948 (t0) REVERT: P 136 GLU cc_start: 0.7102 (mp0) cc_final: 0.6847 (mp0) REVERT: Q 26 LEU cc_start: 0.8441 (mm) cc_final: 0.8212 (mp) REVERT: Q 48 ARG cc_start: 0.7250 (ptt180) cc_final: 0.6850 (ptt90) REVERT: S 122 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.5895 (m-10) REVERT: S 188 GLN cc_start: 0.6890 (mp10) cc_final: 0.6632 (mt0) REVERT: S 220 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7128 (mm) REVERT: S 240 SER cc_start: 0.8653 (t) cc_final: 0.8407 (p) REVERT: S 256 TYR cc_start: 0.8444 (t80) cc_final: 0.8146 (t80) REVERT: S 284 MET cc_start: 0.7703 (ttm) cc_final: 0.7364 (ttm) REVERT: U 514 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7632 (m) REVERT: V 55 SER cc_start: 0.8453 (t) cc_final: 0.8082 (p) REVERT: V 516 ASP cc_start: 0.5676 (OUTLIER) cc_final: 0.5101 (p0) REVERT: X 229 GLU cc_start: 0.7439 (tp30) cc_final: 0.7220 (mm-30) REVERT: Y 83 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7972 (t0) REVERT: Y 440 GLN cc_start: 0.8377 (mt0) cc_final: 0.8076 (mt0) REVERT: Y 441 ARG cc_start: 0.7714 (mpt90) cc_final: 0.7471 (mpt90) outliers start: 112 outliers final: 94 residues processed: 739 average time/residue: 0.5135 time to fit residues: 648.9874 Evaluate side-chains 736 residues out of total 5636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 630 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 1 residue 24 LEU Chi-restraints excluded: chain 1 residue 162 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 240 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 24 VAL Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 3 residue 91 VAL Chi-restraints excluded: chain 4 residue 115 THR Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 146 GLU Chi-restraints excluded: chain 4 residue 197 ASP Chi-restraints excluded: chain 4 residue 247 SER Chi-restraints excluded: chain 5 residue 26 LEU Chi-restraints excluded: chain 5 residue 61 SER Chi-restraints excluded: chain 5 residue 67 SER Chi-restraints excluded: chain 5 residue 113 VAL Chi-restraints excluded: chain 6 residue 139 THR Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 136 GLU Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 7 residue 157 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain D residue 95 ILE Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 128 ASP Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 157 ILE Chi-restraints excluded: chain P residue 207 VAL Chi-restraints excluded: chain P residue 211 THR Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 165 THR Chi-restraints excluded: chain S residue 181 GLU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain S residue 272 SER Chi-restraints excluded: chain S residue 283 GLU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 107 GLU Chi-restraints excluded: chain T residue 164 THR Chi-restraints excluded: chain T residue 187 VAL Chi-restraints excluded: chain T residue 204 THR Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 257 CYS Chi-restraints excluded: chain T residue 376 SER Chi-restraints excluded: chain T residue 496 ARG Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 198 VAL Chi-restraints excluded: chain U residue 273 VAL Chi-restraints excluded: chain U residue 300 PHE Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 514 VAL Chi-restraints excluded: chain V residue 47 GLU Chi-restraints excluded: chain V residue 52 LYS Chi-restraints excluded: chain V residue 67 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 187 VAL Chi-restraints excluded: chain V residue 255 VAL Chi-restraints excluded: chain V residue 516 ASP Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 69 SER Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 266 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 297 VAL Chi-restraints excluded: chain X residue 335 SER Chi-restraints excluded: chain X residue 431 LEU Chi-restraints excluded: chain X residue 484 MET Chi-restraints excluded: chain X residue 502 MET Chi-restraints excluded: chain Y residue 83 ASN Chi-restraints excluded: chain Y residue 141 TRP Chi-restraints excluded: chain Y residue 204 HIS Chi-restraints excluded: chain Y residue 228 ILE Chi-restraints excluded: chain Y residue 471 GLN Chi-restraints excluded: chain Z residue 122 MET Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 198 ASN Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 328 THR Chi-restraints excluded: chain Z residue 358 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.9980 chunk 589 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 510 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 554 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 569 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 60 GLN 1 346 GLN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 HIS ** S 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 246 ASN T 529 ASN ** U 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 199 ASN Z 198 ASN ** Z 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.146207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.120388 restraints weight = 83597.556| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.13 r_work: 0.3258 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 54686 Z= 0.172 Angle : 0.547 9.486 74161 Z= 0.279 Chirality : 0.041 0.196 8689 Planarity : 0.004 0.059 9510 Dihedral : 5.014 72.601 7673 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.05 % Favored : 95.82 % Rotamer: Outliers : 2.04 % Allowed : 18.29 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7038 helix: 1.02 (0.09), residues: 3892 sheet: -0.51 (0.23), residues: 587 loop : -0.58 (0.13), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP V 73 HIS 0.006 0.001 HIS Z 204 PHE 0.029 0.001 PHE V 489 TYR 0.031 0.001 TYR I 102 ARG 0.009 0.000 ARG 2 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12955.99 seconds wall clock time: 225 minutes 37.38 seconds (13537.38 seconds total)