Starting phenix.real_space_refine on Sun Feb 25 13:18:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rql_4984/02_2024/6rql_4984.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rql_4984/02_2024/6rql_4984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rql_4984/02_2024/6rql_4984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rql_4984/02_2024/6rql_4984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rql_4984/02_2024/6rql_4984.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rql_4984/02_2024/6rql_4984.pdb" } resolution = 2.9 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: 5 Type Number sf(0) Gaussians P 83 5.49 5 S 237 5.16 5 C 32522 2.51 5 N 8914 2.21 5 O 9870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 58": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 293": "NH1" <-> "NH2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "S ARG 44": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 221": "NH1" <-> "NH2" Residue "S ARG 257": "NH1" <-> "NH2" Residue "S PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 407": "NH1" <-> "NH2" Residue "S ARG 419": "NH1" <-> "NH2" Residue "S ARG 434": "NH1" <-> "NH2" Residue "S ARG 472": "NH1" <-> "NH2" Residue "S ARG 484": "NH1" <-> "NH2" Residue "S ARG 542": "NH1" <-> "NH2" Residue "S ARG 746": "NH1" <-> "NH2" Residue "S ARG 762": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 441": "NH1" <-> "NH2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51626 Number of models: 1 Model: "" Number of chains: 20 Chain: "T" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 842 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "U" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 877 Classifications: {'DNA': 42} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 41} Chain: "Q" Number of atoms: 3931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3931 Classifications: {'peptide': 476} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "M" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 850 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 11953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 11953 Classifications: {'peptide': 1542} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 62, 'TRANS': 1479} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 137 Chain: "B" Number of atoms: 9371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9371 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1576 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "O" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4086 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 485} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb=" P DG U 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG U 12 " occ=0.00 residue: pdb=" P DA U 19 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 19 " occ=0.00 residue: pdb=" P DA U 31 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 31 " occ=0.00 Time building chain proxies: 27.17, per 1000 atoms: 0.53 Number of scatterers: 51626 At special positions: 0 Unit cell: (160.16, 215.28, 189.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 237 16.00 P 83 15.00 O 9870 8.00 N 8914 7.00 C 32522 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 - 3.50 Amino acid : False - 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: 18.65 Conformation dependent library (CDL) restraints added in 8.7 seconds 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11846 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 60 sheets defined 37.8% alpha, 14.0% beta 20 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 19.40 Creating SS restraints... Processing helix chain 'Q' and resid 78 through 82 removed outlier: 4.114A pdb=" N LEU Q 81 " --> pdb=" O SER Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 90 removed outlier: 4.368A pdb=" N LYS Q 90 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 122 removed outlier: 3.682A pdb=" N LEU Q 105 " --> pdb=" O LYS Q 101 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS Q 106 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER Q 107 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 146 removed outlier: 3.592A pdb=" N LYS Q 134 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN Q 145 " --> pdb=" O LEU Q 141 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP Q 146 " --> pdb=" O LYS Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 172 removed outlier: 3.936A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 187 removed outlier: 5.226A pdb=" N TRP Q 184 " --> pdb=" O ASP Q 180 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS Q 186 " --> pdb=" O ILE Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 209 through 214 removed outlier: 3.534A pdb=" N ILE Q 214 " --> pdb=" O TYR Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 237 removed outlier: 3.547A pdb=" N GLY Q 235 " --> pdb=" O ALA Q 231 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 261 removed outlier: 4.011A pdb=" N LEU Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 275 removed outlier: 3.984A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 4.258A pdb=" N LEU Q 307 " --> pdb=" O GLU Q 303 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 339 removed outlier: 3.691A pdb=" N GLU Q 336 " --> pdb=" O LEU Q 332 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) Processing helix chain 'Q' and resid 344 through 357 removed outlier: 3.580A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL Q 356 " --> pdb=" O ILE Q 352 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR Q 357 " --> pdb=" O VAL Q 353 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 369 removed outlier: 4.073A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 371 through 381 Processing helix chain 'Q' and resid 382 through 384 No H-bonds generated for 'chain 'Q' and resid 382 through 384' Processing helix chain 'Q' and resid 407 through 417 Processing helix chain 'Q' and resid 437 through 447 removed outlier: 3.957A pdb=" N ASP Q 441 " --> pdb=" O THR Q 437 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN Q 443 " --> pdb=" O ILE Q 439 " (cutoff:3.500A) Processing helix chain 'Q' and resid 470 through 490 removed outlier: 3.978A pdb=" N GLU Q 474 " --> pdb=" O PRO Q 470 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Q 479 " --> pdb=" O ALA Q 475 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL Q 489 " --> pdb=" O SER Q 485 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP Q 490 " --> pdb=" O GLN Q 486 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 504 removed outlier: 3.710A pdb=" N CYS Q 501 " --> pdb=" O GLN Q 497 " (cutoff:3.500A) Processing helix chain 'Q' and resid 505 through 514 removed outlier: 3.604A pdb=" N HIS Q 511 " --> pdb=" O ASN Q 507 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 195 removed outlier: 3.731A pdb=" N ARG S 194 " --> pdb=" O ALA S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 576 Processing helix chain 'S' and resid 585 through 604 removed outlier: 4.033A pdb=" N ILE S 589 " --> pdb=" O GLU S 585 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY S 590 " --> pdb=" O LYS S 586 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU S 592 " --> pdb=" O SER S 588 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE S 596 " --> pdb=" O LEU S 592 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU S 598 " --> pdb=" O SER S 594 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU S 600 " --> pdb=" O ILE S 596 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) Processing helix chain 'S' and resid 607 through 612 Processing helix chain 'S' and resid 616 through 643 removed outlier: 4.014A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS S 643 " --> pdb=" O GLU S 639 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.745A pdb=" N PHE S 683 " --> pdb=" O LEU S 679 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN S 684 " --> pdb=" O ASP S 680 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR S 685 " --> pdb=" O GLN S 681 " (cutoff:3.500A) Processing helix chain 'S' and resid 700 through 705 removed outlier: 4.430A pdb=" N LEU S 704 " --> pdb=" O LEU S 700 " (cutoff:3.500A) Processing helix chain 'S' and resid 710 through 720 Processing helix chain 'S' and resid 730 through 742 removed outlier: 3.811A pdb=" N VAL S 737 " --> pdb=" O THR S 733 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 766 removed outlier: 4.017A pdb=" N ILE S 756 " --> pdb=" O LEU S 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN S 757 " --> pdb=" O PHE S 753 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER S 761 " --> pdb=" O GLN S 757 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER S 765 " --> pdb=" O SER S 761 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY S 766 " --> pdb=" O ARG S 762 " (cutoff:3.500A) Processing helix chain 'S' and resid 767 through 773 removed outlier: 4.254A pdb=" N ILE S 772 " --> pdb=" O TYR S 768 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER S 773 " --> pdb=" O GLN S 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 35 removed outlier: 3.632A pdb=" N ARG R 16 " --> pdb=" O LYS R 12 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG R 33 " --> pdb=" O ARG R 29 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 34 " --> pdb=" O ARG R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 130 Processing helix chain 'R' and resid 158 through 174 removed outlier: 3.615A pdb=" N LYS R 167 " --> pdb=" O LYS R 163 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE R 168 " --> pdb=" O LYS R 164 " (cutoff:3.500A) Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 175 through 179 removed outlier: 3.939A pdb=" N LEU R 178 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 removed outlier: 3.720A pdb=" N GLN R 189 " --> pdb=" O LYS R 185 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.640A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 222 " --> pdb=" O ASP R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.604A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 253 removed outlier: 3.786A pdb=" N LEU R 250 " --> pdb=" O GLN R 246 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP R 251 " --> pdb=" O ILE R 247 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 246 through 253' Processing helix chain 'R' and resid 255 through 261 removed outlier: 3.662A pdb=" N LEU R 261 " --> pdb=" O ILE R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 removed outlier: 4.006A pdb=" N LEU R 271 " --> pdb=" O GLY R 267 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.886A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 323 removed outlier: 3.613A pdb=" N CYS R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 353 Processing helix chain 'R' and resid 362 through 379 removed outlier: 3.501A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 403 removed outlier: 4.299A pdb=" N ASN R 402 " --> pdb=" O ASP R 398 " (cutoff:3.500A) Processing helix chain 'R' and resid 403 through 421 removed outlier: 3.886A pdb=" N HIS R 407 " --> pdb=" O GLN R 403 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL R 411 " --> pdb=" O HIS R 407 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE R 417 " --> pdb=" O THR R 413 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS R 421 " --> pdb=" O ILE R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 437 removed outlier: 3.543A pdb=" N GLU R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN R 433 " --> pdb=" O ARG R 429 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 443 removed outlier: 3.535A pdb=" N ARG R 441 " --> pdb=" O SER R 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 28 removed outlier: 4.432A pdb=" N LEU A 27 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.699A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.591A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.510A pdb=" N GLU A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.721A pdb=" N LYS A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 3.672A pdb=" N LEU A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.731A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.993A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 404 removed outlier: 3.747A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.565A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.716A pdb=" N VAL A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.859A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.621A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'A' and resid 640 through 648 removed outlier: 4.190A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.570A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.526A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.821A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.578A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 824 removed outlier: 3.571A pdb=" N LEU A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 849 removed outlier: 3.506A pdb=" N ARG A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 3.505A pdb=" N THR A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 882 Processing helix chain 'A' and resid 891 through 912 removed outlier: 4.088A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.577A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 991 through 1002 Processing helix chain 'A' and resid 1009 through 1013 removed outlier: 3.713A pdb=" N LYS A1012 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR A1013 " --> pdb=" O ALA A1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1009 through 1013' Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 4.203A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1078 removed outlier: 3.818A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1089 removed outlier: 3.562A pdb=" N HIS A1088 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1085 through 1089' Processing helix chain 'A' and resid 1091 through 1108 removed outlier: 4.286A pdb=" N LEU A1095 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 3.538A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1126 Processing helix chain 'A' and resid 1137 through 1150 removed outlier: 3.820A pdb=" N ASP A1142 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A1150 " --> pdb=" O SER A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.744A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A1174 " --> pdb=" O MET A1170 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.755A pdb=" N ARG A1221 " --> pdb=" O LEU A1217 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 Processing helix chain 'A' and resid 1298 through 1306 removed outlier: 3.965A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.580A pdb=" N LEU A1313 " --> pdb=" O SER A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1339 removed outlier: 3.507A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1367 removed outlier: 3.777A pdb=" N GLU A1366 " --> pdb=" O LYS A1363 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1367 " --> pdb=" O ARG A1364 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1363 through 1367' Processing helix chain 'A' and resid 1389 through 1397 Processing helix chain 'A' and resid 1440 through 1454 removed outlier: 3.596A pdb=" N ALA A1449 " --> pdb=" O ASP A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1494 removed outlier: 3.593A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.640A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1554 removed outlier: 3.623A pdb=" N LYS A1551 " --> pdb=" O ALA A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.894A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.653A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1585 " --> pdb=" O HIS A1581 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.844A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1628 Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.914A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 27 Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.569A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 58 through 65 removed outlier: 4.249A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.885A pdb=" N SER B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 84 through 89' Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.531A pdb=" N PHE B 222 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 223 " --> pdb=" O PRO B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 223' Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.597A pdb=" N ALA B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.652A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 310 through 317 removed outlier: 3.575A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.844A pdb=" N VAL B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.696A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.506A pdb=" N LEU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 411 through 430 removed outlier: 3.591A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 456 through 468 removed outlier: 3.691A pdb=" N LYS B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.779A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 removed outlier: 3.674A pdb=" N PHE B 509 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA B 510 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 506 through 511' Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.584A pdb=" N SER B 524 " --> pdb=" O LEU B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.652A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.586A pdb=" N MET B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 removed outlier: 3.532A pdb=" N GLU B 680 " --> pdb=" O THR B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.963A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.507A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR B 717 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 736 removed outlier: 3.673A pdb=" N HIS B 735 " --> pdb=" O ALA B 732 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 736 " --> pdb=" O LEU B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 732 through 736' Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.709A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 760 " --> pdb=" O LEU B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 760' Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.511A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 952 through 958 removed outlier: 4.628A pdb=" N SER B 956 " --> pdb=" O HIS B 952 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 975 removed outlier: 3.804A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 971 " --> pdb=" O LEU B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.630A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 4.322A pdb=" N ASP B1042 " --> pdb=" O MET B1039 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B1043 " --> pdb=" O VAL B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1043' Processing helix chain 'B' and resid 1072 through 1082 removed outlier: 3.561A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1091 removed outlier: 3.759A pdb=" N LEU B1088 " --> pdb=" O THR B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1189 removed outlier: 3.943A pdb=" N LYS B1183 " --> pdb=" O PRO B1179 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.673A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 4.023A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.577A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.282A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.660A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.658A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.602A pdb=" N ARG D 7 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 12 " --> pdb=" O THR D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.580A pdb=" N LEU D 37 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.742A pdb=" N SER D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.698A pdb=" N ILE E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.566A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 4.042A pdb=" N ALA E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.626A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 104 Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.722A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E 124 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.833A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 removed outlier: 4.261A pdb=" N GLU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.643A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 69 removed outlier: 3.539A pdb=" N HIS F 61 " --> pdb=" O ASP F 57 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.733A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 127 removed outlier: 3.689A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 127 " --> pdb=" O LYS F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.612A pdb=" N ILE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 149 through 152 Processing helix chain 'G' and resid 158 through 162 Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'I' and resid 58 through 63 removed outlier: 3.759A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.618A pdb=" N ASN J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.547A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 51 removed outlier: 3.583A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.820A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.727A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE K 139 " --> pdb=" O PHE K 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 154 removed outlier: 3.643A pdb=" N ARG N 154 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 61 removed outlier: 3.705A pdb=" N LYS O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 78 removed outlier: 3.648A pdb=" N ALA O 75 " --> pdb=" O ILE O 71 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 103 Processing helix chain 'O' and resid 112 through 121 removed outlier: 4.192A pdb=" N ILE O 116 " --> pdb=" O GLY O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.560A pdb=" N GLU O 127 " --> pdb=" O LYS O 124 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU O 128 " --> pdb=" O TRP O 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 124 through 128' Processing helix chain 'O' and resid 129 through 147 removed outlier: 4.502A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE O 140 " --> pdb=" O TYR O 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 160 removed outlier: 3.896A pdb=" N SER O 155 " --> pdb=" O TRP O 151 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.954A pdb=" N HIS O 173 " --> pdb=" O THR O 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP O 174 " --> pdb=" O VAL O 170 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 197 removed outlier: 4.050A pdb=" N ASP O 191 " --> pdb=" O MET O 187 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 222 removed outlier: 3.808A pdb=" N ARG O 219 " --> pdb=" O LEU O 215 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 246 removed outlier: 3.758A pdb=" N TRP O 230 " --> pdb=" O GLY O 226 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU O 232 " --> pdb=" O GLN O 228 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU O 235 " --> pdb=" O SER O 231 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU O 244 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN O 245 " --> pdb=" O ASP O 241 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 347 removed outlier: 3.561A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR O 337 " --> pdb=" O ASP O 333 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 353 removed outlier: 3.588A pdb=" N GLU O 353 " --> pdb=" O PRO O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.762A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 383 through 389 Processing helix chain 'O' and resid 392 through 409 removed outlier: 3.573A pdb=" N MET O 396 " --> pdb=" O GLN O 392 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE O 399 " --> pdb=" O LEU O 395 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL O 401 " --> pdb=" O ASP O 397 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR O 402 " --> pdb=" O SER O 398 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 430 removed outlier: 3.621A pdb=" N LYS O 419 " --> pdb=" O GLU O 415 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 452 removed outlier: 3.510A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL O 442 " --> pdb=" O GLN O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 removed outlier: 3.863A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 469' Processing helix chain 'O' and resid 470 through 485 removed outlier: 3.521A pdb=" N PHE O 484 " --> pdb=" O LEU O 480 " (cutoff:3.500A) Processing helix chain 'O' and resid 498 through 500 No H-bonds generated for 'chain 'O' and resid 498 through 500' Processing helix chain 'O' and resid 501 through 511 removed outlier: 3.688A pdb=" N PHE O 506 " --> pdb=" O LEU O 502 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE O 511 " --> pdb=" O GLN O 507 " (cutoff:3.500A) Processing helix chain 'O' and resid 515 through 520 removed outlier: 3.693A pdb=" N PHE O 519 " --> pdb=" O ASN O 515 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS O 520 " --> pdb=" O PRO O 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 515 through 520' Processing helix chain 'O' and resid 521 through 536 Processing helix chain 'O' and resid 540 through 546 removed outlier: 3.567A pdb=" N ILE O 544 " --> pdb=" O CYS O 540 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 591 removed outlier: 3.796A pdb=" N LEU O 588 " --> pdb=" O GLN O 584 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN O 589 " --> pdb=" O PHE O 585 " (cutoff:3.500A) Processing helix chain 'O' and resid 602 through 607 Processing sheet with id=AA1, first strand: chain 'Q' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain 'S' and resid 63 through 67 removed outlier: 7.070A pdb=" N VAL S 547 " --> pdb=" O LEU S 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU S 546 " --> pdb=" O LEU S 541 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU S 541 " --> pdb=" O GLU S 546 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR S 548 " --> pdb=" O VAL S 539 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL S 539 " --> pdb=" O TYR S 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 186 through 187 Processing sheet with id=AA4, first strand: chain 'S' and resid 206 through 207 Processing sheet with id=AA5, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.723A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG S 273 " --> pdb=" O SER S 287 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET S 285 " --> pdb=" O GLU S 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 300 through 304 removed outlier: 6.438A pdb=" N ASP S 319 " --> pdb=" O GLN S 301 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL S 303 " --> pdb=" O ILE S 317 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ILE S 317 " --> pdb=" O VAL S 303 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN S 323 " --> pdb=" O ILE S 320 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TRP S 324 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU S 347 " --> pdb=" O TRP S 324 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE S 326 " --> pdb=" O ASP S 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 362 through 365 removed outlier: 4.042A pdb=" N ARG S 362 " --> pdb=" O PHE S 375 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 402 through 406 removed outlier: 3.677A pdb=" N LEU S 415 " --> pdb=" O LYS S 406 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 450 through 457 removed outlier: 3.630A pdb=" N ALA S 466 " --> pdb=" O HIS S 479 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS S 479 " --> pdb=" O ALA S 466 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER S 495 " --> pdb=" O MET S 478 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL S 480 " --> pdb=" O GLY S 493 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLY S 493 " --> pdb=" O VAL S 480 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER S 482 " --> pdb=" O SER S 491 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER S 491 " --> pdb=" O SER S 482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'N' and resid 52 through 54 removed outlier: 4.180A pdb=" N TYR M 76 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN M 82 " --> pdb=" O SER M 87 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N ILE M 88 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU M 11 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N LEU M 90 " --> pdb=" O GLU M 11 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 101 through 102 removed outlier: 3.690A pdb=" N GLU M 61 " --> pdb=" O VAL M 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 101 through 102 removed outlier: 3.690A pdb=" N GLU M 61 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR M 65 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA M 22 " --> pdb=" O LEU N 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 3.623A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 77 through 86 removed outlier: 6.239A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.626A pdb=" N HIS A 107 " --> pdb=" O CYS A 102 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 243 through 245 removed outlier: 3.614A pdb=" N PHE A 252 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE A 251 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 475 through 476 removed outlier: 4.003A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 7.206A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.348A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AC4, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.518A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.594A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.594A pdb=" N PHE A 826 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AC8, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.617A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1504 through 1508 removed outlier: 3.973A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.691A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 1460 through 1462 Processing sheet with id=AD3, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.892A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 29 through 30 removed outlier: 6.906A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 71 through 72 removed outlier: 4.814A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AD7, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AD8, first strand: chain 'B' and resid 229 through 239 removed outlier: 5.541A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR B 259 " --> pdb=" O HIS B 251 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AE2, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.558A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.410A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AE5, first strand: chain 'B' and resid 823 through 825 removed outlier: 4.226A pdb=" N CYS B 859 " --> pdb=" O LYS B 872 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP B 863 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1099 through 1104 Processing sheet with id=AE7, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AE8, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.201A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 10.764A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N PHE C 298 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N SER C 226 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.544A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AF2, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AF3, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AF4, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.402A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF6, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.764A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AF8, first strand: chain 'G' and resid 131 through 140 removed outlier: 6.918A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU G 147 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER G 244 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL G 236 " --> pdb=" O SER G 244 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ASP G 246 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP G 131 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.520A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU H 126 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AG2, first strand: chain 'I' and resid 81 through 82 Processing sheet with id=AG3, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AG4, first strand: chain 'K' and resid 60 through 66 removed outlier: 3.544A pdb=" N ILE K 103 " --> pdb=" O PHE K 63 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 37 through 38 Processing sheet with id=AG6, first strand: chain 'N' and resid 79 through 81 removed outlier: 4.016A pdb=" N ASP N 86 " --> pdb=" O THR N 142 " (cutoff:3.500A) 1650 hydrogen bonds defined for protein. 4623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 26.55 Time building geometry restraints manager: 20.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8681 1.32 - 1.44: 14093 1.44 - 1.57: 29520 1.57 - 1.69: 168 1.69 - 1.82: 372 Bond restraints: 52834 Sorted by residual: bond pdb=" CA ALA H 140 " pdb=" CB ALA H 140 " ideal model delta sigma weight residual 1.522 1.447 0.074 1.27e-02 6.20e+03 3.43e+01 bond pdb=" C VAL E 124 " pdb=" N PRO E 125 " ideal model delta sigma weight residual 1.331 1.377 -0.045 7.90e-03 1.60e+04 3.31e+01 bond pdb=" C TYR I 37 " pdb=" N PRO I 38 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.69e+01 bond pdb=" C THR F 81 " pdb=" N THR F 82 " ideal model delta sigma weight residual 1.331 1.222 0.109 2.83e-02 1.25e+03 1.49e+01 bond pdb=" C ASP S 443 " pdb=" N PRO S 444 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.25e-02 6.40e+03 1.36e+01 ... (remaining 52829 not shown) Histogram of bond angle deviations from ideal: 96.26 - 104.22: 1026 104.22 - 112.17: 25452 112.17 - 120.13: 23348 120.13 - 128.08: 21420 128.08 - 136.04: 515 Bond angle restraints: 71761 Sorted by residual: angle pdb=" C PHE A 239 " pdb=" N SER A 240 " pdb=" CA SER A 240 " ideal model delta sigma weight residual 120.68 134.16 -13.48 1.52e+00 4.33e-01 7.86e+01 angle pdb=" N LEU A 883 " pdb=" CA LEU A 883 " pdb=" C LEU A 883 " ideal model delta sigma weight residual 114.75 105.75 9.00 1.26e+00 6.30e-01 5.10e+01 angle pdb=" N PRO A1387 " pdb=" CA PRO A1387 " pdb=" CB PRO A1387 " ideal model delta sigma weight residual 103.41 109.50 -6.09 9.40e-01 1.13e+00 4.20e+01 angle pdb=" N VAL A 338 " pdb=" CA VAL A 338 " pdb=" C VAL A 338 " ideal model delta sigma weight residual 111.81 106.71 5.10 8.60e-01 1.35e+00 3.52e+01 angle pdb=" C ASP A 68 " pdb=" N GLU A 69 " pdb=" CA GLU A 69 " ideal model delta sigma weight residual 120.38 128.44 -8.06 1.46e+00 4.69e-01 3.05e+01 ... (remaining 71756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 31291 35.76 - 71.53: 555 71.53 - 107.29: 27 107.29 - 143.06: 3 143.06 - 178.82: 2 Dihedral angle restraints: 31878 sinusoidal: 13613 harmonic: 18265 Sorted by residual: dihedral pdb=" CA ASP Q 180 " pdb=" C ASP Q 180 " pdb=" N TYR Q 181 " pdb=" CA TYR Q 181 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA PHE S 489 " pdb=" C PHE S 489 " pdb=" N GLN S 490 " pdb=" CA GLN S 490 " ideal model delta harmonic sigma weight residual 180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA THR G 238 " pdb=" C THR G 238 " pdb=" N THR G 239 " pdb=" CA THR G 239 " ideal model delta harmonic sigma weight residual -180.00 -150.67 -29.33 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 31875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 7253 0.100 - 0.200: 714 0.200 - 0.299: 45 0.299 - 0.399: 3 0.399 - 0.499: 4 Chirality restraints: 8019 Sorted by residual: chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.50 2.00e-01 2.50e+01 6.22e+00 chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CB ILE R 140 " pdb=" CA ILE R 140 " pdb=" CG1 ILE R 140 " pdb=" CG2 ILE R 140 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 8016 not shown) Planarity restraints: 8922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 933 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C THR B 933 " -0.073 2.00e-02 2.50e+03 pdb=" O THR B 933 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE B 934 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR R 355 " -0.053 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRO R 356 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO R 356 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 356 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP S 441 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C ASP S 441 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP S 441 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU S 442 " -0.018 2.00e-02 2.50e+03 ... (remaining 8919 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 362 2.56 - 3.15: 38462 3.15 - 3.73: 78067 3.73 - 4.32: 112549 4.32 - 4.90: 183695 Nonbonded interactions: 413135 Sorted by model distance: nonbonded pdb=" OE1 GLU B 807 " pdb=" OH TYR B 905 " model vdw 1.977 2.440 nonbonded pdb=" ND2 ASN A 432 " pdb=" OE1 GLN A 444 " model vdw 1.988 2.520 nonbonded pdb=" OH TYR A 697 " pdb=" OE2 GLU A 703 " model vdw 2.228 2.440 nonbonded pdb=" NZ LYS A 964 " pdb=" O MET B 672 " model vdw 2.244 2.520 nonbonded pdb=" OE1 GLN S 21 " pdb=" OG SER S 24 " model vdw 2.255 2.440 ... (remaining 413130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.090 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: 0.050 Extract box with map and model: 14.180 Check model and map are aligned: 0.820 Set scattering table: 0.570 Process input model: 146.630 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.190 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 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 : 0.009 0.109 52834 Z= 0.592 Angle : 1.092 13.479 71761 Z= 0.609 Chirality : 0.062 0.499 8019 Planarity : 0.007 0.079 8922 Dihedral : 13.041 178.821 20032 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.30 % Favored : 91.68 % Rotamer: Outliers : 0.74 % Allowed : 3.41 % Favored : 95.85 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.08), residues: 6144 helix: -4.05 (0.06), residues: 2100 sheet: -2.60 (0.17), residues: 724 loop : -2.65 (0.09), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP B 143 HIS 0.028 0.003 HIS B 532 PHE 0.041 0.004 PHE G 153 TYR 0.044 0.004 TYR B 781 ARG 0.021 0.002 ARG B 796 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1200 time to evaluate : 5.878 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: Q 19 LEU cc_start: 0.3958 (mt) cc_final: 0.3716 (mm) REVERT: Q 35 MET cc_start: 0.3792 (mtm) cc_final: 0.3563 (ptp) REVERT: M 25 SER cc_start: 0.6920 (t) cc_final: 0.6502 (m) REVERT: M 99 LYS cc_start: 0.5637 (pttt) cc_final: 0.4808 (tppp) REVERT: A 103 LEU cc_start: 0.7660 (mp) cc_final: 0.7417 (mt) REVERT: A 108 PHE cc_start: 0.7761 (m-80) cc_final: 0.6859 (m-80) REVERT: A 187 GLU cc_start: 0.7503 (tp30) cc_final: 0.7272 (tt0) REVERT: A 218 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7714 (mtpp) REVERT: A 245 LYS cc_start: 0.5222 (pttp) cc_final: 0.4950 (pptt) REVERT: A 322 ASN cc_start: 0.5515 (m-40) cc_final: 0.5273 (t0) REVERT: A 397 ARG cc_start: 0.6581 (tpt90) cc_final: 0.6190 (tmm160) REVERT: A 424 MET cc_start: 0.5913 (mmp) cc_final: 0.5423 (ttt) REVERT: A 467 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7010 (t80) REVERT: A 646 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8048 (mt-10) REVERT: A 841 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7873 (ttpt) REVERT: A 1086 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6491 (tt) REVERT: A 1088 HIS cc_start: 0.7581 (m170) cc_final: 0.7330 (m-70) REVERT: A 1111 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6306 (mt-10) REVERT: A 1227 MET cc_start: 0.6138 (mtp) cc_final: 0.5373 (mmp) REVERT: A 1290 TYR cc_start: 0.7666 (m-80) cc_final: 0.7422 (m-80) REVERT: A 1314 GLN cc_start: 0.7388 (tp40) cc_final: 0.7167 (tp40) REVERT: A 1521 THR cc_start: 0.8152 (m) cc_final: 0.7946 (p) REVERT: A 1631 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8276 (ttm170) REVERT: B 164 MET cc_start: 0.8574 (ttm) cc_final: 0.8334 (ttp) REVERT: B 306 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7471 (tm) REVERT: B 344 GLN cc_start: 0.7459 (mt0) cc_final: 0.7186 (mt0) REVERT: B 430 MET cc_start: 0.6543 (mtp) cc_final: 0.5833 (ttm) REVERT: B 480 GLN cc_start: 0.7201 (pm20) cc_final: 0.6946 (pm20) REVERT: B 592 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 804 TYR cc_start: 0.8309 (m-80) cc_final: 0.8098 (m-80) REVERT: B 873 THR cc_start: 0.7908 (m) cc_final: 0.7620 (p) REVERT: B 928 SER cc_start: 0.8653 (t) cc_final: 0.8429 (m) REVERT: B 1199 ASN cc_start: 0.8358 (m-40) cc_final: 0.7579 (m110) REVERT: C 33 VAL cc_start: 0.7417 (p) cc_final: 0.7201 (t) REVERT: C 84 TYR cc_start: 0.8568 (m-80) cc_final: 0.8238 (m-80) REVERT: C 154 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7586 (mtpp) REVERT: C 272 LYS cc_start: 0.7707 (tptt) cc_final: 0.7278 (mttm) REVERT: C 311 GLU cc_start: 0.7556 (pm20) cc_final: 0.7280 (pm20) REVERT: C 319 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6502 (mtm110) REVERT: E 17 ARG cc_start: 0.7441 (ttt180) cc_final: 0.6983 (ttp-170) REVERT: E 63 ASN cc_start: 0.6796 (m-40) cc_final: 0.5721 (p0) REVERT: E 71 LYS cc_start: 0.6211 (ttmt) cc_final: 0.5751 (tptp) REVERT: E 91 LYS cc_start: 0.6649 (mttt) cc_final: 0.6084 (ptmt) REVERT: E 99 HIS cc_start: 0.6733 (t70) cc_final: 0.6431 (t-90) REVERT: E 141 VAL cc_start: 0.8498 (t) cc_final: 0.8277 (t) REVERT: E 166 LYS cc_start: 0.8506 (tttt) cc_final: 0.8173 (tppt) REVERT: E 171 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7991 (mttt) REVERT: E 191 LYS cc_start: 0.7967 (mptt) cc_final: 0.7244 (mmmt) REVERT: F 66 ARG cc_start: 0.7445 (mtp180) cc_final: 0.7140 (mmm-85) REVERT: F 67 LYS cc_start: 0.7772 (ttpp) cc_final: 0.6690 (tppt) REVERT: F 68 THR cc_start: 0.8188 (m) cc_final: 0.7971 (p) REVERT: F 76 LYS cc_start: 0.7321 (ttmm) cc_final: 0.7060 (tmtt) REVERT: F 79 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.5938 (ptt90) REVERT: G 19 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7431 (mppt) REVERT: G 70 VAL cc_start: 0.8028 (m) cc_final: 0.7678 (t) REVERT: G 134 GLU cc_start: 0.5625 (mt-10) cc_final: 0.5207 (mm-30) REVERT: G 136 TYR cc_start: 0.3780 (m-80) cc_final: 0.3363 (t80) REVERT: H 9 ILE cc_start: 0.7715 (mp) cc_final: 0.7455 (mt) REVERT: H 61 SER cc_start: 0.7946 (t) cc_final: 0.7682 (m) REVERT: H 80 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7525 (mtp180) REVERT: H 112 ILE cc_start: 0.7552 (mt) cc_final: 0.7302 (tp) REVERT: I 4 VAL cc_start: 0.8111 (t) cc_final: 0.7900 (p) REVERT: K 60 SER cc_start: 0.8127 (m) cc_final: 0.7880 (p) REVERT: N 36 LYS cc_start: 0.4534 (mmtm) cc_final: 0.4016 (tmtm) REVERT: N 120 LYS cc_start: 0.5080 (mttt) cc_final: 0.4872 (mtmt) REVERT: N 134 ASP cc_start: 0.3494 (m-30) cc_final: 0.2426 (t70) REVERT: N 152 LYS cc_start: 0.6312 (ttmt) cc_final: 0.5949 (tmtp) REVERT: O 124 LYS cc_start: 0.6397 (mmtp) cc_final: 0.5807 (mtpt) REVERT: O 137 ILE cc_start: 0.7673 (mt) cc_final: 0.7402 (mm) REVERT: O 149 LYS cc_start: 0.5880 (ttpt) cc_final: 0.5082 (tptp) REVERT: O 158 LEU cc_start: 0.7472 (mt) cc_final: 0.7060 (tt) REVERT: O 178 TYR cc_start: 0.6397 (t80) cc_final: 0.6195 (t80) REVERT: O 181 ARG cc_start: 0.5972 (ttm-80) cc_final: 0.5385 (tpp80) REVERT: O 187 MET cc_start: 0.7005 (mmt) cc_final: 0.6660 (mmm) REVERT: O 211 TYR cc_start: 0.5834 (t80) cc_final: 0.5230 (t80) REVERT: O 223 SER cc_start: 0.5979 (p) cc_final: 0.5690 (t) REVERT: O 235 GLU cc_start: 0.6587 (tp30) cc_final: 0.6236 (pt0) REVERT: O 311 MET cc_start: 0.3183 (mmm) cc_final: 0.2770 (tpp) REVERT: O 360 VAL cc_start: 0.7071 (t) cc_final: 0.6688 (t) REVERT: O 459 GLU cc_start: 0.5539 (pt0) cc_final: 0.5339 (mp0) REVERT: O 502 LEU cc_start: 0.5014 (mt) cc_final: 0.4638 (tt) REVERT: O 551 ARG cc_start: 0.5582 (ttp80) cc_final: 0.5365 (ptt180) outliers start: 41 outliers final: 9 residues processed: 1234 average time/residue: 1.6685 time to fit residues: 2570.7786 Evaluate side-chains 612 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 598 time to evaluate : 5.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 209 ASN Chi-restraints excluded: chain Q residue 293 ARG Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 444 GLN Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain J residue 2 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 527 optimal weight: 0.5980 chunk 473 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 161 optimal weight: 0.0870 chunk 319 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 chunk 489 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 364 optimal weight: 1.9990 chunk 567 optimal weight: 10.0000 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 14 ASN Q 42 ASN Q 149 GLN Q 206 GLN Q 294 HIS Q 435 GLN Q 482 HIS Q 507 ASN S 222 GLN S 267 ASN ** S 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 461 HIS S 483 HIS S 571 HIS R 179 HIS ** R 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 207 ASN R 223 ASN R 263 ASN R 286 GLN R 298 GLN R 304 HIS R 382 GLN R 409 HIS M 74 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS A 332 GLN A 431 GLN A 560 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN A 880 GLN A1062 HIS A1072 ASN A1116 GLN A1199 GLN A1299 ASN A1323 HIS A1336 GLN A1662 ASN B 62 ASN ** B 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 HIS B 282 HIS B 351 GLN B 361 HIS B 427 GLN B 439 ASN B 504 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 575 HIS B 682 GLN B 686 HIS B 886 ASN B 899 GLN B 923 GLN B1008 HIS B1041 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN D 38 GLN D 88 GLN E 32 GLN E 147 HIS G 56 ASN G 65 HIS G 75 ASN G 121 ASN G 144 HIS G 235 ASN H 134 ASN I 21 ASN I 95 ASN I 100 GLN K 106 GLN O 66 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 ASN O 472 HIS ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 547 ASN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 52834 Z= 0.193 Angle : 0.645 11.280 71761 Z= 0.344 Chirality : 0.044 0.213 8019 Planarity : 0.005 0.057 8922 Dihedral : 13.093 174.123 7713 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.83 % Allowed : 11.35 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.00 % 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: -3.30 (0.09), residues: 6144 helix: -2.26 (0.09), residues: 2166 sheet: -2.02 (0.17), residues: 733 loop : -2.16 (0.10), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP Q 118 HIS 0.009 0.001 HIS B 532 PHE 0.032 0.002 PHE A 108 TYR 0.025 0.002 TYR A1302 ARG 0.008 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 697 time to evaluate : 5.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 31 TYR cc_start: 0.7131 (m-80) cc_final: 0.6917 (m-80) REVERT: Q 35 MET cc_start: 0.3890 (mtm) cc_final: 0.3650 (ptp) REVERT: M 61 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.5114 (pp20) REVERT: M 99 LYS cc_start: 0.5669 (pttt) cc_final: 0.4733 (tppp) REVERT: A 218 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8031 (mtpp) REVERT: A 232 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5615 (tppt) REVERT: A 366 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7289 (ptp-110) REVERT: A 424 MET cc_start: 0.5484 (mmp) cc_final: 0.4943 (ttm) REVERT: A 442 LYS cc_start: 0.6339 (mptm) cc_final: 0.6132 (mtpt) REVERT: A 458 GLN cc_start: 0.5186 (OUTLIER) cc_final: 0.4762 (mm110) REVERT: A 467 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7023 (t80) REVERT: A 762 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7505 (ttmm) REVERT: A 944 MET cc_start: 0.7988 (mtt) cc_final: 0.7750 (mtt) REVERT: A 1086 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6372 (tt) REVERT: A 1111 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6275 (mt-10) REVERT: A 1121 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6466 (m-30) REVERT: A 1307 ASP cc_start: 0.7089 (t0) cc_final: 0.6682 (t70) REVERT: A 1439 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6284 (mtp) REVERT: A 1631 ARG cc_start: 0.8539 (ttm170) cc_final: 0.8320 (ttm170) REVERT: B 16 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.5814 (p90) REVERT: B 136 LYS cc_start: 0.8014 (tppt) cc_final: 0.7794 (tptt) REVERT: B 278 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7350 (mttt) REVERT: B 306 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7609 (mt) REVERT: B 344 GLN cc_start: 0.7517 (mt0) cc_final: 0.7074 (mt0) REVERT: B 447 SER cc_start: 0.7911 (m) cc_final: 0.7634 (p) REVERT: B 448 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6785 (mtt180) REVERT: B 480 GLN cc_start: 0.7058 (pm20) cc_final: 0.6823 (pm20) REVERT: B 560 ARG cc_start: 0.6987 (mmp-170) cc_final: 0.6401 (mmm-85) REVERT: B 783 MET cc_start: 0.8180 (mtt) cc_final: 0.7978 (mtm) REVERT: B 863 ASP cc_start: 0.7134 (p0) cc_final: 0.6895 (p0) REVERT: B 875 HIS cc_start: 0.6830 (OUTLIER) cc_final: 0.6612 (p90) REVERT: B 1114 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7170 (pt0) REVERT: B 1199 ASN cc_start: 0.8351 (m-40) cc_final: 0.7950 (m110) REVERT: C 272 LYS cc_start: 0.7484 (tptt) cc_final: 0.7041 (mttm) REVERT: C 319 ARG cc_start: 0.6788 (mtm-85) cc_final: 0.6564 (mtm110) REVERT: D 15 THR cc_start: 0.7931 (p) cc_final: 0.7695 (m) REVERT: E 17 ARG cc_start: 0.7270 (ttt180) cc_final: 0.6950 (ttp-170) REVERT: E 40 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.5573 (pt0) REVERT: E 50 MET cc_start: 0.4609 (mmt) cc_final: 0.4392 (ptm) REVERT: E 63 ASN cc_start: 0.7209 (m-40) cc_final: 0.5977 (p0) REVERT: E 69 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7025 (mm) REVERT: E 71 LYS cc_start: 0.6071 (ttmt) cc_final: 0.5720 (tptp) REVERT: E 166 LYS cc_start: 0.8429 (tttt) cc_final: 0.8103 (tppt) REVERT: E 171 LYS cc_start: 0.8093 (mmtm) cc_final: 0.7882 (mttt) REVERT: F 67 LYS cc_start: 0.7504 (ttpp) cc_final: 0.6677 (tppt) REVERT: F 79 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7553 (ptt180) REVERT: G 19 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7424 (mppt) REVERT: G 56 ASN cc_start: 0.7819 (OUTLIER) cc_final: 0.7130 (m-40) REVERT: G 219 ASP cc_start: 0.5457 (t0) cc_final: 0.4959 (t0) REVERT: H 7 ASP cc_start: 0.7728 (t0) cc_final: 0.7301 (t70) REVERT: H 53 ASP cc_start: 0.6057 (m-30) cc_final: 0.5749 (m-30) REVERT: H 61 SER cc_start: 0.7922 (t) cc_final: 0.7695 (m) REVERT: I 18 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6337 (tm-30) REVERT: J 19 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7542 (mt-10) REVERT: J 67 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: K 60 SER cc_start: 0.8282 (m) cc_final: 0.7991 (p) REVERT: K 67 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6201 (mp0) REVERT: K 87 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7305 (tm-30) REVERT: N 36 LYS cc_start: 0.4614 (mmtm) cc_final: 0.3813 (tmtm) REVERT: N 134 ASP cc_start: 0.3474 (m-30) cc_final: 0.2224 (t70) REVERT: N 152 LYS cc_start: 0.6509 (ttmt) cc_final: 0.6228 (tmtp) REVERT: O 51 MET cc_start: 0.5809 (tpp) cc_final: 0.5355 (mmm) REVERT: O 124 LYS cc_start: 0.6399 (mmtp) cc_final: 0.5807 (mtpt) REVERT: O 131 HIS cc_start: 0.5992 (m-70) cc_final: 0.5498 (m-70) REVERT: O 137 ILE cc_start: 0.7557 (mt) cc_final: 0.7344 (mm) REVERT: O 149 LYS cc_start: 0.5770 (ttpt) cc_final: 0.5083 (tptp) REVERT: O 158 LEU cc_start: 0.7232 (mt) cc_final: 0.6842 (tt) REVERT: O 181 ARG cc_start: 0.5757 (ttm-80) cc_final: 0.5256 (tpm170) REVERT: O 211 TYR cc_start: 0.5900 (t80) cc_final: 0.5145 (t80) REVERT: O 222 CYS cc_start: 0.6305 (t) cc_final: 0.5867 (p) REVERT: O 223 SER cc_start: 0.6013 (p) cc_final: 0.5652 (t) REVERT: O 228 GLN cc_start: 0.6726 (mt0) cc_final: 0.6305 (mm110) REVERT: O 235 GLU cc_start: 0.6542 (tp30) cc_final: 0.6218 (pt0) REVERT: O 311 MET cc_start: 0.3308 (mmm) cc_final: 0.3002 (tpp) REVERT: O 459 GLU cc_start: 0.5629 (pt0) cc_final: 0.5199 (mp0) outliers start: 212 outliers final: 60 residues processed: 856 average time/residue: 1.5801 time to fit residues: 1722.5867 Evaluate side-chains 616 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 536 time to evaluate : 6.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 CYS Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 213 VAL Chi-restraints excluded: chain S residue 744 LEU Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1439 MET Chi-restraints excluded: chain A residue 1466 SER Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 278 LYS Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain G residue 56 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 607 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 315 optimal weight: 0.8980 chunk 176 optimal weight: 4.9990 chunk 472 optimal weight: 7.9990 chunk 386 optimal weight: 0.9980 chunk 156 optimal weight: 0.0770 chunk 568 optimal weight: 3.9990 chunk 614 optimal weight: 2.9990 chunk 506 optimal weight: 4.9990 chunk 563 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 chunk 456 optimal weight: 0.2980 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 185 GLN ** S 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 665 ASN ** R 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 407 HIS M 89 GLN A 92 ASN A 489 ASN A 560 GLN A 640 ASN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN A1323 HIS B 166 GLN B 209 GLN B 231 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 899 GLN B 923 GLN B 987 ASN C 32 ASN C 93 GLN C 130 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN E 114 ASN F 63 GLN G 20 HIS H 43 ASN H 137 GLN I 21 ASN I 100 GLN O 94 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 534 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 52834 Z= 0.220 Angle : 0.602 11.575 71761 Z= 0.319 Chirality : 0.044 0.228 8019 Planarity : 0.005 0.063 8922 Dihedral : 12.824 179.071 7695 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.10 % Favored : 93.88 % Rotamer: Outliers : 3.74 % Allowed : 13.95 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 6144 helix: -1.23 (0.10), residues: 2176 sheet: -1.73 (0.17), residues: 766 loop : -1.88 (0.10), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 143 HIS 0.010 0.001 HIS B 532 PHE 0.029 0.002 PHE O 55 TYR 0.023 0.002 TYR A1302 ARG 0.008 0.001 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 594 time to evaluate : 5.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 43 LYS cc_start: 0.4659 (ttmt) cc_final: 0.3926 (mmmt) REVERT: M 61 GLU cc_start: 0.5528 (OUTLIER) cc_final: 0.5220 (pp20) REVERT: A 43 HIS cc_start: 0.3867 (t70) cc_final: 0.2852 (m90) REVERT: A 93 GLN cc_start: 0.6108 (mm110) cc_final: 0.5802 (mm-40) REVERT: A 218 LYS cc_start: 0.8571 (mtpt) cc_final: 0.8029 (mtpp) REVERT: A 342 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.6823 (mpp-170) REVERT: A 359 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7515 (t) REVERT: A 366 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7250 (ptp-110) REVERT: A 424 MET cc_start: 0.5282 (mmp) cc_final: 0.4909 (ttm) REVERT: A 442 LYS cc_start: 0.6483 (mptm) cc_final: 0.6180 (mtpt) REVERT: A 458 GLN cc_start: 0.5109 (OUTLIER) cc_final: 0.4556 (mm110) REVERT: A 591 ARG cc_start: 0.7979 (tpt90) cc_final: 0.7597 (tpt90) REVERT: A 727 THR cc_start: 0.8462 (m) cc_final: 0.8174 (p) REVERT: A 762 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7402 (ttmm) REVERT: A 944 MET cc_start: 0.8164 (mtt) cc_final: 0.7921 (mtt) REVERT: A 1003 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8020 (ttm170) REVERT: A 1086 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6403 (tt) REVERT: A 1111 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6408 (mt-10) REVERT: A 1121 ASP cc_start: 0.7248 (OUTLIER) cc_final: 0.6642 (m-30) REVERT: A 1307 ASP cc_start: 0.7134 (t0) cc_final: 0.6669 (t70) REVERT: A 1631 ARG cc_start: 0.8514 (ttm170) cc_final: 0.7953 (ttm170) REVERT: B 16 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.6050 (p90) REVERT: B 100 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6211 (mt-10) REVERT: B 290 ASP cc_start: 0.6810 (m-30) cc_final: 0.6063 (t70) REVERT: B 306 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 344 GLN cc_start: 0.7692 (mt0) cc_final: 0.7290 (mt0) REVERT: B 368 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7226 (mt0) REVERT: B 429 ARG cc_start: 0.6214 (ttm110) cc_final: 0.5856 (tpt90) REVERT: B 432 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7327 (mt) REVERT: B 443 LYS cc_start: 0.7186 (ttpt) cc_final: 0.6879 (ttpp) REVERT: B 447 SER cc_start: 0.8108 (m) cc_final: 0.7819 (p) REVERT: B 448 ARG cc_start: 0.7204 (mtp180) cc_final: 0.6933 (mtt180) REVERT: B 592 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8041 (mt) REVERT: B 795 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8097 (mm-30) REVERT: B 908 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7098 (ptm-80) REVERT: B 909 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7331 (mtp85) REVERT: B 1114 GLN cc_start: 0.7662 (tm-30) cc_final: 0.7423 (pt0) REVERT: B 1199 ASN cc_start: 0.8349 (m-40) cc_final: 0.7982 (m110) REVERT: C 272 LYS cc_start: 0.7592 (tptt) cc_final: 0.7073 (mttm) REVERT: C 309 THR cc_start: 0.8268 (t) cc_final: 0.7896 (p) REVERT: C 311 GLU cc_start: 0.7531 (pm20) cc_final: 0.7159 (pm20) REVERT: D 2 MET cc_start: 0.1766 (ttt) cc_final: 0.1532 (ttt) REVERT: E 11 ARG cc_start: 0.6230 (mtt180) cc_final: 0.5538 (mtp180) REVERT: E 17 ARG cc_start: 0.7408 (ttt180) cc_final: 0.6917 (ttp-170) REVERT: E 50 MET cc_start: 0.4721 (mmt) cc_final: 0.4298 (ptm) REVERT: E 63 ASN cc_start: 0.7230 (m-40) cc_final: 0.6073 (p0) REVERT: E 69 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7004 (mm) REVERT: E 71 LYS cc_start: 0.6294 (ttmt) cc_final: 0.5931 (tptp) REVERT: E 158 SER cc_start: 0.7258 (p) cc_final: 0.7051 (t) REVERT: E 162 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7450 (ttm110) REVERT: E 166 LYS cc_start: 0.8452 (tttt) cc_final: 0.7951 (tptt) REVERT: E 171 LYS cc_start: 0.8158 (mmtm) cc_final: 0.7898 (mttt) REVERT: F 60 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6312 (tm-30) REVERT: F 67 LYS cc_start: 0.7699 (ttpp) cc_final: 0.6989 (mmpt) REVERT: F 79 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7564 (ptt180) REVERT: G 19 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7452 (mppt) REVERT: G 56 ASN cc_start: 0.7718 (p0) cc_final: 0.6999 (m-40) REVERT: G 219 ASP cc_start: 0.5563 (t70) cc_final: 0.5158 (t0) REVERT: H 53 ASP cc_start: 0.6125 (m-30) cc_final: 0.5750 (m-30) REVERT: H 86 ASP cc_start: 0.6138 (OUTLIER) cc_final: 0.5905 (t0) REVERT: H 110 ASP cc_start: 0.5401 (OUTLIER) cc_final: 0.5146 (m-30) REVERT: I 18 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6344 (tm-30) REVERT: I 64 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6861 (mmtp) REVERT: J 19 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: K 67 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6333 (mp0) REVERT: K 122 LYS cc_start: 0.7575 (tptp) cc_final: 0.7305 (tptp) REVERT: N 36 LYS cc_start: 0.4774 (mmtm) cc_final: 0.4097 (tmtm) REVERT: N 134 ASP cc_start: 0.3606 (m-30) cc_final: 0.2306 (t70) REVERT: N 141 GLU cc_start: 0.5526 (tm-30) cc_final: 0.5239 (tm-30) REVERT: N 152 LYS cc_start: 0.6857 (ttmt) cc_final: 0.6541 (tmtp) REVERT: O 124 LYS cc_start: 0.6281 (mmtp) cc_final: 0.5888 (mtpt) REVERT: O 131 HIS cc_start: 0.6097 (m-70) cc_final: 0.5541 (m-70) REVERT: O 137 ILE cc_start: 0.7524 (mt) cc_final: 0.7295 (mm) REVERT: O 149 LYS cc_start: 0.5814 (ttpt) cc_final: 0.5075 (tptp) REVERT: O 158 LEU cc_start: 0.7369 (mt) cc_final: 0.7137 (tt) REVERT: O 178 TYR cc_start: 0.6803 (t80) cc_final: 0.6560 (t80) REVERT: O 181 ARG cc_start: 0.5753 (ttm-80) cc_final: 0.5211 (tpm170) REVERT: O 211 TYR cc_start: 0.6500 (t80) cc_final: 0.5678 (t80) REVERT: O 222 CYS cc_start: 0.6275 (t) cc_final: 0.5807 (p) REVERT: O 228 GLN cc_start: 0.6600 (mt0) cc_final: 0.5970 (mm110) REVERT: O 232 LEU cc_start: 0.8262 (tp) cc_final: 0.7945 (pp) REVERT: O 311 MET cc_start: 0.2890 (mmm) cc_final: 0.2681 (tpp) REVERT: O 329 SER cc_start: 0.4672 (t) cc_final: 0.4455 (m) REVERT: O 356 GLU cc_start: 0.4817 (OUTLIER) cc_final: 0.4615 (pp20) REVERT: O 457 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5523 (ttp-110) REVERT: O 458 GLU cc_start: 0.4612 (mt-10) cc_final: 0.2203 (mm-30) REVERT: O 459 GLU cc_start: 0.5939 (pt0) cc_final: 0.5351 (mp0) REVERT: O 550 GLU cc_start: 0.6608 (tp30) cc_final: 0.6336 (mm-30) outliers start: 207 outliers final: 92 residues processed: 741 average time/residue: 1.5512 time to fit residues: 1464.3648 Evaluate side-chains 637 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 518 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain S residue 49 THR Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 213 VAL Chi-restraints excluded: chain S residue 744 LEU Chi-restraints excluded: chain R residue 168 ILE Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 221 HIS Chi-restraints excluded: chain A residue 329 ARG Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 743 ASP Chi-restraints excluded: chain A residue 762 LYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 625 GLU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 795 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 909 ARG Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 37 CYS Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 356 GLU Chi-restraints excluded: chain O residue 457 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 561 optimal weight: 0.7980 chunk 427 optimal weight: 4.9990 chunk 295 optimal weight: 0.6980 chunk 62 optimal weight: 40.0000 chunk 271 optimal weight: 0.9980 chunk 381 optimal weight: 1.9990 chunk 570 optimal weight: 4.9990 chunk 604 optimal weight: 0.0050 chunk 298 optimal weight: 2.9990 chunk 540 optimal weight: 0.9990 chunk 162 optimal weight: 0.0030 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 665 ASN R 184 ASN M 74 ASN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1314 GLN A1323 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 987 ASN C 32 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN D 38 GLN H 137 GLN I 21 ASN O 103 ASN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 52834 Z= 0.154 Angle : 0.539 12.681 71761 Z= 0.284 Chirality : 0.042 0.283 8019 Planarity : 0.004 0.053 8922 Dihedral : 12.535 175.645 7693 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.43 % Allowed : 15.45 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.87 (0.10), residues: 6144 helix: -0.53 (0.11), residues: 2163 sheet: -1.49 (0.17), residues: 782 loop : -1.66 (0.10), residues: 3199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 118 HIS 0.009 0.001 HIS B 575 PHE 0.028 0.001 PHE O 55 TYR 0.022 0.001 TYR A1302 ARG 0.010 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 565 time to evaluate : 5.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 27 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.5730 (ptt-90) REVERT: M 43 LYS cc_start: 0.4578 (ttmt) cc_final: 0.3855 (mmmt) REVERT: M 61 GLU cc_start: 0.5545 (OUTLIER) cc_final: 0.5245 (pp20) REVERT: A 5 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.7978 (mtpm) REVERT: A 43 HIS cc_start: 0.3775 (t70) cc_final: 0.2844 (m90) REVERT: A 218 LYS cc_start: 0.8548 (mtpt) cc_final: 0.7917 (mtpt) REVERT: A 232 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5787 (ttmt) REVERT: A 366 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7289 (ptp-110) REVERT: A 386 LEU cc_start: 0.5471 (tt) cc_final: 0.4807 (tp) REVERT: A 424 MET cc_start: 0.5389 (mmp) cc_final: 0.4901 (ttm) REVERT: A 442 LYS cc_start: 0.6460 (mptm) cc_final: 0.6111 (mtpt) REVERT: A 727 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8076 (p) REVERT: A 886 ASN cc_start: 0.7990 (t0) cc_final: 0.7785 (t0) REVERT: A 944 MET cc_start: 0.8146 (mtt) cc_final: 0.7913 (mtt) REVERT: A 1086 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6285 (tt) REVERT: A 1111 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6332 (mt-10) REVERT: A 1120 TYR cc_start: 0.7697 (m-80) cc_final: 0.7153 (m-80) REVERT: A 1121 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6623 (m-30) REVERT: A 1183 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: A 1227 MET cc_start: 0.5864 (mtp) cc_final: 0.5353 (mmm) REVERT: A 1307 ASP cc_start: 0.7034 (t0) cc_final: 0.6685 (t70) REVERT: A 1332 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6881 (mp0) REVERT: A 1455 ARG cc_start: 0.6304 (OUTLIER) cc_final: 0.5654 (ttp-170) REVERT: A 1631 ARG cc_start: 0.8320 (ttm170) cc_final: 0.8042 (ttm170) REVERT: B 16 PHE cc_start: 0.7516 (OUTLIER) cc_final: 0.6111 (p90) REVERT: B 70 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5800 (mt-10) REVERT: B 290 ASP cc_start: 0.6733 (m-30) cc_final: 0.5973 (t70) REVERT: B 344 GLN cc_start: 0.7693 (mt0) cc_final: 0.7296 (mt0) REVERT: B 368 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7224 (mt0) REVERT: B 429 ARG cc_start: 0.6166 (ttm110) cc_final: 0.5803 (tpt90) REVERT: B 432 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7255 (mt) REVERT: B 447 SER cc_start: 0.8106 (m) cc_final: 0.7821 (p) REVERT: B 592 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 708 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8858 (p0) REVERT: B 805 LYS cc_start: 0.8440 (ttmt) cc_final: 0.7594 (tptt) REVERT: B 908 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7126 (ptm-80) REVERT: B 1114 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7377 (pt0) REVERT: B 1199 ASN cc_start: 0.8337 (m-40) cc_final: 0.8010 (m110) REVERT: C 97 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7845 (mt) REVERT: C 272 LYS cc_start: 0.7589 (tptt) cc_final: 0.7041 (mttm) REVERT: C 309 THR cc_start: 0.8260 (t) cc_final: 0.7885 (p) REVERT: C 311 GLU cc_start: 0.7527 (pm20) cc_final: 0.7137 (pm20) REVERT: D 95 ASP cc_start: 0.5782 (p0) cc_final: 0.5576 (p0) REVERT: E 11 ARG cc_start: 0.6286 (mtt180) cc_final: 0.5685 (mtp180) REVERT: E 17 ARG cc_start: 0.7462 (ttt180) cc_final: 0.6982 (ttp-170) REVERT: E 50 MET cc_start: 0.4770 (mmt) cc_final: 0.4300 (ptm) REVERT: E 63 ASN cc_start: 0.7206 (m-40) cc_final: 0.6034 (p0) REVERT: E 69 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.6937 (mm) REVERT: E 72 PHE cc_start: 0.7183 (m-80) cc_final: 0.6833 (m-80) REVERT: E 166 LYS cc_start: 0.8465 (tttt) cc_final: 0.7997 (tptt) REVERT: E 171 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7881 (mttt) REVERT: F 60 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6419 (tm-30) REVERT: F 67 LYS cc_start: 0.7634 (ttpp) cc_final: 0.6896 (mmpt) REVERT: G 55 GLU cc_start: 0.7510 (tp30) cc_final: 0.7026 (mt-10) REVERT: G 56 ASN cc_start: 0.7532 (p0) cc_final: 0.6963 (m-40) REVERT: H 7 ASP cc_start: 0.7718 (t0) cc_final: 0.7361 (t70) REVERT: H 86 ASP cc_start: 0.6129 (OUTLIER) cc_final: 0.5866 (t0) REVERT: I 18 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6484 (tm-30) REVERT: N 36 LYS cc_start: 0.4913 (mmtm) cc_final: 0.4161 (tmtm) REVERT: N 134 ASP cc_start: 0.3608 (m-30) cc_final: 0.2397 (t70) REVERT: N 141 GLU cc_start: 0.5521 (tm-30) cc_final: 0.5203 (tm-30) REVERT: N 152 LYS cc_start: 0.6705 (ttmt) cc_final: 0.6450 (tmtp) REVERT: O 114 PHE cc_start: 0.5117 (t80) cc_final: 0.4911 (t80) REVERT: O 124 LYS cc_start: 0.6274 (mmtp) cc_final: 0.5845 (mtpt) REVERT: O 131 HIS cc_start: 0.6241 (m-70) cc_final: 0.5718 (m-70) REVERT: O 137 ILE cc_start: 0.7544 (mt) cc_final: 0.7330 (mm) REVERT: O 149 LYS cc_start: 0.5874 (ttpt) cc_final: 0.5123 (tptp) REVERT: O 158 LEU cc_start: 0.7353 (mt) cc_final: 0.7119 (tt) REVERT: O 181 ARG cc_start: 0.5883 (ttm-80) cc_final: 0.5240 (tpm170) REVERT: O 211 TYR cc_start: 0.6377 (t80) cc_final: 0.5759 (t80) REVERT: O 222 CYS cc_start: 0.6370 (t) cc_final: 0.5782 (p) REVERT: O 228 GLN cc_start: 0.6652 (mt0) cc_final: 0.6028 (mm110) REVERT: O 232 LEU cc_start: 0.8200 (tp) cc_final: 0.7982 (pp) REVERT: O 342 HIS cc_start: 0.6452 (t70) cc_final: 0.6211 (t70) REVERT: O 369 LYS cc_start: 0.7149 (ptpt) cc_final: 0.6419 (pttm) REVERT: O 458 GLU cc_start: 0.4516 (mt-10) cc_final: 0.2356 (mm-30) REVERT: O 459 GLU cc_start: 0.5888 (pt0) cc_final: 0.5292 (mp0) outliers start: 190 outliers final: 84 residues processed: 709 average time/residue: 1.5195 time to fit residues: 1387.0182 Evaluate side-chains 628 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 523 time to evaluate : 5.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 CYS Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain S residue 292 LEU Chi-restraints excluded: chain S residue 468 VAL Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 175 MET Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 503 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 449 optimal weight: 0.7980 chunk 249 optimal weight: 2.9990 chunk 515 optimal weight: 3.9990 chunk 417 optimal weight: 0.0040 chunk 0 optimal weight: 20.0000 chunk 308 optimal weight: 0.9990 chunk 542 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 661 ASN M 74 ASN A 673 HIS ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1323 HIS B 231 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 HIS B 899 GLN C 32 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN I 21 ASN O 105 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 422 GLN O 478 GLN ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 52834 Z= 0.194 Angle : 0.562 12.885 71761 Z= 0.293 Chirality : 0.043 0.270 8019 Planarity : 0.004 0.049 8922 Dihedral : 12.429 177.751 7687 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.02 % Allowed : 15.79 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.58 (0.10), residues: 6144 helix: -0.18 (0.11), residues: 2172 sheet: -1.31 (0.17), residues: 780 loop : -1.59 (0.11), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 143 HIS 0.013 0.001 HIS B 575 PHE 0.025 0.001 PHE O 55 TYR 0.021 0.001 TYR O 178 ARG 0.008 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 769 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 546 time to evaluate : 5.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 43 LYS cc_start: 0.4618 (ttmt) cc_final: 0.3884 (mmmt) REVERT: M 61 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.5218 (pp20) REVERT: A 43 HIS cc_start: 0.3899 (t70) cc_final: 0.2901 (m-70) REVERT: A 232 LYS cc_start: 0.5911 (ptpt) cc_final: 0.5708 (ttmt) REVERT: A 359 VAL cc_start: 0.7804 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 366 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7284 (ptp-110) REVERT: A 424 MET cc_start: 0.5241 (mmp) cc_final: 0.4938 (ttm) REVERT: A 442 LYS cc_start: 0.6455 (mptm) cc_final: 0.6098 (mtpt) REVERT: A 727 THR cc_start: 0.8504 (m) cc_final: 0.8229 (p) REVERT: A 944 MET cc_start: 0.8200 (mtt) cc_final: 0.7947 (mtt) REVERT: A 1003 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7994 (ttm170) REVERT: A 1111 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6370 (mt-10) REVERT: A 1121 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: A 1307 ASP cc_start: 0.7072 (t0) cc_final: 0.6715 (t70) REVERT: A 1332 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: A 1455 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5720 (ttp-170) REVERT: A 1475 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: B 16 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6033 (p90) REVERT: B 70 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: B 153 PHE cc_start: 0.7914 (m-10) cc_final: 0.7709 (m-10) REVERT: B 344 GLN cc_start: 0.7952 (mt0) cc_final: 0.7463 (mt0) REVERT: B 368 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7202 (mt0) REVERT: B 429 ARG cc_start: 0.6167 (ttm110) cc_final: 0.5805 (tpt90) REVERT: B 430 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6338 (ttm) REVERT: B 432 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7120 (mt) REVERT: B 448 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6897 (mtt180) REVERT: B 592 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8264 (mt) REVERT: B 708 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8885 (p0) REVERT: B 805 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7627 (tptt) REVERT: B 908 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7114 (ptm-80) REVERT: B 909 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7360 (mtp85) REVERT: B 1114 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7509 (pt0) REVERT: B 1199 ASN cc_start: 0.8223 (m-40) cc_final: 0.7907 (m110) REVERT: C 97 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7913 (mt) REVERT: C 123 ASP cc_start: 0.8033 (m-30) cc_final: 0.7808 (t0) REVERT: C 168 LYS cc_start: 0.8498 (tttp) cc_final: 0.8162 (tttt) REVERT: C 272 LYS cc_start: 0.7630 (tptt) cc_final: 0.7087 (mttm) REVERT: C 309 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8024 (p) REVERT: C 311 GLU cc_start: 0.7499 (pm20) cc_final: 0.7109 (pm20) REVERT: E 11 ARG cc_start: 0.6283 (mtt180) cc_final: 0.5684 (mtp180) REVERT: E 17 ARG cc_start: 0.7483 (ttt180) cc_final: 0.6978 (ttp-170) REVERT: E 50 MET cc_start: 0.4786 (mmt) cc_final: 0.4290 (ptp) REVERT: E 63 ASN cc_start: 0.7235 (m-40) cc_final: 0.6109 (p0) REVERT: E 69 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7008 (mm) REVERT: E 91 LYS cc_start: 0.6971 (mttt) cc_final: 0.6217 (ptmt) REVERT: E 166 LYS cc_start: 0.8590 (tttt) cc_final: 0.8043 (tptp) REVERT: E 171 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7886 (mttt) REVERT: F 60 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: F 67 LYS cc_start: 0.7712 (ttpp) cc_final: 0.6991 (mmpt) REVERT: G 55 GLU cc_start: 0.7575 (tp30) cc_final: 0.7090 (mt-10) REVERT: G 56 ASN cc_start: 0.7537 (p0) cc_final: 0.6923 (m110) REVERT: H 7 ASP cc_start: 0.7779 (t0) cc_final: 0.7388 (t70) REVERT: H 86 ASP cc_start: 0.6087 (OUTLIER) cc_final: 0.5783 (t0) REVERT: I 18 GLU cc_start: 0.6880 (tm-30) cc_final: 0.6409 (tm-30) REVERT: I 64 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.6967 (mmtp) REVERT: J 67 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: K 47 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7905 (tt) REVERT: K 48 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7462 (mtmp) REVERT: L 56 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8351 (mt) REVERT: N 36 LYS cc_start: 0.4805 (mmtm) cc_final: 0.4118 (tmtm) REVERT: N 134 ASP cc_start: 0.3673 (m-30) cc_final: 0.2317 (t70) REVERT: N 152 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6826 (tmtp) REVERT: O 117 GLN cc_start: 0.5863 (mm-40) cc_final: 0.5325 (tm130) REVERT: O 124 LYS cc_start: 0.6069 (mmtp) cc_final: 0.5845 (mtpt) REVERT: O 131 HIS cc_start: 0.6271 (m-70) cc_final: 0.5736 (m-70) REVERT: O 137 ILE cc_start: 0.7495 (mt) cc_final: 0.7260 (mm) REVERT: O 149 LYS cc_start: 0.5973 (ttpt) cc_final: 0.5250 (tptp) REVERT: O 181 ARG cc_start: 0.6007 (ttm-80) cc_final: 0.5312 (tpm170) REVERT: O 211 TYR cc_start: 0.6486 (t80) cc_final: 0.5938 (t80) REVERT: O 222 CYS cc_start: 0.6388 (t) cc_final: 0.5646 (p) REVERT: O 228 GLN cc_start: 0.6675 (mt0) cc_final: 0.6005 (mm110) REVERT: O 311 MET cc_start: 0.3265 (tpp) cc_final: 0.1937 (mtt) REVERT: O 342 HIS cc_start: 0.6497 (t70) cc_final: 0.6251 (t70) REVERT: O 369 LYS cc_start: 0.7195 (ptpt) cc_final: 0.6318 (pttm) REVERT: O 397 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.5670 (p0) REVERT: O 458 GLU cc_start: 0.4813 (mt-10) cc_final: 0.2811 (mm-30) REVERT: O 459 GLU cc_start: 0.6147 (pt0) cc_final: 0.5630 (mp0) outliers start: 223 outliers final: 106 residues processed: 711 average time/residue: 1.5321 time to fit residues: 1396.7189 Evaluate side-chains 637 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 504 time to evaluate : 5.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 CYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1334 LYS Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1614 SER Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 70 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 909 ARG Chi-restraints excluded: chain B residue 933 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1038 HIS Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 363 THR Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 397 ASP Chi-restraints excluded: chain O residue 526 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 203 optimal weight: 0.3980 chunk 544 optimal weight: 1.9990 chunk 119 optimal weight: 30.0000 chunk 354 optimal weight: 0.5980 chunk 149 optimal weight: 0.0370 chunk 604 optimal weight: 0.7980 chunk 501 optimal weight: 0.0370 chunk 279 optimal weight: 0.9980 chunk 50 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 317 optimal weight: 4.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1323 HIS B 151 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN C 32 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN I 21 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 318 ASN ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 52834 Z= 0.143 Angle : 0.524 12.347 71761 Z= 0.273 Chirality : 0.042 0.291 8019 Planarity : 0.004 0.045 8922 Dihedral : 12.296 176.582 7685 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.09 % Allowed : 17.42 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.25 (0.11), residues: 6144 helix: 0.15 (0.11), residues: 2173 sheet: -1.09 (0.18), residues: 764 loop : -1.45 (0.11), residues: 3207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 613 HIS 0.008 0.001 HIS B 575 PHE 0.024 0.001 PHE O 55 TYR 0.021 0.001 TYR A1302 ARG 0.010 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 555 time to evaluate : 6.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 27 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5767 (ptt-90) REVERT: Q 35 MET cc_start: 0.5017 (ptp) cc_final: 0.4601 (ptm) REVERT: M 43 LYS cc_start: 0.4494 (ttmt) cc_final: 0.3787 (mmmt) REVERT: M 61 GLU cc_start: 0.5477 (OUTLIER) cc_final: 0.5242 (pp20) REVERT: A 5 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7954 (mtpm) REVERT: A 43 HIS cc_start: 0.3813 (t70) cc_final: 0.2827 (m-70) REVERT: A 218 LYS cc_start: 0.8676 (mtmt) cc_final: 0.7961 (mtpt) REVERT: A 226 LYS cc_start: 0.7173 (ttmm) cc_final: 0.6951 (ttmt) REVERT: A 232 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5438 (ttmm) REVERT: A 355 PHE cc_start: 0.7271 (m-80) cc_final: 0.6969 (m-80) REVERT: A 366 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7207 (ptp-110) REVERT: A 424 MET cc_start: 0.5157 (mmp) cc_final: 0.4784 (ttm) REVERT: A 442 LYS cc_start: 0.6378 (mptm) cc_final: 0.6064 (mtpt) REVERT: A 458 GLN cc_start: 0.5126 (OUTLIER) cc_final: 0.4468 (mm110) REVERT: A 727 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 780 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8053 (pt) REVERT: A 1003 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: A 1086 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6040 (tt) REVERT: A 1111 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6331 (mt-10) REVERT: A 1121 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6595 (m-30) REVERT: A 1227 MET cc_start: 0.5996 (mtp) cc_final: 0.5500 (mmm) REVERT: A 1290 TYR cc_start: 0.7458 (m-80) cc_final: 0.7089 (m-80) REVERT: A 1307 ASP cc_start: 0.6908 (t0) cc_final: 0.6619 (t70) REVERT: A 1332 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7100 (mp0) REVERT: A 1439 MET cc_start: 0.6026 (mtp) cc_final: 0.4690 (mpt) REVERT: A 1455 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5620 (ttp-170) REVERT: A 1475 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6578 (pt0) REVERT: A 1524 VAL cc_start: 0.8393 (t) cc_final: 0.8139 (m) REVERT: A 1628 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6365 (t0) REVERT: B 16 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.5960 (p90) REVERT: B 75 ASP cc_start: 0.6387 (OUTLIER) cc_final: 0.5720 (m-30) REVERT: B 344 GLN cc_start: 0.7878 (mt0) cc_final: 0.7430 (mt0) REVERT: B 368 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7218 (mt0) REVERT: B 429 ARG cc_start: 0.6123 (ttm110) cc_final: 0.5872 (tpt90) REVERT: B 432 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7231 (mt) REVERT: B 438 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6129 (mt) REVERT: B 448 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6886 (mtt180) REVERT: B 592 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8364 (mt) REVERT: B 708 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8778 (p0) REVERT: B 805 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7651 (tptt) REVERT: B 872 LYS cc_start: 0.7716 (mtpp) cc_final: 0.7362 (mttm) REVERT: B 908 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7091 (ptm-80) REVERT: B 1114 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7378 (pt0) REVERT: B 1199 ASN cc_start: 0.8228 (m-40) cc_final: 0.7971 (m110) REVERT: C 97 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7871 (mt) REVERT: C 123 ASP cc_start: 0.7898 (m-30) cc_final: 0.7670 (t70) REVERT: C 168 LYS cc_start: 0.8360 (tttp) cc_final: 0.8130 (tttt) REVERT: C 272 LYS cc_start: 0.7698 (tptt) cc_final: 0.7124 (mttm) REVERT: C 309 THR cc_start: 0.8261 (t) cc_final: 0.7964 (p) REVERT: C 311 GLU cc_start: 0.7486 (pm20) cc_final: 0.7094 (pm20) REVERT: E 17 ARG cc_start: 0.7507 (ttt180) cc_final: 0.6992 (ttp-170) REVERT: E 50 MET cc_start: 0.4869 (mmt) cc_final: 0.4321 (ptp) REVERT: E 63 ASN cc_start: 0.7269 (m-40) cc_final: 0.6083 (p0) REVERT: E 69 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.6970 (mm) REVERT: E 71 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6980 (mptp) REVERT: E 91 LYS cc_start: 0.6987 (mttt) cc_final: 0.6234 (ptmt) REVERT: E 166 LYS cc_start: 0.8556 (tttt) cc_final: 0.8023 (tptp) REVERT: E 171 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7833 (mtpt) REVERT: F 60 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6535 (tm-30) REVERT: F 67 LYS cc_start: 0.7757 (ttpp) cc_final: 0.6740 (tppt) REVERT: G 55 GLU cc_start: 0.7549 (tp30) cc_final: 0.7078 (mt-10) REVERT: G 56 ASN cc_start: 0.7485 (p0) cc_final: 0.6943 (m110) REVERT: G 219 ASP cc_start: 0.5823 (t70) cc_final: 0.5486 (t0) REVERT: H 86 ASP cc_start: 0.6103 (OUTLIER) cc_final: 0.5789 (t0) REVERT: I 18 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: I 42 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.5350 (p90) REVERT: N 36 LYS cc_start: 0.4777 (mmtm) cc_final: 0.4032 (tmtm) REVERT: N 134 ASP cc_start: 0.3780 (m-30) cc_final: 0.2497 (t70) REVERT: N 141 GLU cc_start: 0.5411 (tm-30) cc_final: 0.5126 (tm-30) REVERT: O 117 GLN cc_start: 0.5805 (mm-40) cc_final: 0.5342 (tm130) REVERT: O 124 LYS cc_start: 0.6045 (mmtp) cc_final: 0.5836 (mtpt) REVERT: O 131 HIS cc_start: 0.6162 (m-70) cc_final: 0.5696 (m-70) REVERT: O 149 LYS cc_start: 0.5984 (ttpt) cc_final: 0.5253 (tptp) REVERT: O 181 ARG cc_start: 0.6026 (ttm-80) cc_final: 0.5334 (tmm160) REVERT: O 211 TYR cc_start: 0.6209 (t80) cc_final: 0.5710 (t80) REVERT: O 311 MET cc_start: 0.3252 (tpp) cc_final: 0.1679 (mtt) REVERT: O 342 HIS cc_start: 0.6461 (t70) cc_final: 0.6194 (t70) REVERT: O 369 LYS cc_start: 0.7248 (ptpt) cc_final: 0.6364 (pttm) REVERT: O 457 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.5664 (mtp85) REVERT: O 458 GLU cc_start: 0.5039 (mt-10) cc_final: 0.2903 (mm-30) REVERT: O 459 GLU cc_start: 0.6129 (pt0) cc_final: 0.5582 (mp0) REVERT: O 527 MET cc_start: 0.3135 (ttp) cc_final: 0.2788 (tpp) REVERT: O 545 GLU cc_start: 0.6351 (tm-30) cc_final: 0.6150 (tm-30) REVERT: O 548 ASN cc_start: 0.3244 (OUTLIER) cc_final: 0.2809 (p0) outliers start: 171 outliers final: 76 residues processed: 678 average time/residue: 1.5078 time to fit residues: 1315.4656 Evaluate side-chains 619 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 512 time to evaluate : 5.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 CYS Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain S residue 178 VAL Chi-restraints excluded: chain S residue 363 ILE Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 232 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 363 THR Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 457 ARG Chi-restraints excluded: chain O residue 548 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 583 optimal weight: 0.8980 chunk 68 optimal weight: 50.0000 chunk 344 optimal weight: 0.9990 chunk 441 optimal weight: 0.5980 chunk 342 optimal weight: 0.0060 chunk 509 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 602 optimal weight: 3.9990 chunk 376 optimal weight: 0.9980 chunk 367 optimal weight: 0.5980 chunk 278 optimal weight: 4.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN A 235 ASN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A1116 GLN A1323 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 480 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 HIS I 21 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 52834 Z= 0.158 Angle : 0.530 11.930 71761 Z= 0.275 Chirality : 0.042 0.273 8019 Planarity : 0.004 0.045 8922 Dihedral : 12.253 177.439 7685 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.19 % Allowed : 17.72 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.09 (0.11), residues: 6144 helix: 0.32 (0.11), residues: 2181 sheet: -0.94 (0.18), residues: 761 loop : -1.40 (0.11), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP O 151 HIS 0.009 0.001 HIS B 575 PHE 0.037 0.001 PHE O 114 TYR 0.021 0.001 TYR A1302 ARG 0.009 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 534 time to evaluate : 5.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 43 LYS cc_start: 0.4515 (ttmt) cc_final: 0.3798 (mmmt) REVERT: M 61 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.5282 (pp20) REVERT: M 97 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7359 (p) REVERT: A 5 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7938 (mtpm) REVERT: A 43 HIS cc_start: 0.3847 (t70) cc_final: 0.2854 (m-70) REVERT: A 184 LYS cc_start: 0.7117 (mttt) cc_final: 0.6903 (mptm) REVERT: A 218 LYS cc_start: 0.8667 (mtmt) cc_final: 0.7938 (mtpt) REVERT: A 355 PHE cc_start: 0.7283 (m-80) cc_final: 0.6972 (m-80) REVERT: A 366 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7160 (ptp-110) REVERT: A 384 GLN cc_start: 0.6575 (tt0) cc_final: 0.6295 (tm-30) REVERT: A 424 MET cc_start: 0.5161 (mmp) cc_final: 0.4788 (ttm) REVERT: A 442 LYS cc_start: 0.6383 (mptm) cc_final: 0.6090 (mtpt) REVERT: A 458 GLN cc_start: 0.5187 (OUTLIER) cc_final: 0.4623 (mm110) REVERT: A 727 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8159 (p) REVERT: A 944 MET cc_start: 0.8142 (mtt) cc_final: 0.7909 (mtt) REVERT: A 1003 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7933 (ttm170) REVERT: A 1111 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6194 (mt-10) REVERT: A 1121 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6592 (m-30) REVERT: A 1227 MET cc_start: 0.6027 (mtp) cc_final: 0.5524 (mmm) REVERT: A 1288 ARG cc_start: 0.6951 (mmt90) cc_final: 0.6689 (ttt180) REVERT: A 1290 TYR cc_start: 0.7436 (m-80) cc_final: 0.7179 (m-80) REVERT: A 1307 ASP cc_start: 0.6915 (t0) cc_final: 0.6631 (t70) REVERT: A 1332 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: A 1439 MET cc_start: 0.6001 (mtp) cc_final: 0.4609 (mpt) REVERT: A 1455 ARG cc_start: 0.6398 (OUTLIER) cc_final: 0.5732 (ttp-170) REVERT: A 1475 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6516 (pt0) REVERT: A 1524 VAL cc_start: 0.8302 (t) cc_final: 0.8014 (m) REVERT: A 1628 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6342 (t0) REVERT: B 16 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.6001 (p90) REVERT: B 75 ASP cc_start: 0.6238 (OUTLIER) cc_final: 0.5527 (m-30) REVERT: B 152 LEU cc_start: 0.7476 (mt) cc_final: 0.7262 (mp) REVERT: B 257 GLN cc_start: 0.6188 (tt0) cc_final: 0.5888 (mm110) REVERT: B 304 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.7156 (t0) REVERT: B 344 GLN cc_start: 0.7899 (mt0) cc_final: 0.7479 (mt0) REVERT: B 368 GLN cc_start: 0.7528 (mm-40) cc_final: 0.7212 (mt0) REVERT: B 429 ARG cc_start: 0.6161 (ttm110) cc_final: 0.5842 (tpt90) REVERT: B 432 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7195 (mt) REVERT: B 438 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.6052 (mt) REVERT: B 592 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (mt) REVERT: B 708 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8853 (p0) REVERT: B 795 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7950 (mt-10) REVERT: B 805 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7629 (tptt) REVERT: B 872 LYS cc_start: 0.7704 (mtpp) cc_final: 0.7314 (mttm) REVERT: B 908 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7076 (ptm-80) REVERT: B 1092 LEU cc_start: 0.8097 (mt) cc_final: 0.7852 (tp) REVERT: B 1114 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7385 (pt0) REVERT: B 1199 ASN cc_start: 0.8217 (m-40) cc_final: 0.7924 (m110) REVERT: C 97 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7926 (mt) REVERT: C 123 ASP cc_start: 0.7895 (m-30) cc_final: 0.7695 (t70) REVERT: C 168 LYS cc_start: 0.8371 (tttp) cc_final: 0.8136 (tttt) REVERT: C 272 LYS cc_start: 0.7667 (tptt) cc_final: 0.7118 (mttm) REVERT: C 309 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7937 (p) REVERT: C 311 GLU cc_start: 0.7488 (pm20) cc_final: 0.7097 (pm20) REVERT: E 17 ARG cc_start: 0.7477 (ttt180) cc_final: 0.6951 (ttp-170) REVERT: E 50 MET cc_start: 0.4876 (mmt) cc_final: 0.4270 (ptp) REVERT: E 63 ASN cc_start: 0.7337 (m-40) cc_final: 0.6154 (p0) REVERT: E 69 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.6941 (mm) REVERT: E 91 LYS cc_start: 0.6998 (mttt) cc_final: 0.6244 (ptmt) REVERT: E 166 LYS cc_start: 0.8547 (tttt) cc_final: 0.8017 (tptp) REVERT: E 171 LYS cc_start: 0.8078 (mmtm) cc_final: 0.7820 (mtpt) REVERT: F 60 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: F 67 LYS cc_start: 0.7720 (ttpp) cc_final: 0.6787 (tppt) REVERT: G 55 GLU cc_start: 0.7546 (tp30) cc_final: 0.7079 (mt-10) REVERT: G 56 ASN cc_start: 0.7526 (p0) cc_final: 0.7003 (m-40) REVERT: G 138 PHE cc_start: 0.6332 (m-80) cc_final: 0.5882 (m-80) REVERT: G 219 ASP cc_start: 0.5836 (t70) cc_final: 0.5498 (t0) REVERT: H 86 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5799 (t0) REVERT: I 18 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: I 42 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5345 (p90) REVERT: J 67 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: N 36 LYS cc_start: 0.4875 (mmtm) cc_final: 0.4127 (tmtm) REVERT: N 134 ASP cc_start: 0.3714 (m-30) cc_final: 0.2387 (t70) REVERT: N 141 GLU cc_start: 0.5401 (tm-30) cc_final: 0.5086 (tm-30) REVERT: O 117 GLN cc_start: 0.5654 (mm-40) cc_final: 0.5234 (tm130) REVERT: O 124 LYS cc_start: 0.6056 (mmtp) cc_final: 0.5849 (mtpt) REVERT: O 131 HIS cc_start: 0.6187 (m-70) cc_final: 0.5706 (m-70) REVERT: O 149 LYS cc_start: 0.6038 (ttpt) cc_final: 0.5253 (tptp) REVERT: O 181 ARG cc_start: 0.6204 (ttm-80) cc_final: 0.5401 (tmm160) REVERT: O 211 TYR cc_start: 0.6185 (t80) cc_final: 0.5790 (t80) REVERT: O 311 MET cc_start: 0.3230 (tpp) cc_final: 0.1708 (mtt) REVERT: O 342 HIS cc_start: 0.6462 (t70) cc_final: 0.6176 (t70) REVERT: O 366 THR cc_start: 0.8015 (p) cc_final: 0.7555 (t) REVERT: O 369 LYS cc_start: 0.7262 (ptpt) cc_final: 0.6358 (pttm) REVERT: O 457 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.5713 (mtp85) REVERT: O 458 GLU cc_start: 0.5292 (mt-10) cc_final: 0.3155 (mm-30) REVERT: O 459 GLU cc_start: 0.6035 (pt0) cc_final: 0.5560 (mp0) REVERT: O 527 MET cc_start: 0.3186 (ttp) cc_final: 0.2825 (tpp) REVERT: O 548 ASN cc_start: 0.3262 (OUTLIER) cc_final: 0.2836 (p0) outliers start: 177 outliers final: 91 residues processed: 663 average time/residue: 1.5534 time to fit residues: 1323.3405 Evaluate side-chains 628 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 507 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 CYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain S residue 347 LEU Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 479 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 683 ASN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 940 GLU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 53 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 363 THR Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 457 ARG Chi-restraints excluded: chain O residue 548 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 372 optimal weight: 0.6980 chunk 240 optimal weight: 0.5980 chunk 359 optimal weight: 0.0040 chunk 181 optimal weight: 0.2980 chunk 118 optimal weight: 50.0000 chunk 116 optimal weight: 30.0000 chunk 382 optimal weight: 0.7980 chunk 410 optimal weight: 0.8980 chunk 297 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 473 optimal weight: 4.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN A 116 HIS ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1323 HIS A1620 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN C 53 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 546 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 52834 Z= 0.146 Angle : 0.521 11.994 71761 Z= 0.270 Chirality : 0.041 0.272 8019 Planarity : 0.004 0.044 8922 Dihedral : 12.172 177.066 7685 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.87 % Allowed : 18.28 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.88 (0.11), residues: 6144 helix: 0.52 (0.11), residues: 2186 sheet: -0.75 (0.18), residues: 748 loop : -1.33 (0.11), residues: 3210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 151 HIS 0.007 0.001 HIS B 575 PHE 0.025 0.001 PHE B 862 TYR 0.020 0.001 TYR A1302 ARG 0.009 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 536 time to evaluate : 5.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 43 LYS cc_start: 0.4526 (ttmt) cc_final: 0.3809 (mmmt) REVERT: M 61 GLU cc_start: 0.5458 (OUTLIER) cc_final: 0.5218 (pp20) REVERT: M 97 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7354 (p) REVERT: A 5 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7979 (mtpm) REVERT: A 43 HIS cc_start: 0.3834 (t70) cc_final: 0.2867 (m-70) REVERT: A 184 LYS cc_start: 0.7264 (mttt) cc_final: 0.6916 (mptm) REVERT: A 218 LYS cc_start: 0.8633 (mtmt) cc_final: 0.7892 (mtpt) REVERT: A 355 PHE cc_start: 0.7282 (m-80) cc_final: 0.6954 (m-80) REVERT: A 366 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7123 (ptp-110) REVERT: A 384 GLN cc_start: 0.6523 (tt0) cc_final: 0.6022 (tm-30) REVERT: A 424 MET cc_start: 0.5154 (mmp) cc_final: 0.4749 (ttm) REVERT: A 442 LYS cc_start: 0.6251 (mptm) cc_final: 0.5988 (mtpt) REVERT: A 458 GLN cc_start: 0.5148 (OUTLIER) cc_final: 0.4609 (mm110) REVERT: A 727 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 1003 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7942 (ttm170) REVERT: A 1078 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7579 (ptpt) REVERT: A 1086 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6507 (pp) REVERT: A 1111 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6205 (mt-10) REVERT: A 1121 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: A 1227 MET cc_start: 0.5961 (mtp) cc_final: 0.5467 (mmm) REVERT: A 1290 TYR cc_start: 0.7313 (m-80) cc_final: 0.7005 (m-80) REVERT: A 1307 ASP cc_start: 0.7050 (t0) cc_final: 0.6764 (t70) REVERT: A 1332 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 1439 MET cc_start: 0.5974 (mtp) cc_final: 0.4534 (mpt) REVERT: A 1455 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5723 (ttp-170) REVERT: A 1475 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6476 (pp20) REVERT: A 1524 VAL cc_start: 0.8195 (t) cc_final: 0.7935 (m) REVERT: B 16 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6002 (p90) REVERT: B 75 ASP cc_start: 0.6017 (OUTLIER) cc_final: 0.5251 (m-30) REVERT: B 304 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7164 (t0) REVERT: B 344 GLN cc_start: 0.7941 (mt0) cc_final: 0.7488 (mt0) REVERT: B 368 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7241 (mt0) REVERT: B 429 ARG cc_start: 0.6227 (ttm110) cc_final: 0.5906 (tpt90) REVERT: B 432 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7155 (mt) REVERT: B 438 ILE cc_start: 0.6426 (OUTLIER) cc_final: 0.6124 (mt) REVERT: B 708 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8767 (p0) REVERT: B 795 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7955 (mt-10) REVERT: B 805 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7620 (tptt) REVERT: B 872 LYS cc_start: 0.7720 (mtpp) cc_final: 0.7336 (mttm) REVERT: B 908 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7056 (ptm-80) REVERT: B 1199 ASN cc_start: 0.8167 (m-40) cc_final: 0.7867 (m110) REVERT: C 97 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7915 (mt) REVERT: C 168 LYS cc_start: 0.8310 (tttp) cc_final: 0.8073 (tttt) REVERT: C 272 LYS cc_start: 0.7653 (tptt) cc_final: 0.7113 (mttm) REVERT: C 309 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.7904 (p) REVERT: C 311 GLU cc_start: 0.7460 (pm20) cc_final: 0.7107 (pm20) REVERT: E 17 ARG cc_start: 0.7468 (ttt180) cc_final: 0.6990 (ttp-170) REVERT: E 50 MET cc_start: 0.4872 (mmt) cc_final: 0.4255 (ptp) REVERT: E 63 ASN cc_start: 0.7365 (m-40) cc_final: 0.6096 (p0) REVERT: E 71 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6884 (mptp) REVERT: E 91 LYS cc_start: 0.7028 (mttt) cc_final: 0.6283 (ptmt) REVERT: E 166 LYS cc_start: 0.8579 (tttt) cc_final: 0.8025 (tptp) REVERT: E 171 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7820 (mtpt) REVERT: F 60 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: F 67 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7048 (mmpt) REVERT: G 55 GLU cc_start: 0.7486 (tp30) cc_final: 0.7031 (mt-10) REVERT: G 56 ASN cc_start: 0.7604 (p0) cc_final: 0.7043 (m110) REVERT: G 217 TRP cc_start: 0.3608 (m100) cc_final: 0.2926 (m100) REVERT: G 219 ASP cc_start: 0.5690 (t70) cc_final: 0.5312 (t0) REVERT: H 86 ASP cc_start: 0.6103 (OUTLIER) cc_final: 0.5889 (t0) REVERT: H 112 ILE cc_start: 0.7988 (tp) cc_final: 0.7684 (tp) REVERT: I 18 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6395 (tm-30) REVERT: I 42 PHE cc_start: 0.5786 (OUTLIER) cc_final: 0.5374 (p90) REVERT: I 64 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.7105 (mmtp) REVERT: J 67 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: N 36 LYS cc_start: 0.4676 (mmtm) cc_final: 0.3974 (tmtm) REVERT: N 134 ASP cc_start: 0.3746 (m-30) cc_final: 0.2376 (t70) REVERT: N 141 GLU cc_start: 0.5279 (tm-30) cc_final: 0.4979 (tm-30) REVERT: O 117 GLN cc_start: 0.5676 (mm-40) cc_final: 0.5186 (tm130) REVERT: O 131 HIS cc_start: 0.6191 (m-70) cc_final: 0.5754 (m-70) REVERT: O 149 LYS cc_start: 0.6113 (ttpt) cc_final: 0.5303 (tptp) REVERT: O 181 ARG cc_start: 0.6196 (ttm-80) cc_final: 0.5246 (tmm160) REVERT: O 211 TYR cc_start: 0.6139 (t80) cc_final: 0.5883 (t80) REVERT: O 311 MET cc_start: 0.3434 (tpp) cc_final: 0.1824 (mtt) REVERT: O 342 HIS cc_start: 0.6419 (t70) cc_final: 0.6136 (t70) REVERT: O 352 LEU cc_start: 0.5828 (mt) cc_final: 0.5425 (tt) REVERT: O 366 THR cc_start: 0.7959 (p) cc_final: 0.7587 (t) REVERT: O 369 LYS cc_start: 0.7232 (ptpt) cc_final: 0.6346 (pttm) REVERT: O 458 GLU cc_start: 0.5539 (mt-10) cc_final: 0.3664 (mm-30) REVERT: O 459 GLU cc_start: 0.6008 (pt0) cc_final: 0.5605 (mp0) REVERT: O 527 MET cc_start: 0.3063 (ttp) cc_final: 0.2755 (tpp) REVERT: O 548 ASN cc_start: 0.3259 (OUTLIER) cc_final: 0.2814 (p0) outliers start: 159 outliers final: 86 residues processed: 652 average time/residue: 1.5167 time to fit residues: 1269.2983 Evaluate side-chains 617 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 501 time to evaluate : 6.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 15 CYS Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1086 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1475 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 42 PHE Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 363 THR Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 457 ARG Chi-restraints excluded: chain O residue 548 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 547 optimal weight: 0.6980 chunk 577 optimal weight: 0.0020 chunk 526 optimal weight: 4.9990 chunk 561 optimal weight: 2.9990 chunk 576 optimal weight: 10.0000 chunk 337 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 chunk 507 optimal weight: 0.4980 chunk 530 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 206 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 GLN A1323 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 480 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 695 ASN B 899 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** G 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 52834 Z= 0.160 Angle : 0.537 13.544 71761 Z= 0.277 Chirality : 0.042 0.301 8019 Planarity : 0.004 0.044 8922 Dihedral : 12.148 177.948 7683 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.74 % Allowed : 18.84 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.77 (0.11), residues: 6144 helix: 0.62 (0.12), residues: 2191 sheet: -0.71 (0.18), residues: 762 loop : -1.27 (0.11), residues: 3191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP O 151 HIS 0.008 0.001 HIS S 473 PHE 0.048 0.001 PHE O 114 TYR 0.020 0.001 TYR A1302 ARG 0.009 0.000 ARG G 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 528 time to evaluate : 5.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 27 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5756 (ptt-90) REVERT: Q 38 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.5119 (t70) REVERT: M 43 LYS cc_start: 0.4542 (ttmt) cc_final: 0.3822 (mmmt) REVERT: M 61 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.5255 (pp20) REVERT: M 97 VAL cc_start: 0.7645 (OUTLIER) cc_final: 0.7353 (p) REVERT: A 5 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.7969 (mtpm) REVERT: A 43 HIS cc_start: 0.3884 (t70) cc_final: 0.2892 (m-70) REVERT: A 184 LYS cc_start: 0.7223 (mttt) cc_final: 0.6880 (mptm) REVERT: A 218 LYS cc_start: 0.8729 (mtmt) cc_final: 0.7973 (mtpt) REVERT: A 355 PHE cc_start: 0.7295 (m-80) cc_final: 0.7002 (m-80) REVERT: A 359 VAL cc_start: 0.7723 (m) cc_final: 0.7458 (t) REVERT: A 366 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7153 (ptp-110) REVERT: A 384 GLN cc_start: 0.6573 (tt0) cc_final: 0.5989 (tm-30) REVERT: A 397 ARG cc_start: 0.5775 (tmt-80) cc_final: 0.5472 (tmm160) REVERT: A 424 MET cc_start: 0.5068 (mmp) cc_final: 0.4671 (ttm) REVERT: A 458 GLN cc_start: 0.5155 (OUTLIER) cc_final: 0.4599 (mm110) REVERT: A 727 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8197 (p) REVERT: A 944 MET cc_start: 0.8117 (mtt) cc_final: 0.7899 (mtt) REVERT: A 1003 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7935 (ttm170) REVERT: A 1078 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7578 (ptpt) REVERT: A 1111 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6258 (mt-10) REVERT: A 1121 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6580 (m-30) REVERT: A 1227 MET cc_start: 0.6052 (mtp) cc_final: 0.5568 (mmm) REVERT: A 1290 TYR cc_start: 0.7345 (m-80) cc_final: 0.7033 (m-80) REVERT: A 1307 ASP cc_start: 0.7059 (t0) cc_final: 0.6762 (t70) REVERT: A 1332 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 1439 MET cc_start: 0.5993 (mtp) cc_final: 0.4544 (mpt) REVERT: A 1455 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5676 (ttp-170) REVERT: A 1524 VAL cc_start: 0.8192 (t) cc_final: 0.7937 (m) REVERT: B 16 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.6022 (p90) REVERT: B 75 ASP cc_start: 0.6053 (OUTLIER) cc_final: 0.5303 (m-30) REVERT: B 304 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7244 (t0) REVERT: B 344 GLN cc_start: 0.7973 (mt0) cc_final: 0.7526 (mt0) REVERT: B 368 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7231 (mt0) REVERT: B 429 ARG cc_start: 0.6399 (ttm110) cc_final: 0.6073 (tpt90) REVERT: B 432 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7113 (mt) REVERT: B 438 ILE cc_start: 0.6388 (OUTLIER) cc_final: 0.6034 (mt) REVERT: B 491 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6782 (mp) REVERT: B 708 ASP cc_start: 0.9221 (OUTLIER) cc_final: 0.8823 (p0) REVERT: B 724 GLN cc_start: 0.7892 (mt0) cc_final: 0.7375 (mm110) REVERT: B 805 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7624 (tptt) REVERT: B 872 LYS cc_start: 0.7726 (mtpp) cc_final: 0.7324 (mttm) REVERT: B 908 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7008 (ptm-80) REVERT: B 909 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7324 (mtp85) REVERT: B 1134 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6532 (mtt-85) REVERT: B 1163 GLN cc_start: 0.6352 (tt0) cc_final: 0.6048 (tm-30) REVERT: B 1199 ASN cc_start: 0.8168 (m-40) cc_final: 0.7737 (m110) REVERT: C 97 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7938 (mt) REVERT: C 168 LYS cc_start: 0.8320 (tttp) cc_final: 0.8079 (tttt) REVERT: C 272 LYS cc_start: 0.7670 (tptt) cc_final: 0.7115 (mttm) REVERT: C 311 GLU cc_start: 0.7444 (pm20) cc_final: 0.7223 (pm20) REVERT: E 17 ARG cc_start: 0.7477 (ttt180) cc_final: 0.6995 (ttp-170) REVERT: E 50 MET cc_start: 0.4909 (mmt) cc_final: 0.4375 (ptp) REVERT: E 63 ASN cc_start: 0.7327 (m-40) cc_final: 0.6039 (p0) REVERT: E 71 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6771 (mptp) REVERT: E 91 LYS cc_start: 0.7026 (mttt) cc_final: 0.6293 (ptmt) REVERT: E 166 LYS cc_start: 0.8625 (tttt) cc_final: 0.8039 (tptp) REVERT: E 171 LYS cc_start: 0.8123 (mmtm) cc_final: 0.7831 (mtpt) REVERT: F 60 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6550 (tm-30) REVERT: F 67 LYS cc_start: 0.7836 (ttpp) cc_final: 0.7062 (mmpt) REVERT: G 55 GLU cc_start: 0.7481 (tp30) cc_final: 0.7030 (mt-10) REVERT: G 56 ASN cc_start: 0.7608 (p0) cc_final: 0.7025 (m110) REVERT: G 217 TRP cc_start: 0.3654 (m100) cc_final: 0.2949 (m100) REVERT: G 219 ASP cc_start: 0.5635 (t70) cc_final: 0.5268 (t0) REVERT: H 86 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.5932 (t0) REVERT: H 126 GLU cc_start: 0.7313 (pt0) cc_final: 0.7023 (pt0) REVERT: I 18 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: I 64 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7051 (mmtp) REVERT: J 67 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: N 36 LYS cc_start: 0.4723 (mmtm) cc_final: 0.3981 (tmtm) REVERT: N 134 ASP cc_start: 0.3750 (m-30) cc_final: 0.2342 (t70) REVERT: N 141 GLU cc_start: 0.5276 (tm-30) cc_final: 0.4983 (tm-30) REVERT: O 117 GLN cc_start: 0.5552 (mm-40) cc_final: 0.5103 (tm130) REVERT: O 131 HIS cc_start: 0.6334 (m-70) cc_final: 0.5909 (m-70) REVERT: O 149 LYS cc_start: 0.6078 (ttpt) cc_final: 0.5309 (tptp) REVERT: O 156 MET cc_start: 0.5180 (OUTLIER) cc_final: 0.4884 (tpp) REVERT: O 180 LEU cc_start: 0.5826 (OUTLIER) cc_final: 0.5352 (pp) REVERT: O 181 ARG cc_start: 0.6118 (ttm-80) cc_final: 0.5190 (tmm160) REVERT: O 205 ARG cc_start: 0.6335 (mtm110) cc_final: 0.6068 (mtm110) REVERT: O 211 TYR cc_start: 0.6127 (t80) cc_final: 0.5885 (t80) REVERT: O 311 MET cc_start: 0.3486 (tpp) cc_final: 0.2048 (mtt) REVERT: O 342 HIS cc_start: 0.6431 (t70) cc_final: 0.6140 (t70) REVERT: O 366 THR cc_start: 0.7928 (p) cc_final: 0.7575 (t) REVERT: O 369 LYS cc_start: 0.7243 (ptpt) cc_final: 0.6323 (pttm) REVERT: O 458 GLU cc_start: 0.5575 (mt-10) cc_final: 0.3781 (mm-30) REVERT: O 459 GLU cc_start: 0.5966 (pt0) cc_final: 0.5639 (mp0) REVERT: O 527 MET cc_start: 0.3165 (ttp) cc_final: 0.2865 (tpp) REVERT: O 548 ASN cc_start: 0.3279 (OUTLIER) cc_final: 0.2858 (p0) outliers start: 152 outliers final: 86 residues processed: 637 average time/residue: 1.4445 time to fit residues: 1177.9308 Evaluate side-chains 616 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 497 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 38 ASP Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 203 ILE Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1078 LYS Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 909 ARG Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 64 LYS Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 363 THR Chi-restraints excluded: chain O residue 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 559 optimal weight: 0.0470 chunk 368 optimal weight: 0.0000 chunk 593 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 412 optimal weight: 2.9990 chunk 622 optimal weight: 5.9990 chunk 573 optimal weight: 4.9990 chunk 495 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 382 optimal weight: 1.9990 overall best weight: 0.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN C 216 HIS I 21 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 52834 Z= 0.181 Angle : 0.555 12.366 71761 Z= 0.285 Chirality : 0.043 0.369 8019 Planarity : 0.004 0.044 8922 Dihedral : 12.151 177.617 7683 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.60 % Allowed : 19.04 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.75 (0.11), residues: 6144 helix: 0.62 (0.11), residues: 2193 sheet: -0.64 (0.18), residues: 750 loop : -1.26 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP O 151 HIS 0.009 0.001 HIS B 575 PHE 0.026 0.001 PHE B 862 TYR 0.032 0.001 TYR O 178 ARG 0.009 0.000 ARG G 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 516 time to evaluate : 5.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 43 LYS cc_start: 0.4558 (ttmt) cc_final: 0.3825 (mmmt) REVERT: M 61 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5287 (pp20) REVERT: M 97 VAL cc_start: 0.7643 (t) cc_final: 0.7356 (p) REVERT: A 5 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.7955 (mtpm) REVERT: A 43 HIS cc_start: 0.3962 (t70) cc_final: 0.2863 (m-70) REVERT: A 184 LYS cc_start: 0.7213 (mttt) cc_final: 0.6867 (mptm) REVERT: A 218 LYS cc_start: 0.8741 (mtmt) cc_final: 0.7973 (mtpt) REVERT: A 355 PHE cc_start: 0.7257 (m-80) cc_final: 0.6948 (m-80) REVERT: A 359 VAL cc_start: 0.7714 (m) cc_final: 0.7451 (t) REVERT: A 366 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7152 (ptp-110) REVERT: A 384 GLN cc_start: 0.6535 (tt0) cc_final: 0.6006 (tm-30) REVERT: A 397 ARG cc_start: 0.5843 (tmt-80) cc_final: 0.5512 (tmm160) REVERT: A 424 MET cc_start: 0.5065 (mmp) cc_final: 0.4667 (ttm) REVERT: A 458 GLN cc_start: 0.5149 (OUTLIER) cc_final: 0.4598 (mm110) REVERT: A 727 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8239 (p) REVERT: A 1003 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7972 (ttm170) REVERT: A 1111 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6262 (mt-10) REVERT: A 1121 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6561 (m-30) REVERT: A 1227 MET cc_start: 0.6066 (mtp) cc_final: 0.5542 (mmm) REVERT: A 1290 TYR cc_start: 0.7422 (m-80) cc_final: 0.7106 (m-80) REVERT: A 1307 ASP cc_start: 0.7054 (t0) cc_final: 0.6755 (t70) REVERT: A 1332 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: A 1439 MET cc_start: 0.6078 (mtp) cc_final: 0.4598 (mpt) REVERT: A 1455 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5774 (ttp-170) REVERT: A 1524 VAL cc_start: 0.8198 (t) cc_final: 0.7943 (m) REVERT: B 16 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.6102 (p90) REVERT: B 304 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7271 (t0) REVERT: B 344 GLN cc_start: 0.8069 (mt0) cc_final: 0.7640 (mt0) REVERT: B 368 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7224 (mt0) REVERT: B 429 ARG cc_start: 0.6482 (ttm110) cc_final: 0.6021 (tpt170) REVERT: B 432 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7113 (mt) REVERT: B 438 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6053 (mt) REVERT: B 491 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6824 (mp) REVERT: B 708 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8857 (p0) REVERT: B 805 LYS cc_start: 0.8362 (ttmt) cc_final: 0.7627 (tptt) REVERT: B 872 LYS cc_start: 0.7686 (mtpp) cc_final: 0.7292 (mttm) REVERT: B 908 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.6948 (ptm-80) REVERT: B 909 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7164 (mtp85) REVERT: B 1163 GLN cc_start: 0.6345 (tt0) cc_final: 0.6017 (tm-30) REVERT: B 1199 ASN cc_start: 0.8111 (m-40) cc_final: 0.7773 (m110) REVERT: C 168 LYS cc_start: 0.8337 (tttp) cc_final: 0.8101 (tttt) REVERT: C 272 LYS cc_start: 0.7646 (tptt) cc_final: 0.7129 (mttm) REVERT: C 309 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8137 (m) REVERT: C 311 GLU cc_start: 0.7440 (pm20) cc_final: 0.6959 (pm20) REVERT: E 1 MET cc_start: 0.1798 (OUTLIER) cc_final: 0.1583 (ttt) REVERT: E 17 ARG cc_start: 0.7485 (ttt180) cc_final: 0.6966 (ttp-170) REVERT: E 50 MET cc_start: 0.4913 (mmt) cc_final: 0.4380 (ptp) REVERT: E 63 ASN cc_start: 0.7280 (m-40) cc_final: 0.6088 (p0) REVERT: E 91 LYS cc_start: 0.7048 (mttt) cc_final: 0.6333 (ptmt) REVERT: E 166 LYS cc_start: 0.8660 (tttt) cc_final: 0.8076 (tptp) REVERT: E 171 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7837 (mtpt) REVERT: F 60 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: F 67 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7104 (mmpt) REVERT: G 55 GLU cc_start: 0.7487 (tp30) cc_final: 0.7036 (mt-10) REVERT: G 56 ASN cc_start: 0.7607 (p0) cc_final: 0.7001 (m110) REVERT: G 138 PHE cc_start: 0.6410 (m-80) cc_final: 0.6078 (m-80) REVERT: G 217 TRP cc_start: 0.3500 (m100) cc_final: 0.3084 (m100) REVERT: G 219 ASP cc_start: 0.5609 (t70) cc_final: 0.5253 (t0) REVERT: H 126 GLU cc_start: 0.7506 (pt0) cc_final: 0.7232 (pt0) REVERT: I 18 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6396 (tm-30) REVERT: I 101 LEU cc_start: 0.7284 (mm) cc_final: 0.7068 (mm) REVERT: J 67 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: N 36 LYS cc_start: 0.4744 (mmtm) cc_final: 0.3981 (tmtm) REVERT: N 134 ASP cc_start: 0.3916 (m-30) cc_final: 0.2567 (t70) REVERT: N 141 GLU cc_start: 0.5329 (tm-30) cc_final: 0.5000 (tm-30) REVERT: O 117 GLN cc_start: 0.5586 (mm-40) cc_final: 0.5055 (tm130) REVERT: O 131 HIS cc_start: 0.6374 (m-70) cc_final: 0.5928 (m-70) REVERT: O 149 LYS cc_start: 0.6124 (ttpt) cc_final: 0.5258 (tptp) REVERT: O 156 MET cc_start: 0.5157 (OUTLIER) cc_final: 0.4870 (tpp) REVERT: O 181 ARG cc_start: 0.6099 (ttm-80) cc_final: 0.5294 (tmm160) REVERT: O 211 TYR cc_start: 0.6123 (t80) cc_final: 0.5869 (t80) REVERT: O 311 MET cc_start: 0.3377 (tpp) cc_final: 0.1861 (mtt) REVERT: O 342 HIS cc_start: 0.6494 (t70) cc_final: 0.6188 (t70) REVERT: O 366 THR cc_start: 0.7976 (p) cc_final: 0.7709 (t) REVERT: O 369 LYS cc_start: 0.7276 (ptpt) cc_final: 0.6320 (pttm) REVERT: O 458 GLU cc_start: 0.5711 (mt-10) cc_final: 0.4178 (mm-30) REVERT: O 459 GLU cc_start: 0.6141 (pt0) cc_final: 0.5762 (mp0) REVERT: O 527 MET cc_start: 0.3080 (ttp) cc_final: 0.2786 (tpp) REVERT: O 548 ASN cc_start: 0.2953 (OUTLIER) cc_final: 0.2547 (p0) outliers start: 144 outliers final: 88 residues processed: 619 average time/residue: 1.3786 time to fit residues: 1087.4203 Evaluate side-chains 607 residues out of total 5627 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 495 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 359 MET Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 458 GLN Chi-restraints excluded: chain A residue 600 MET Chi-restraints excluded: chain A residue 631 ASP Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 957 VAL Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1004 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1016 SER Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1455 ARG Chi-restraints excluded: chain A residue 1584 LEU Chi-restraints excluded: chain A residue 1643 VAL Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 456 ASN Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 668 GLU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 908 ARG Chi-restraints excluded: chain B residue 909 ARG Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1044 PHE Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1134 ARG Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain F residue 60 GLN Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 128 GLN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain I residue 71 LEU Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 20 SER Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 59 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 98 GLU Chi-restraints excluded: chain K residue 137 GLU Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 153 ASP Chi-restraints excluded: chain O residue 156 MET Chi-restraints excluded: chain O residue 329 SER Chi-restraints excluded: chain O residue 363 THR Chi-restraints excluded: chain O residue 548 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 625 random chunks: chunk 304 optimal weight: 1.9990 chunk 393 optimal weight: 0.7980 chunk 528 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 457 optimal weight: 1.9990 chunk 73 optimal weight: 50.0000 chunk 137 optimal weight: 40.0000 chunk 496 optimal weight: 2.9990 chunk 207 optimal weight: 0.0000 chunk 509 optimal weight: 0.7980 chunk 62 optimal weight: 40.0000 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 HIS ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN I 21 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.245581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.202380 restraints weight = 69407.261| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.00 r_work: 0.3751 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 52834 Z= 0.174 Angle : 0.551 12.833 71761 Z= 0.283 Chirality : 0.042 0.250 8019 Planarity : 0.004 0.044 8922 Dihedral : 12.130 175.630 7683 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.47 % Allowed : 19.35 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.69 (0.11), residues: 6144 helix: 0.68 (0.11), residues: 2200 sheet: -0.62 (0.18), residues: 762 loop : -1.22 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 842 HIS 0.008 0.001 HIS B 575 PHE 0.044 0.001 PHE O 114 TYR 0.021 0.001 TYR A1302 ARG 0.017 0.000 ARG B 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20246.74 seconds wall clock time: 357 minutes 48.26 seconds (21468.26 seconds total)